Starting phenix.real_space_refine on Fri Mar 14 01:53:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uva_20906/03_2025/6uva_20906.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uva_20906/03_2025/6uva_20906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uva_20906/03_2025/6uva_20906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uva_20906/03_2025/6uva_20906.map" model { file = "/net/cci-nas-00/data/ceres_data/6uva_20906/03_2025/6uva_20906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uva_20906/03_2025/6uva_20906.cif" } resolution = 2.3 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= 0.004 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 72 5.16 5 C 6095 2.51 5 N 1657 2.21 5 O 1737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 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: 9561 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1604 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 6, 'TRANS': 183} Chain breaks: 4 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 380 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "E" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "P" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 326 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 4, 'TRANS': 38} Chain: "R" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2819 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 9, 'TRANS': 334} Chain breaks: 4 Time building chain proxies: 6.04, per 1000 atoms: 0.63 Number of scatterers: 9561 At special positions: 0 Unit cell: (115.37, 97.11, 146.08, 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 72 16.00 O 1737 8.00 N 1657 7.00 C 6095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 10 " - pdb=" SG CYS P 15 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 74 " distance=2.03 Simple disulfide: pdb=" SG CYS R 65 " - pdb=" SG CYS R 105 " distance=2.03 Simple disulfide: pdb=" SG CYS R 88 " - pdb=" SG CYS R 127 " distance=2.03 Simple disulfide: pdb=" SG CYS R 212 " - pdb=" SG CYS R 282 " distance=2.02 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: 2.53 Conformation dependent library (CDL) restraints added in 1.2 seconds 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2258 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 11 sheets defined 40.2% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 16 through 39 removed outlier: 3.803A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.637A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.746A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.788A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 15 through 23 Processing helix chain 'G' and resid 29 through 43 removed outlier: 3.509A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.714A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'E' and resid 36 through 48 removed outlier: 4.188A pdb=" N CYS E 40 " --> pdb=" O ARG E 36 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA E 43 " --> pdb=" O LEU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 58 removed outlier: 3.632A pdb=" N TRP E 56 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N CYS E 57 " --> pdb=" O TRP E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 76 Processing helix chain 'E' and resid 86 through 99 removed outlier: 4.531A pdb=" N GLY E 91 " --> pdb=" O PRO E 87 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N PHE E 92 " --> pdb=" O LEU E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 142 Proline residue: E 126 - end of helix removed outlier: 3.951A pdb=" N LYS E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 28 Processing helix chain 'R' and resid 36 through 52 Processing helix chain 'R' and resid 124 through 128 removed outlier: 3.551A pdb=" N CYS R 127 " --> pdb=" O TYR R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 167 removed outlier: 3.707A pdb=" N LYS R 134 " --> pdb=" O ASN R 130 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS R 167 " --> pdb=" O PHE R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 198 Processing helix chain 'R' and resid 204 through 208 removed outlier: 4.205A pdb=" N THR R 207 " --> pdb=" O LEU R 204 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN R 208 " --> pdb=" O VAL R 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 204 through 208' Processing helix chain 'R' and resid 210 through 242 Processing helix chain 'R' and resid 252 through 261 Processing helix chain 'R' and resid 263 through 277 Processing helix chain 'R' and resid 280 through 284 removed outlier: 3.670A pdb=" N TRP R 283 " --> pdb=" O ASP R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 290 No H-bonds generated for 'chain 'R' and resid 288 through 290' Processing helix chain 'R' and resid 291 through 321 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 330 through 346 Proline residue: R 343 - end of helix Processing helix chain 'R' and resid 347 through 350 Processing helix chain 'R' and resid 363 through 385 removed outlier: 5.205A pdb=" N GLY R 377 " --> pdb=" O MET R 373 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU R 378 " --> pdb=" O HIS R 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 388 through 399 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.970A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 9.350A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.528A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.501A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.670A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.202A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.775A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.523A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.527A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 5 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.672A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 84 through 87 456 hydrogen bonds defined for protein. 1293 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: 2.57 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3099 1.34 - 1.46: 2237 1.46 - 1.58: 4344 1.58 - 1.70: 0 1.70 - 1.81: 100 Bond restraints: 9780 Sorted by residual: bond pdb=" C ASP P 40 " pdb=" N PRO P 41 " ideal model delta sigma weight residual 1.334 1.356 -0.023 2.34e-02 1.83e+03 9.30e-01 bond pdb=" CA GLY B 244 " pdb=" C GLY B 244 " ideal model delta sigma weight residual 1.520 1.514 0.006 7.30e-03 1.88e+04 7.45e-01 bond pdb=" CA GLU E 74 " pdb=" C GLU E 74 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.28e-02 6.10e+03 6.82e-01 bond pdb=" C VAL E 124 " pdb=" N ILE E 125 " ideal model delta sigma weight residual 1.329 1.338 -0.009 1.13e-02 7.83e+03 6.31e-01 bond pdb=" CA VAL E 51 " pdb=" CB VAL E 51 " ideal model delta sigma weight residual 1.538 1.546 -0.008 1.10e-02 8.26e+03 5.83e-01 ... (remaining 9775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 13037 1.66 - 3.32: 181 3.32 - 4.98: 33 4.98 - 6.64: 9 6.64 - 8.31: 2 Bond angle restraints: 13262 Sorted by residual: angle pdb=" CA TYR R 367 " pdb=" CB TYR R 367 " pdb=" CG TYR R 367 " ideal model delta sigma weight residual 113.90 119.60 -5.70 1.80e+00 3.09e-01 1.00e+01 angle pdb=" N VAL R 205 " pdb=" CA VAL R 205 " pdb=" C VAL R 205 " ideal model delta sigma weight residual 112.29 109.46 2.83 9.40e-01 1.13e+00 9.08e+00 angle pdb=" C THR E 73 " pdb=" N GLU E 74 " pdb=" CA GLU E 74 " ideal model delta sigma weight residual 122.37 118.02 4.35 1.54e+00 4.22e-01 7.97e+00 angle pdb=" C PHE R 166 " pdb=" N LYS R 167 " pdb=" CA LYS R 167 " ideal model delta sigma weight residual 121.54 126.14 -4.60 1.91e+00 2.74e-01 5.81e+00 angle pdb=" CA LEU R 395 " pdb=" CB LEU R 395 " pdb=" CG LEU R 395 " ideal model delta sigma weight residual 116.30 124.61 -8.31 3.50e+00 8.16e-02 5.63e+00 ... (remaining 13257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4970 17.98 - 35.96: 561 35.96 - 53.94: 193 53.94 - 71.92: 49 71.92 - 89.89: 15 Dihedral angle restraints: 5788 sinusoidal: 2300 harmonic: 3488 Sorted by residual: dihedral pdb=" CB CYS E 57 " pdb=" SG CYS E 57 " pdb=" SG CYS E 104 " pdb=" CB CYS E 104 " ideal model delta sinusoidal sigma weight residual -86.00 -167.11 81.11 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" CB CYS R 88 " pdb=" SG CYS R 88 " pdb=" SG CYS R 127 " pdb=" CB CYS R 127 " ideal model delta sinusoidal sigma weight residual 93.00 142.59 -49.59 1 1.00e+01 1.00e-02 3.38e+01 dihedral pdb=" CB CYS R 48 " pdb=" SG CYS R 48 " pdb=" SG CYS R 74 " pdb=" CB CYS R 74 " ideal model delta sinusoidal sigma weight residual 93.00 52.92 40.08 1 1.00e+01 1.00e-02 2.25e+01 ... (remaining 5785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 915 0.030 - 0.060: 377 0.060 - 0.091: 109 0.091 - 0.121: 68 0.121 - 0.151: 6 Chirality restraints: 1475 Sorted by residual: chirality pdb=" CA LYS E 42 " pdb=" N LYS E 42 " pdb=" C LYS E 42 " pdb=" CB LYS E 42 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CA ILE R 352 " pdb=" N ILE R 352 " pdb=" C ILE R 352 " pdb=" CB ILE R 352 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILE E 123 " pdb=" N ILE E 123 " pdb=" C ILE E 123 " pdb=" CB ILE E 123 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 ... (remaining 1472 not shown) Planarity restraints: 1684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 367 " 0.016 2.00e-02 2.50e+03 1.22e-02 2.99e+00 pdb=" CG TYR R 367 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR R 367 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR R 367 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR R 367 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR R 367 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR R 367 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR R 367 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO E 114 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO E 115 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO E 115 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 115 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 113 " -0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO E 114 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO E 114 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 114 " -0.017 5.00e-02 4.00e+02 ... (remaining 1681 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 887 2.75 - 3.28: 9414 3.28 - 3.82: 16408 3.82 - 4.36: 19653 4.36 - 4.90: 32748 Nonbonded interactions: 79110 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.207 3.040 nonbonded pdb=" O TRP R 72 " pdb=" OH TYR R 91 " model vdw 2.296 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.307 3.040 nonbonded pdb=" OG SER B 227 " pdb=" O PRO N 100 " model vdw 2.318 3.040 nonbonded pdb=" O HIS R 370 " pdb=" ND1 HIS R 374 " model vdw 2.321 3.120 ... (remaining 79105 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.030 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 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 : 0.002 0.030 9780 Z= 0.140 Angle : 0.547 8.305 13262 Z= 0.313 Chirality : 0.040 0.151 1475 Planarity : 0.003 0.033 1684 Dihedral : 18.040 89.894 3503 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.36 % Allowed : 26.30 % Favored : 70.35 % 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: -2.29 (0.22), residues: 1169 helix: -0.89 (0.22), residues: 434 sheet: -1.42 (0.30), residues: 225 loop : -2.05 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 234 HIS 0.004 0.001 HIS R 374 PHE 0.011 0.001 PHE R 308 TYR 0.030 0.001 TYR R 367 ARG 0.006 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 1.053 Fit side-chains REVERT: A 17 LYS cc_start: 0.5897 (pmtt) cc_final: 0.5426 (mmtm) REVERT: B 96 ARG cc_start: 0.6594 (mtm180) cc_final: 0.6373 (mtm110) REVERT: B 134 ARG cc_start: 0.6435 (ptp-110) cc_final: 0.6043 (ppt170) REVERT: E 142 LYS cc_start: 0.5737 (mtmp) cc_final: 0.5497 (mtmt) REVERT: R 42 MET cc_start: 0.3583 (mtm) cc_final: 0.3213 (ttm) REVERT: R 339 LEU cc_start: 0.7314 (mp) cc_final: 0.7093 (mm) outliers start: 35 outliers final: 9 residues processed: 164 average time/residue: 1.6532 time to fit residues: 287.2212 Evaluate side-chains 115 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 98 SER Chi-restraints excluded: chain R residue 136 LYS Chi-restraints excluded: chain R residue 310 LEU Chi-restraints excluded: chain R residue 342 VAL Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 351 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.5980 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 55 optimal weight: 0.0370 chunk 68 optimal weight: 0.0170 chunk 106 optimal weight: 0.6980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 357 HIS B 88 ASN B 259 GLN E 86 ASN E 110 HIS ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 250 GLN ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.223719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.175703 restraints weight = 9778.087| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.43 r_work: 0.3838 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9780 Z= 0.153 Angle : 0.546 7.820 13262 Z= 0.289 Chirality : 0.042 0.152 1475 Planarity : 0.004 0.036 1684 Dihedral : 5.265 49.506 1312 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.93 % Allowed : 25.24 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.24), residues: 1169 helix: 0.31 (0.24), residues: 441 sheet: -0.88 (0.31), residues: 232 loop : -1.60 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 56 HIS 0.005 0.001 HIS R 374 PHE 0.015 0.001 PHE E 100 TYR 0.009 0.001 TYR R 227 ARG 0.007 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 0.944 Fit side-chains REVERT: A 35 GLN cc_start: 0.6819 (mm-40) cc_final: 0.6395 (mm-40) REVERT: A 216 LYS cc_start: 0.6650 (OUTLIER) cc_final: 0.6190 (mppt) REVERT: A 317 ARG cc_start: 0.5379 (mtm180) cc_final: 0.4841 (mmt-90) REVERT: B 44 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.6908 (mt0) REVERT: B 96 ARG cc_start: 0.7427 (mtm180) cc_final: 0.7130 (mtm110) REVERT: B 134 ARG cc_start: 0.6888 (ptp-110) cc_final: 0.5813 (ppt170) REVERT: G 29 LYS cc_start: 0.5125 (OUTLIER) cc_final: 0.4781 (mtpp) REVERT: N 67 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6429 (ttp80) REVERT: N 83 MET cc_start: 0.6825 (mtp) cc_final: 0.6576 (mtm) REVERT: N 85 SER cc_start: 0.6921 (m) cc_final: 0.6347 (m) REVERT: P 18 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7135 (mp10) REVERT: R 42 MET cc_start: 0.4640 (mtm) cc_final: 0.4141 (ttm) REVERT: R 53 MET cc_start: 0.3103 (ptm) cc_final: 0.2354 (ptm) REVERT: R 339 LEU cc_start: 0.7363 (mp) cc_final: 0.7130 (mm) outliers start: 41 outliers final: 9 residues processed: 148 average time/residue: 1.3355 time to fit residues: 210.4350 Evaluate side-chains 122 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 299 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 54 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 218 ASN A 267 GLN A 357 HIS B 259 GLN B 266 HIS N 35 ASN N 82 GLN E 71 ASN E 86 ASN E 97 HIS ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.216923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.169946 restraints weight = 9713.957| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 1.59 r_work: 0.3751 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9780 Z= 0.212 Angle : 0.601 7.233 13262 Z= 0.320 Chirality : 0.044 0.147 1475 Planarity : 0.004 0.041 1684 Dihedral : 4.906 28.388 1299 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.09 % Allowed : 24.66 % Favored : 70.25 % 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: -0.59 (0.24), residues: 1169 helix: 0.76 (0.25), residues: 443 sheet: -0.49 (0.31), residues: 241 loop : -1.37 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.009 0.001 HIS E 97 PHE 0.013 0.002 PHE A 212 TYR 0.011 0.001 TYR R 227 ARG 0.006 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 112 time to evaluate : 1.092 Fit side-chains REVERT: A 35 GLN cc_start: 0.6884 (mm-40) cc_final: 0.6341 (mm-40) REVERT: A 216 LYS cc_start: 0.6683 (OUTLIER) cc_final: 0.6090 (mmtm) REVERT: A 278 ASN cc_start: 0.8388 (m-40) cc_final: 0.8067 (m110) REVERT: A 344 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7186 (mm-30) REVERT: B 59 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: B 96 ARG cc_start: 0.7642 (mtm180) cc_final: 0.7062 (mmt-90) REVERT: B 132 ASN cc_start: 0.5869 (OUTLIER) cc_final: 0.5525 (m-40) REVERT: B 134 ARG cc_start: 0.6904 (ptp-110) cc_final: 0.5744 (ppt170) REVERT: B 266 HIS cc_start: 0.7218 (t-90) cc_final: 0.6877 (t70) REVERT: N 83 MET cc_start: 0.6942 (mtp) cc_final: 0.6703 (mtm) REVERT: E 75 MET cc_start: 0.2673 (OUTLIER) cc_final: 0.2428 (mpm) REVERT: E 97 HIS cc_start: 0.3705 (OUTLIER) cc_final: 0.3182 (t-170) REVERT: E 118 VAL cc_start: 0.5643 (t) cc_final: 0.5350 (t) REVERT: E 139 TRP cc_start: 0.6045 (t60) cc_final: 0.5811 (t60) REVERT: E 140 ARG cc_start: 0.5514 (OUTLIER) cc_final: 0.4311 (mmm160) REVERT: P 18 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7192 (mp10) REVERT: R 42 MET cc_start: 0.4550 (mtm) cc_final: 0.4109 (ttm) REVERT: R 53 MET cc_start: 0.2913 (ptm) cc_final: 0.2330 (ptm) REVERT: R 287 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7105 (t0) REVERT: R 339 LEU cc_start: 0.7371 (mp) cc_final: 0.7134 (mm) REVERT: R 369 MET cc_start: 0.5600 (OUTLIER) cc_final: 0.5134 (mmt) outliers start: 53 outliers final: 17 residues processed: 153 average time/residue: 1.4324 time to fit residues: 233.1883 Evaluate side-chains 137 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain R residue 351 LEU Chi-restraints excluded: chain R residue 369 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 112 optimal weight: 0.0980 chunk 75 optimal weight: 0.0570 chunk 26 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 73 optimal weight: 0.0770 chunk 23 optimal weight: 4.9990 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 264 ASN A 357 HIS B 32 GLN N 35 ASN E 71 ASN E 86 ASN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.221055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.172163 restraints weight = 9760.474| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.47 r_work: 0.3785 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9780 Z= 0.134 Angle : 0.516 6.790 13262 Z= 0.272 Chirality : 0.041 0.145 1475 Planarity : 0.003 0.039 1684 Dihedral : 4.490 25.566 1299 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.13 % Allowed : 25.82 % Favored : 70.06 % 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: -0.18 (0.25), residues: 1169 helix: 1.18 (0.25), residues: 443 sheet: -0.25 (0.32), residues: 237 loop : -1.24 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.006 0.001 HIS R 374 PHE 0.011 0.001 PHE B 199 TYR 0.009 0.001 TYR R 227 ARG 0.003 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 121 time to evaluate : 1.078 Fit side-chains REVERT: A 35 GLN cc_start: 0.6921 (mm-40) cc_final: 0.6428 (mm-40) REVERT: A 344 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7153 (mm-30) REVERT: B 96 ARG cc_start: 0.7634 (mtm180) cc_final: 0.7070 (mmt-90) REVERT: B 146 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8121 (mm) REVERT: B 266 HIS cc_start: 0.7326 (t-90) cc_final: 0.6904 (t70) REVERT: N 83 MET cc_start: 0.6947 (mtp) cc_final: 0.6697 (mtm) REVERT: E 75 MET cc_start: 0.2529 (OUTLIER) cc_final: 0.2267 (mpm) REVERT: E 118 VAL cc_start: 0.5676 (OUTLIER) cc_final: 0.5339 (t) REVERT: E 140 ARG cc_start: 0.5501 (OUTLIER) cc_final: 0.4280 (mmm160) REVERT: R 53 MET cc_start: 0.2927 (ptm) cc_final: 0.2358 (ptm) REVERT: R 287 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7132 (t0) REVERT: R 303 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7816 (mt) REVERT: R 339 LEU cc_start: 0.7409 (mp) cc_final: 0.7180 (mm) REVERT: R 392 GLN cc_start: 0.5973 (OUTLIER) cc_final: 0.5713 (mt0) outliers start: 43 outliers final: 12 residues processed: 152 average time/residue: 1.4346 time to fit residues: 231.5240 Evaluate side-chains 132 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain R residue 351 LEU Chi-restraints excluded: chain R residue 392 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 112 optimal weight: 0.0060 chunk 55 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 264 ASN A 357 HIS A 387 HIS B 155 ASN B 176 GLN B 220 GLN B 340 ASN G 59 ASN E 86 ASN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 172 GLN R 187 ASN ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.214659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.164547 restraints weight = 9632.607| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.43 r_work: 0.3709 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9780 Z= 0.292 Angle : 0.672 7.317 13262 Z= 0.361 Chirality : 0.047 0.217 1475 Planarity : 0.005 0.045 1684 Dihedral : 5.404 29.547 1299 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.57 % Allowed : 24.95 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.24), residues: 1169 helix: 0.88 (0.24), residues: 446 sheet: -0.48 (0.31), residues: 249 loop : -1.11 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.006 0.002 HIS B 54 PHE 0.014 0.002 PHE R 262 TYR 0.012 0.002 TYR R 227 ARG 0.007 0.001 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 103 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.6911 (mm-40) cc_final: 0.6372 (mm-40) REVERT: A 209 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6485 (mt-10) REVERT: A 216 LYS cc_start: 0.6661 (OUTLIER) cc_final: 0.5991 (mmtm) REVERT: A 264 ASN cc_start: 0.5214 (OUTLIER) cc_final: 0.4946 (t0) REVERT: A 344 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7239 (mm-30) REVERT: B 46 ARG cc_start: 0.7837 (mtm-85) cc_final: 0.7556 (mtt-85) REVERT: B 146 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8268 (mm) REVERT: B 266 HIS cc_start: 0.7419 (t-90) cc_final: 0.6962 (t70) REVERT: N 83 MET cc_start: 0.6975 (mtp) cc_final: 0.6672 (mtm) REVERT: E 75 MET cc_start: 0.2549 (OUTLIER) cc_final: 0.1468 (tmm) REVERT: E 140 ARG cc_start: 0.5521 (OUTLIER) cc_final: 0.4313 (mmm160) REVERT: P 18 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7318 (mp10) REVERT: R 287 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7166 (t0) REVERT: R 333 LYS cc_start: 0.5159 (mttp) cc_final: 0.4560 (mmtt) outliers start: 58 outliers final: 24 residues processed: 146 average time/residue: 1.4231 time to fit residues: 221.3817 Evaluate side-chains 130 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 136 LYS Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 177 HIS Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain R residue 314 ARG Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain R residue 351 LEU Chi-restraints excluded: chain R residue 369 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 36 optimal weight: 2.9990 chunk 88 optimal weight: 0.0980 chunk 111 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 76 optimal weight: 20.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 264 ASN A 357 HIS B 176 GLN E 86 ASN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 ASN ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.215776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.170089 restraints weight = 9639.994| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.49 r_work: 0.3735 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9780 Z= 0.191 Angle : 0.588 7.134 13262 Z= 0.312 Chirality : 0.044 0.150 1475 Planarity : 0.004 0.042 1684 Dihedral : 5.123 32.306 1299 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.22 % Allowed : 26.10 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -0.12 (0.25), residues: 1169 helix: 1.15 (0.25), residues: 440 sheet: -0.38 (0.31), residues: 249 loop : -1.02 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 139 HIS 0.007 0.001 HIS R 374 PHE 0.013 0.002 PHE B 199 TYR 0.009 0.001 TYR A 311 ARG 0.011 0.001 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 107 time to evaluate : 1.098 Fit side-chains REVERT: A 35 GLN cc_start: 0.6866 (mm-40) cc_final: 0.6312 (mm-40) REVERT: A 209 GLU cc_start: 0.6719 (mt-10) cc_final: 0.6388 (mt-10) REVERT: A 216 LYS cc_start: 0.6663 (OUTLIER) cc_final: 0.6022 (mmtm) REVERT: A 344 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7217 (mm-30) REVERT: A 392 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7734 (mt-10) REVERT: B 146 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8242 (mm) REVERT: B 266 HIS cc_start: 0.7482 (t-90) cc_final: 0.7041 (t70) REVERT: G 29 LYS cc_start: 0.5586 (mtpp) cc_final: 0.5235 (mtpp) REVERT: N 83 MET cc_start: 0.6921 (mtp) cc_final: 0.6611 (mtm) REVERT: E 62 PHE cc_start: 0.1987 (OUTLIER) cc_final: 0.1338 (p90) REVERT: E 75 MET cc_start: 0.2626 (OUTLIER) cc_final: 0.1514 (tmm) REVERT: E 140 ARG cc_start: 0.5390 (OUTLIER) cc_final: 0.4223 (mmm160) REVERT: R 287 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7139 (t0) REVERT: R 303 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7906 (mt) REVERT: R 333 LYS cc_start: 0.5083 (mttp) cc_final: 0.4459 (mmpt) REVERT: R 390 GLU cc_start: 0.6079 (OUTLIER) cc_final: 0.5759 (mt-10) outliers start: 44 outliers final: 22 residues processed: 139 average time/residue: 1.3710 time to fit residues: 202.8130 Evaluate side-chains 132 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain E residue 62 PHE Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 136 LYS Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain R residue 314 ARG Chi-restraints excluded: chain R residue 351 LEU Chi-restraints excluded: chain R residue 369 MET Chi-restraints excluded: chain R residue 390 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 54 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 264 ASN A 357 HIS B 176 GLN E 86 ASN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.215466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.163798 restraints weight = 9653.340| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.40 r_work: 0.3732 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9780 Z= 0.206 Angle : 0.598 7.130 13262 Z= 0.318 Chirality : 0.044 0.149 1475 Planarity : 0.004 0.043 1684 Dihedral : 5.153 31.814 1299 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.80 % Allowed : 26.10 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -0.08 (0.25), residues: 1169 helix: 1.18 (0.25), residues: 440 sheet: -0.34 (0.31), residues: 247 loop : -1.01 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 139 HIS 0.007 0.001 HIS R 374 PHE 0.013 0.002 PHE B 199 TYR 0.008 0.001 TYR N 32 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 106 time to evaluate : 1.390 Fit side-chains REVERT: A 35 GLN cc_start: 0.6848 (mm-40) cc_final: 0.6304 (mm-40) REVERT: A 209 GLU cc_start: 0.6810 (mt-10) cc_final: 0.6591 (mt-10) REVERT: A 216 LYS cc_start: 0.6659 (OUTLIER) cc_final: 0.6139 (mmtm) REVERT: A 392 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7686 (mt-10) REVERT: B 46 ARG cc_start: 0.7791 (mtm-85) cc_final: 0.7341 (mmt-90) REVERT: B 146 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8247 (mm) REVERT: B 266 HIS cc_start: 0.7408 (t-90) cc_final: 0.7060 (t70) REVERT: G 29 LYS cc_start: 0.5666 (mtpp) cc_final: 0.5405 (mtpp) REVERT: N 67 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6508 (ttp80) REVERT: N 83 MET cc_start: 0.6919 (mtp) cc_final: 0.6657 (mtm) REVERT: N 85 SER cc_start: 0.7187 (m) cc_final: 0.6701 (p) REVERT: E 62 PHE cc_start: 0.2187 (OUTLIER) cc_final: 0.1563 (p90) REVERT: E 75 MET cc_start: 0.2715 (OUTLIER) cc_final: 0.1601 (tmm) REVERT: E 140 ARG cc_start: 0.5430 (OUTLIER) cc_final: 0.4267 (mmm160) REVERT: P 18 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7148 (mp10) REVERT: R 287 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7096 (t0) REVERT: R 303 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7915 (mt) REVERT: R 333 LYS cc_start: 0.5167 (mttp) cc_final: 0.4512 (mmpt) REVERT: R 369 MET cc_start: 0.5628 (OUTLIER) cc_final: 0.5309 (mmt) REVERT: R 390 GLU cc_start: 0.6070 (OUTLIER) cc_final: 0.5760 (mt-10) outliers start: 50 outliers final: 22 residues processed: 144 average time/residue: 1.7791 time to fit residues: 272.9198 Evaluate side-chains 137 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain E residue 62 PHE Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 15 CYS Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain R residue 314 ARG Chi-restraints excluded: chain R residue 351 LEU Chi-restraints excluded: chain R residue 369 MET Chi-restraints excluded: chain R residue 390 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 99 optimal weight: 0.0050 chunk 35 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN A 357 HIS B 176 GLN E 86 ASN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.214128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.168754 restraints weight = 9774.731| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.45 r_work: 0.3721 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9780 Z= 0.240 Angle : 0.632 7.941 13262 Z= 0.336 Chirality : 0.045 0.150 1475 Planarity : 0.005 0.044 1684 Dihedral : 5.340 32.495 1299 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.32 % Allowed : 26.49 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -0.11 (0.24), residues: 1169 helix: 1.18 (0.25), residues: 434 sheet: -0.24 (0.33), residues: 233 loop : -1.06 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 139 HIS 0.007 0.001 HIS R 374 PHE 0.014 0.002 PHE B 199 TYR 0.010 0.002 TYR N 32 ARG 0.005 0.001 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 103 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.6862 (mm-40) cc_final: 0.6312 (mm-40) REVERT: A 209 GLU cc_start: 0.6867 (mt-10) cc_final: 0.6645 (mt-10) REVERT: A 216 LYS cc_start: 0.6625 (OUTLIER) cc_final: 0.5978 (mmtm) REVERT: A 344 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6799 (mm-30) REVERT: B 46 ARG cc_start: 0.7809 (mtm-85) cc_final: 0.7605 (mtt-85) REVERT: B 146 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8243 (mm) REVERT: B 217 MET cc_start: 0.7196 (OUTLIER) cc_final: 0.6959 (mtt) REVERT: N 67 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6509 (ttp80) REVERT: N 83 MET cc_start: 0.6945 (mtp) cc_final: 0.6624 (mtm) REVERT: N 85 SER cc_start: 0.7161 (m) cc_final: 0.6770 (p) REVERT: E 75 MET cc_start: 0.2627 (OUTLIER) cc_final: 0.1498 (tmm) REVERT: E 140 ARG cc_start: 0.5483 (OUTLIER) cc_final: 0.4273 (mmm160) REVERT: P 18 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7149 (tp40) REVERT: R 287 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7104 (t0) REVERT: R 333 LYS cc_start: 0.5267 (mttp) cc_final: 0.4592 (mmpt) REVERT: R 369 MET cc_start: 0.5662 (OUTLIER) cc_final: 0.5334 (mmt) REVERT: R 390 GLU cc_start: 0.6171 (OUTLIER) cc_final: 0.5861 (mt-10) outliers start: 45 outliers final: 26 residues processed: 138 average time/residue: 1.6268 time to fit residues: 239.1573 Evaluate side-chains 137 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain E residue 62 PHE Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 15 CYS Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain R residue 314 ARG Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain R residue 351 LEU Chi-restraints excluded: chain R residue 369 MET Chi-restraints excluded: chain R residue 390 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 51 optimal weight: 0.2980 chunk 7 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 53 optimal weight: 10.0000 chunk 111 optimal weight: 0.7980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 264 ASN A 357 HIS B 176 GLN B 266 HIS E 86 ASN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.216487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.165882 restraints weight = 9704.765| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.40 r_work: 0.3747 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9780 Z= 0.174 Angle : 0.571 6.888 13262 Z= 0.301 Chirality : 0.043 0.145 1475 Planarity : 0.004 0.043 1684 Dihedral : 5.018 30.852 1299 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.65 % Allowed : 27.16 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: 0.08 (0.25), residues: 1169 helix: 1.41 (0.25), residues: 434 sheet: -0.31 (0.32), residues: 241 loop : -0.95 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 139 HIS 0.007 0.001 HIS R 374 PHE 0.013 0.001 PHE R 262 TYR 0.007 0.001 TYR A 311 ARG 0.003 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.6864 (mm-40) cc_final: 0.6309 (mm-40) REVERT: A 209 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6565 (mt-10) REVERT: A 265 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.7012 (ttp-170) REVERT: A 344 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6838 (mm-30) REVERT: B 46 ARG cc_start: 0.7785 (mtm-85) cc_final: 0.7304 (mmt-90) REVERT: B 146 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8215 (mm) REVERT: B 217 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6824 (mtt) REVERT: B 266 HIS cc_start: 0.7364 (t-90) cc_final: 0.6991 (t70) REVERT: N 67 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6494 (ttp80) REVERT: N 83 MET cc_start: 0.6942 (mtp) cc_final: 0.6665 (mtm) REVERT: N 85 SER cc_start: 0.7307 (m) cc_final: 0.6761 (p) REVERT: E 33 MET cc_start: 0.2394 (tmm) cc_final: 0.2100 (ppp) REVERT: E 62 PHE cc_start: 0.2148 (OUTLIER) cc_final: 0.1488 (p90) REVERT: E 140 ARG cc_start: 0.5387 (OUTLIER) cc_final: 0.4229 (mmm160) REVERT: R 287 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7080 (t0) REVERT: R 303 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7887 (mt) REVERT: R 333 LYS cc_start: 0.5188 (mttp) cc_final: 0.4547 (mmpt) REVERT: R 339 LEU cc_start: 0.7475 (mp) cc_final: 0.7115 (mm) REVERT: R 369 MET cc_start: 0.5638 (OUTLIER) cc_final: 0.5307 (mmt) REVERT: R 390 GLU cc_start: 0.6144 (OUTLIER) cc_final: 0.5838 (mt-10) outliers start: 38 outliers final: 21 residues processed: 135 average time/residue: 1.3808 time to fit residues: 198.4310 Evaluate side-chains 134 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain E residue 62 PHE Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 15 CYS Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain R residue 314 ARG Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain R residue 351 LEU Chi-restraints excluded: chain R residue 369 MET Chi-restraints excluded: chain R residue 390 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 2.9990 chunk 99 optimal weight: 0.0570 chunk 116 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 264 ASN A 357 HIS B 176 GLN E 86 ASN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.215975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.164594 restraints weight = 9802.565| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.38 r_work: 0.3750 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9780 Z= 0.180 Angle : 0.580 7.042 13262 Z= 0.306 Chirality : 0.043 0.148 1475 Planarity : 0.004 0.044 1684 Dihedral : 5.011 30.465 1299 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.74 % Allowed : 26.97 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: 0.13 (0.25), residues: 1169 helix: 1.43 (0.25), residues: 434 sheet: -0.26 (0.32), residues: 241 loop : -0.92 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 139 HIS 0.006 0.001 HIS E 97 PHE 0.013 0.001 PHE R 262 TYR 0.007 0.001 TYR R 227 ARG 0.003 0.000 ARG N 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2338 Ramachandran restraints generated. 1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 100 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.6911 (mm-40) cc_final: 0.6390 (mm-40) REVERT: A 209 GLU cc_start: 0.6801 (mt-10) cc_final: 0.6581 (mt-10) REVERT: A 265 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.7045 (ttp-110) REVERT: A 344 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6863 (mm-30) REVERT: B 46 ARG cc_start: 0.7820 (mtm-85) cc_final: 0.7345 (mmt-90) REVERT: B 59 TYR cc_start: 0.8402 (OUTLIER) cc_final: 0.7880 (m-80) REVERT: B 146 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8224 (mm) REVERT: B 217 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6875 (mtt) REVERT: B 266 HIS cc_start: 0.7464 (t-90) cc_final: 0.7064 (t70) REVERT: N 67 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.6509 (ttp80) REVERT: N 83 MET cc_start: 0.6938 (mtp) cc_final: 0.6653 (mtm) REVERT: N 85 SER cc_start: 0.7209 (m) cc_final: 0.6747 (p) REVERT: E 33 MET cc_start: 0.2430 (tmm) cc_final: 0.2135 (ppp) REVERT: E 75 MET cc_start: 0.2999 (mmp) cc_final: 0.2056 (tmm) REVERT: E 140 ARG cc_start: 0.5439 (OUTLIER) cc_final: 0.4228 (mmm160) REVERT: R 287 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7085 (t0) REVERT: R 303 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7906 (mt) REVERT: R 333 LYS cc_start: 0.5185 (mttp) cc_final: 0.4535 (mmpt) REVERT: R 339 LEU cc_start: 0.7465 (mp) cc_final: 0.7152 (mm) REVERT: R 369 MET cc_start: 0.5626 (OUTLIER) cc_final: 0.5297 (mmt) REVERT: R 390 GLU cc_start: 0.6124 (OUTLIER) cc_final: 0.5812 (mt-10) outliers start: 39 outliers final: 24 residues processed: 132 average time/residue: 1.4130 time to fit residues: 198.4206 Evaluate side-chains 132 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain E residue 62 PHE Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 140 ARG Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 15 CYS Chi-restraints excluded: chain P residue 39 VAL Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain R residue 314 ARG Chi-restraints excluded: chain R residue 336 ARG Chi-restraints excluded: chain R residue 351 LEU Chi-restraints excluded: chain R residue 369 MET Chi-restraints excluded: chain R residue 390 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 97 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 88 optimal weight: 0.0770 chunk 89 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 264 ASN A 357 HIS B 176 GLN E 86 ASN ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.217008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.166141 restraints weight = 9858.356| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 1.45 r_work: 0.3749 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9780 Z= 0.159 Angle : 0.554 6.646 13262 Z= 0.291 Chirality : 0.042 0.144 1475 Planarity : 0.004 0.043 1684 Dihedral : 4.839 29.358 1299 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.74 % Allowed : 26.87 % Favored : 69.39 % 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: 0.19 (0.25), residues: 1169 helix: 1.48 (0.25), residues: 439 sheet: -0.24 (0.32), residues: 241 loop : -0.89 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 139 HIS 0.007 0.001 HIS E 97 PHE 0.011 0.001 PHE B 199 TYR 0.006 0.001 TYR R 227 ARG 0.003 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11794.41 seconds wall clock time: 206 minutes 13.09 seconds (12373.09 seconds total)