Starting phenix.real_space_refine on Thu Feb 13 22:12:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uva_20906/02_2025/6uva_20906.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uva_20906/02_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_20906/02_2025/6uva_20906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uva_20906/02_2025/6uva_20906.map" model { file = "/net/cci-nas-00/data/ceres_data/6uva_20906/02_2025/6uva_20906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uva_20906/02_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-5592/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: 5.46, per 1000 atoms: 0.57 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: 2.25 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: 0.94 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: 2.76 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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: 1.170 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.600 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.540 ------------------------------------------------------------------------------- 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 : 1.040 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: 1.4495 time to fit residues: 252.0539 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 : 1.087 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.175710 restraints weight = 9778.087| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.43 r_work: 0.3841 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 : 1.142 Fit side-chains REVERT: A 35 GLN cc_start: 0.6838 (mm-40) cc_final: 0.6425 (mm-40) REVERT: A 216 LYS cc_start: 0.6663 (OUTLIER) cc_final: 0.6204 (mppt) REVERT: A 317 ARG cc_start: 0.5399 (mtm180) cc_final: 0.4863 (mmt-90) REVERT: B 44 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.6915 (mt0) REVERT: B 96 ARG cc_start: 0.7416 (mtm180) cc_final: 0.7119 (mtm110) REVERT: B 134 ARG cc_start: 0.6886 (ptp-110) cc_final: 0.5835 (ppt170) REVERT: G 29 LYS cc_start: 0.5134 (OUTLIER) cc_final: 0.4796 (mtpp) REVERT: N 67 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6427 (ttp80) REVERT: N 83 MET cc_start: 0.6823 (mtp) cc_final: 0.6576 (mtm) REVERT: N 85 SER cc_start: 0.6922 (m) cc_final: 0.6348 (m) REVERT: P 18 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7135 (mp10) REVERT: R 42 MET cc_start: 0.4631 (mtm) cc_final: 0.4129 (ttm) REVERT: R 53 MET cc_start: 0.3106 (ptm) cc_final: 0.2353 (ptm) REVERT: R 339 LEU cc_start: 0.7370 (mp) cc_final: 0.7135 (mm) outliers start: 41 outliers final: 9 residues processed: 148 average time/residue: 1.4451 time to fit residues: 227.2601 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 : 1.136 ------------------------------------------------------------------------------- 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: 0.3980 chunk 90 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 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: 0.7980 chunk 112 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4387 r_free = 0.4387 target = 0.218028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.169465 restraints weight = 9732.523| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 1.57 r_work: 0.3734 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9780 Z= 0.195 Angle : 0.580 7.139 13262 Z= 0.308 Chirality : 0.043 0.144 1475 Planarity : 0.004 0.040 1684 Dihedral : 4.783 27.949 1299 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.99 % Allowed : 24.86 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.24), residues: 1169 helix: 0.81 (0.25), residues: 443 sheet: -0.50 (0.31), residues: 241 loop : -1.36 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 84 HIS 0.010 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 164 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 112 time to evaluate : 0.854 Fit side-chains REVERT: A 35 GLN cc_start: 0.6891 (mm-40) cc_final: 0.6353 (mm-40) REVERT: A 216 LYS cc_start: 0.6692 (OUTLIER) cc_final: 0.6010 (mmtm) REVERT: A 278 ASN cc_start: 0.8429 (m-40) cc_final: 0.8071 (m110) REVERT: A 344 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7181 (mm-30) REVERT: B 132 ASN cc_start: 0.5839 (OUTLIER) cc_final: 0.5566 (m-40) REVERT: B 134 ARG cc_start: 0.6893 (ptp-110) cc_final: 0.5699 (ppt170) REVERT: B 146 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8243 (mm) REVERT: B 266 HIS cc_start: 0.7224 (t-90) cc_final: 0.6867 (t70) REVERT: N 83 MET cc_start: 0.6955 (mtp) cc_final: 0.6699 (mtm) REVERT: E 75 MET cc_start: 0.2676 (OUTLIER) cc_final: 0.2437 (mpm) REVERT: E 97 HIS cc_start: 0.3533 (OUTLIER) cc_final: 0.3005 (t-170) REVERT: E 118 VAL cc_start: 0.5634 (t) cc_final: 0.5344 (t) REVERT: E 139 TRP cc_start: 0.6010 (t60) cc_final: 0.5783 (t60) REVERT: E 140 ARG cc_start: 0.5495 (OUTLIER) cc_final: 0.4303 (mmm160) REVERT: P 18 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7198 (mp10) REVERT: R 42 MET cc_start: 0.4552 (mtm) cc_final: 0.4115 (ttm) REVERT: R 53 MET cc_start: 0.2899 (ptm) cc_final: 0.2352 (ptm) REVERT: R 287 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7135 (t0) REVERT: R 339 LEU cc_start: 0.7403 (mp) cc_final: 0.7166 (mm) outliers start: 52 outliers final: 17 residues processed: 152 average time/residue: 1.4507 time to fit residues: 234.6257 Evaluate side-chains 134 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 132 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 31 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 31 optimal weight: 0.0170 chunk 27 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 75 optimal weight: 0.0000 chunk 26 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.4222 ------------------------------------------------------------------------------- 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 B 176 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.220748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.170078 restraints weight = 9740.355| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 1.38 r_work: 0.3818 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3723 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1941 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= 0.141 Angle : 0.523 6.801 13262 Z= 0.276 Chirality : 0.041 0.144 1475 Planarity : 0.003 0.040 1684 Dihedral : 4.518 25.626 1299 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.51 % Allowed : 25.34 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1169 helix: 1.18 (0.25), residues: 443 sheet: -0.24 (0.33), residues: 237 loop : -1.23 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.011 0.001 HIS E 97 PHE 0.011 0.001 PHE B 199 TYR 0.009 0.001 TYR R 227 ARG 0.004 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: 47 poor density : 117 time to evaluate : 1.019 Fit side-chains REVERT: A 35 GLN cc_start: 0.6889 (mm-40) cc_final: 0.6399 (mm-40) REVERT: A 344 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7140 (mm-30) REVERT: B 134 ARG cc_start: 0.6750 (ptp-110) cc_final: 0.5667 (ppt170) REVERT: B 146 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8131 (mm) REVERT: B 266 HIS cc_start: 0.7330 (t-90) cc_final: 0.6914 (t70) REVERT: N 83 MET cc_start: 0.6908 (mtp) cc_final: 0.6664 (mtm) REVERT: E 75 MET cc_start: 0.2455 (OUTLIER) cc_final: 0.2198 (mpm) REVERT: E 118 VAL cc_start: 0.5693 (OUTLIER) cc_final: 0.5361 (t) REVERT: E 140 ARG cc_start: 0.5447 (OUTLIER) cc_final: 0.4221 (mmm160) REVERT: R 42 MET cc_start: 0.4512 (mtm) cc_final: 0.4052 (ttm) REVERT: R 53 MET cc_start: 0.2971 (ptm) cc_final: 0.2397 (ptm) REVERT: R 287 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7091 (t0) REVERT: R 303 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7787 (mt) REVERT: R 339 LEU cc_start: 0.7409 (mp) cc_final: 0.7181 (mm) REVERT: R 392 GLN cc_start: 0.5960 (OUTLIER) cc_final: 0.5697 (mt0) outliers start: 47 outliers final: 14 residues processed: 151 average time/residue: 1.3863 time to fit residues: 222.9315 Evaluate side-chains 131 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 GLU 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 79 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 105 THR 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 310 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: 0.8980 chunk 57 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 95 optimal weight: 0.0970 chunk 112 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 89 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 340 ASN G 59 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.219580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.168929 restraints weight = 9738.435| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 1.27 r_work: 0.3803 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3709 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9780 Z= 0.152 Angle : 0.529 6.731 13262 Z= 0.279 Chirality : 0.042 0.156 1475 Planarity : 0.004 0.039 1684 Dihedral : 4.551 24.012 1299 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.32 % Allowed : 25.91 % Favored : 69.77 % 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: 0.03 (0.25), residues: 1169 helix: 1.38 (0.25), residues: 443 sheet: -0.25 (0.32), residues: 249 loop : -1.09 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 139 HIS 0.007 0.001 HIS E 97 PHE 0.012 0.001 PHE R 262 TYR 0.010 0.001 TYR R 124 ARG 0.003 0.000 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 157 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 112 time to evaluate : 1.038 Fit side-chains REVERT: A 35 GLN cc_start: 0.6950 (mm-40) cc_final: 0.6443 (mm-40) REVERT: A 264 ASN cc_start: 0.4909 (OUTLIER) cc_final: 0.4658 (t0) REVERT: A 344 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7141 (mm-30) REVERT: B 134 ARG cc_start: 0.6741 (ptp-110) cc_final: 0.5696 (ppt170) REVERT: B 146 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8145 (mm) REVERT: B 266 HIS cc_start: 0.7310 (t-90) cc_final: 0.6853 (t70) REVERT: N 67 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6481 (ttp80) REVERT: N 83 MET cc_start: 0.6894 (mtp) cc_final: 0.6625 (mtm) REVERT: E 75 MET cc_start: 0.2722 (OUTLIER) cc_final: 0.1569 (tmm) REVERT: E 97 HIS cc_start: 0.3681 (OUTLIER) cc_final: 0.3184 (t-170) REVERT: E 118 VAL cc_start: 0.5577 (OUTLIER) cc_final: 0.5233 (t) REVERT: E 140 ARG cc_start: 0.5352 (OUTLIER) cc_final: 0.4163 (mmm160) REVERT: R 53 MET cc_start: 0.3124 (ptm) cc_final: 0.2527 (ptm) REVERT: R 136 LYS cc_start: 0.6012 (OUTLIER) cc_final: 0.4983 (mtmm) REVERT: R 287 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7046 (t0) REVERT: R 303 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7888 (mt) REVERT: R 369 MET cc_start: 0.5595 (OUTLIER) cc_final: 0.5295 (mmt) outliers start: 45 outliers final: 16 residues processed: 145 average time/residue: 1.3338 time to fit residues: 207.0364 Evaluate side-chains 135 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 320 THR 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 331 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 67 ARG 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 118 VAL Chi-restraints excluded: chain E residue 140 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 136 LYS Chi-restraints excluded: chain R residue 144 LEU 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 310 LEU 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: 7.9990 chunk 88 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 0.0020 overall best weight: 1.7996 ------------------------------------------------------------------------------- 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 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 295 HIS ** 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 = 0.4358 r_free = 0.4358 target = 0.214656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.165224 restraints weight = 9658.852| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.25 r_work: 0.3739 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9780 Z= 0.284 Angle : 0.662 7.190 13262 Z= 0.355 Chirality : 0.047 0.217 1475 Planarity : 0.005 0.043 1684 Dihedral : 5.303 30.328 1299 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 5.28 % Allowed : 24.95 % Favored : 69.77 % 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: -0.20 (0.24), residues: 1169 helix: 1.05 (0.25), residues: 444 sheet: -0.39 (0.31), residues: 250 loop : -1.06 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 139 HIS 0.007 0.002 HIS R 374 PHE 0.016 0.002 PHE B 199 TYR 0.011 0.002 TYR N 32 ARG 0.008 0.001 ARG N 72 *********************** 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 162 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 107 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.6885 (mm-40) cc_final: 0.6384 (mm-40) REVERT: A 216 LYS cc_start: 0.6655 (OUTLIER) cc_final: 0.5991 (mmtm) REVERT: A 392 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7640 (mt-10) REVERT: B 46 ARG cc_start: 0.7789 (mtm-85) cc_final: 0.7581 (mtt-85) REVERT: B 112 VAL cc_start: 0.8063 (OUTLIER) cc_final: 0.7810 (m) REVERT: B 266 HIS cc_start: 0.7409 (t-90) cc_final: 0.6955 (t70) REVERT: N 67 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.6506 (ttp80) REVERT: N 83 MET cc_start: 0.6922 (mtp) cc_final: 0.6670 (mtm) REVERT: N 85 SER cc_start: 0.7276 (m) cc_final: 0.6853 (p) REVERT: E 75 MET cc_start: 0.2650 (OUTLIER) cc_final: 0.1491 (tmm) REVERT: E 96 ILE cc_start: 0.5132 (OUTLIER) cc_final: 0.4907 (tt) REVERT: E 140 ARG cc_start: 0.5438 (OUTLIER) cc_final: 0.4226 (mmm160) REVERT: P 18 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7232 (mp10) REVERT: R 287 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7090 (t0) REVERT: R 333 LYS cc_start: 0.5173 (mttp) cc_final: 0.4548 (mmtt) outliers start: 55 outliers final: 26 residues processed: 149 average time/residue: 1.4140 time to fit residues: 223.9949 Evaluate side-chains 136 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 27 ASP Chi-restraints excluded: chain B residue 112 VAL 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 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 88 LEU Chi-restraints excluded: chain E residue 96 ILE 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 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 287 ASP Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain R residue 310 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 54 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4374 r_free = 0.4374 target = 0.216141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.170986 restraints weight = 9675.623| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 1.54 r_work: 0.3718 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9780 Z= 0.186 Angle : 0.570 6.857 13262 Z= 0.303 Chirality : 0.043 0.146 1475 Planarity : 0.004 0.041 1684 Dihedral : 4.957 29.626 1298 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.41 % Allowed : 25.91 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.25), residues: 1169 helix: 1.32 (0.25), residues: 440 sheet: -0.28 (0.32), residues: 243 loop : -1.00 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 139 HIS 0.006 0.001 HIS R 374 PHE 0.013 0.001 PHE B 199 TYR 0.008 0.001 TYR N 95 ARG 0.004 0.000 ARG A 265 *********************** 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 151 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 105 time to evaluate : 1.074 Fit side-chains REVERT: A 35 GLN cc_start: 0.6965 (mm-40) cc_final: 0.6396 (mm-40) REVERT: A 216 LYS cc_start: 0.6691 (OUTLIER) cc_final: 0.6071 (mmtm) REVERT: A 264 ASN cc_start: 0.5164 (OUTLIER) cc_final: 0.4941 (t0) REVERT: A 392 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7762 (mt-10) REVERT: B 217 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6920 (mtt) REVERT: B 266 HIS cc_start: 0.7464 (t-90) cc_final: 0.7091 (t70) REVERT: G 29 LYS cc_start: 0.5726 (mtpp) cc_final: 0.5332 (mtpp) REVERT: N 67 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.6523 (ttp80) REVERT: N 83 MET cc_start: 0.6976 (mtp) cc_final: 0.6628 (mtm) REVERT: N 85 SER cc_start: 0.7209 (m) cc_final: 0.6681 (p) REVERT: E 62 PHE cc_start: 0.2096 (OUTLIER) cc_final: 0.1474 (p90) REVERT: E 75 MET cc_start: 0.2717 (OUTLIER) cc_final: 0.1552 (tmm) REVERT: E 140 ARG cc_start: 0.5409 (OUTLIER) cc_final: 0.4239 (mmm160) REVERT: R 287 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7190 (t0) REVERT: R 303 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7935 (mt) REVERT: R 333 LYS cc_start: 0.5080 (mttp) cc_final: 0.4497 (mmpt) REVERT: R 390 GLU cc_start: 0.6130 (OUTLIER) cc_final: 0.5870 (mt-10) outliers start: 46 outliers final: 22 residues processed: 143 average time/residue: 1.3883 time to fit residues: 211.9169 Evaluate side-chains 135 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 217 MET 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 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 E residue 143 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 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 310 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: 2.9990 chunk 83 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 75 optimal weight: 0.0040 chunk 99 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 R 50 GLN ** 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 = 0.4370 r_free = 0.4370 target = 0.216093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.167310 restraints weight = 9803.422| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.50 r_work: 0.3741 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9780 Z= 0.171 Angle : 0.560 6.919 13262 Z= 0.296 Chirality : 0.043 0.145 1475 Planarity : 0.004 0.042 1684 Dihedral : 4.857 28.426 1298 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.84 % Allowed : 26.39 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.25), residues: 1169 helix: 1.43 (0.25), residues: 438 sheet: -0.25 (0.32), residues: 243 loop : -0.99 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 139 HIS 0.006 0.001 HIS E 97 PHE 0.012 0.001 PHE R 262 TYR 0.007 0.001 TYR R 227 ARG 0.003 0.000 ARG A 265 *********************** 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 146 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.6938 (mm-40) cc_final: 0.6384 (mm-40) REVERT: A 216 LYS cc_start: 0.6709 (OUTLIER) cc_final: 0.6118 (mmtm) REVERT: A 389 ARG cc_start: 0.7802 (ttp-110) cc_final: 0.7598 (ttm110) REVERT: A 392 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7678 (mt-10) REVERT: B 146 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8255 (mm) REVERT: B 217 MET cc_start: 0.7123 (OUTLIER) cc_final: 0.6909 (mtt) REVERT: B 266 HIS cc_start: 0.7444 (t-90) cc_final: 0.7068 (t70) REVERT: G 29 LYS cc_start: 0.5692 (mtpp) cc_final: 0.5383 (mtpp) REVERT: N 67 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6508 (ttp80) REVERT: N 83 MET cc_start: 0.6930 (mtp) cc_final: 0.6584 (mtm) REVERT: N 85 SER cc_start: 0.7199 (m) cc_final: 0.6675 (p) REVERT: E 62 PHE cc_start: 0.2162 (OUTLIER) cc_final: 0.1552 (p90) REVERT: E 75 MET cc_start: 0.2716 (OUTLIER) cc_final: 0.1605 (tmm) REVERT: E 140 ARG cc_start: 0.5385 (OUTLIER) cc_final: 0.4205 (mmm160) REVERT: R 287 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7153 (t0) REVERT: R 303 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7913 (mt) REVERT: R 333 LYS cc_start: 0.5176 (mttp) cc_final: 0.4577 (mmpt) REVERT: R 339 LEU cc_start: 0.7475 (mp) cc_final: 0.7161 (mm) REVERT: R 369 MET cc_start: 0.5601 (OUTLIER) cc_final: 0.5275 (mmt) REVERT: R 390 GLU cc_start: 0.6134 (OUTLIER) cc_final: 0.5870 (mt-10) outliers start: 40 outliers final: 23 residues processed: 138 average time/residue: 1.4740 time to fit residues: 216.0935 Evaluate side-chains 138 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 E residue 143 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 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 310 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: 9.9990 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ** 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 = 0.4380 r_free = 0.4380 target = 0.217372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.166572 restraints weight = 9712.511| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.26 r_work: 0.3777 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9780 Z= 0.169 Angle : 0.557 6.573 13262 Z= 0.294 Chirality : 0.042 0.145 1475 Planarity : 0.004 0.042 1684 Dihedral : 4.799 27.391 1298 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.03 % Allowed : 26.10 % Favored : 69.87 % 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: 0.16 (0.25), residues: 1169 helix: 1.48 (0.25), residues: 438 sheet: -0.20 (0.32), residues: 241 loop : -0.98 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 139 HIS 0.006 0.001 HIS R 374 PHE 0.013 0.001 PHE R 257 TYR 0.007 0.001 TYR R 227 ARG 0.004 0.000 ARG A 265 *********************** 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 147 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 105 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.6956 (mm-40) cc_final: 0.6448 (mm-40) REVERT: A 216 LYS cc_start: 0.6692 (OUTLIER) cc_final: 0.6161 (mmtm) REVERT: B 59 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: B 146 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8219 (mm) REVERT: B 266 HIS cc_start: 0.7409 (t-90) cc_final: 0.7052 (t70) REVERT: N 67 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6507 (ttp80) REVERT: N 83 MET cc_start: 0.6891 (mtp) cc_final: 0.6612 (mtm) REVERT: N 85 SER cc_start: 0.7165 (m) cc_final: 0.6714 (p) REVERT: E 75 MET cc_start: 0.2719 (OUTLIER) cc_final: 0.1552 (tmm) REVERT: E 140 ARG cc_start: 0.5346 (OUTLIER) cc_final: 0.4194 (mmm160) REVERT: R 85 MET cc_start: 0.4003 (pp-130) cc_final: 0.3176 (mpp) REVERT: R 287 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7096 (t0) REVERT: R 303 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7900 (mt) REVERT: R 333 LYS cc_start: 0.5197 (mttp) cc_final: 0.4603 (mmpt) REVERT: R 369 MET cc_start: 0.5594 (OUTLIER) cc_final: 0.5267 (mmt) outliers start: 42 outliers final: 23 residues processed: 139 average time/residue: 1.4130 time to fit residues: 209.1616 Evaluate side-chains 136 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LYS 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 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 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 39 VAL Chi-restraints excluded: chain R residue 68 THR 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 310 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.0470 chunk 99 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 66 optimal weight: 0.0770 chunk 8 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 overall best weight: 0.4836 ------------------------------------------------------------------------------- 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 ** 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 = 0.4393 r_free = 0.4393 target = 0.218839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.171741 restraints weight = 9819.638| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 1.49 r_work: 0.3762 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2654 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= 0.150 Angle : 0.536 6.503 13262 Z= 0.281 Chirality : 0.042 0.145 1475 Planarity : 0.004 0.042 1684 Dihedral : 4.626 30.756 1298 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.69 % Allowed : 27.35 % Favored : 69.96 % 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: 0.27 (0.25), residues: 1169 helix: 1.62 (0.25), residues: 437 sheet: -0.21 (0.32), residues: 242 loop : -0.92 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 139 HIS 0.005 0.001 HIS R 374 PHE 0.012 0.001 PHE R 262 TYR 0.006 0.001 TYR B 145 ARG 0.002 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 138 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.6954 (mm-40) cc_final: 0.6395 (mm-40) REVERT: A 209 GLU cc_start: 0.6474 (mt-10) cc_final: 0.5964 (mp0) REVERT: B 46 ARG cc_start: 0.7845 (mtm-85) cc_final: 0.7345 (mmt-90) REVERT: B 59 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.7928 (m-80) REVERT: B 146 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8200 (mm) REVERT: B 266 HIS cc_start: 0.7408 (t-90) cc_final: 0.6929 (t70) REVERT: N 83 MET cc_start: 0.6911 (mtp) cc_final: 0.6597 (mtm) REVERT: E 62 PHE cc_start: 0.2168 (OUTLIER) cc_final: 0.1541 (p90) REVERT: E 75 MET cc_start: 0.2655 (OUTLIER) cc_final: 0.1524 (tmm) REVERT: E 140 ARG cc_start: 0.5335 (OUTLIER) cc_final: 0.4207 (mmm160) REVERT: R 85 MET cc_start: 0.4072 (pp-130) cc_final: 0.3370 (mpp) REVERT: R 287 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7146 (t0) REVERT: R 333 LYS cc_start: 0.5124 (mttp) cc_final: 0.4555 (mmpt) REVERT: R 339 LEU cc_start: 0.7388 (mp) cc_final: 0.7078 (mm) REVERT: R 369 MET cc_start: 0.5431 (OUTLIER) cc_final: 0.4885 (mmm) outliers start: 28 outliers final: 15 residues processed: 132 average time/residue: 1.4355 time to fit residues: 201.4800 Evaluate side-chains 126 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR 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 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 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 144 LEU Chi-restraints excluded: chain R residue 287 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 97 optimal weight: 0.0020 chunk 12 optimal weight: 0.0040 chunk 23 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 55 optimal weight: 0.0050 overall best weight: 0.2814 ------------------------------------------------------------------------------- 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 268 ASN E 86 ASN ** R 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 ASN ** 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 = 0.4406 r_free = 0.4406 target = 0.220395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.171894 restraints weight = 9923.249| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 1.58 r_work: 0.3782 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2668 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= 0.136 Angle : 0.520 6.804 13262 Z= 0.272 Chirality : 0.041 0.145 1475 Planarity : 0.003 0.041 1684 Dihedral : 4.390 27.876 1298 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.40 % Allowed : 27.45 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.25), residues: 1169 helix: 1.65 (0.26), residues: 443 sheet: -0.25 (0.32), residues: 248 loop : -0.80 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 139 HIS 0.005 0.001 HIS R 374 PHE 0.011 0.001 PHE E 101 TYR 0.007 0.001 TYR B 145 ARG 0.003 0.000 ARG N 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10740.62 seconds wall clock time: 189 minutes 12.51 seconds (11352.51 seconds total)