Starting phenix.real_space_refine on Wed Sep 17 10:14:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lrb_63324/09_2025/9lrb_63324_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lrb_63324/09_2025/9lrb_63324.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lrb_63324/09_2025/9lrb_63324_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lrb_63324/09_2025/9lrb_63324_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lrb_63324/09_2025/9lrb_63324.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lrb_63324/09_2025/9lrb_63324.map" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.119 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5146 2.51 5 N 1415 2.21 5 O 1485 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8102 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1924 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 1 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2598 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 393 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 968 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2211 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 9, 'TRANS': 257} Chain breaks: 2 Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.09, per 1000 atoms: 0.26 Number of scatterers: 8102 At special positions: 0 Unit cell: (79.4033, 100.707, 133.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1485 8.00 N 1415 7.00 C 5146 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, 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 R 100 " - pdb=" SG CYS R 180 " distance=2.03 Simple disulfide: pdb=" SG CYS R 441 " - pdb=" SG CYS R 444 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 423.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1922 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 42.9% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 Processing helix chain 'A' and resid 52 through 57 removed outlier: 3.641A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 52 through 57' Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.617A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.657A pdb=" N ALA A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 removed outlier: 3.594A pdb=" N LEU A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 302 through 308 removed outlier: 3.911A pdb=" N ALA A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 343 removed outlier: 3.740A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 381 Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 11 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.944A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.603A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 56 removed outlier: 4.347A pdb=" N ARG R 56 " --> pdb=" O VAL R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 91 removed outlier: 5.178A pdb=" N MET R 81 " --> pdb=" O GLY R 77 " (cutoff:3.500A) Proline residue: R 82 - end of helix Processing helix chain 'R' and resid 95 through 131 removed outlier: 4.483A pdb=" N LEU R 99 " --> pdb=" O LEU R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 136 removed outlier: 3.543A pdb=" N LEU R 136 " --> pdb=" O PRO R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 157 Processing helix chain 'R' and resid 158 through 165 removed outlier: 3.908A pdb=" N ILE R 162 " --> pdb=" O TRP R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 199 Processing helix chain 'R' and resid 199 through 222 Processing helix chain 'R' and resid 410 through 442 Proline residue: R 430 - end of helix Processing helix chain 'R' and resid 446 through 464 removed outlier: 3.701A pdb=" N HIS R 450 " --> pdb=" O ASN R 446 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER R 461 " --> pdb=" O GLY R 457 " (cutoff:3.500A) Processing helix chain 'R' and resid 465 through 467 No H-bonds generated for 'chain 'R' and resid 465 through 467' Processing helix chain 'R' and resid 468 through 471 removed outlier: 3.531A pdb=" N CYS R 471 " --> pdb=" O TYR R 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 468 through 471' Processing helix chain 'R' and resid 472 through 482 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 9.087A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.569A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.793A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.733A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.226A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.916A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.372A 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: 6.381A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.617A 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: 3.656A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.311A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1179 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.34 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2644 1.34 - 1.46: 1997 1.46 - 1.58: 3555 1.58 - 1.70: 0 1.70 - 1.82: 79 Bond restraints: 8275 Sorted by residual: bond pdb=" N GLN B 1 " pdb=" CA GLN B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N GLN R 26 " pdb=" CA GLN R 26 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N THR A 9 " pdb=" CA THR A 9 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N ALA G 10 " pdb=" CA ALA G 10 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N GLN N 1 " pdb=" CA GLN N 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 ... (remaining 8270 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 10982 1.37 - 2.74: 187 2.74 - 4.11: 27 4.11 - 5.48: 6 5.48 - 6.85: 1 Bond angle restraints: 11203 Sorted by residual: angle pdb=" CA GLY B 185 " pdb=" C GLY B 185 " pdb=" N ASP B 186 " ideal model delta sigma weight residual 114.65 117.04 -2.39 9.20e-01 1.18e+00 6.77e+00 angle pdb=" C ILE A 298 " pdb=" CA ILE A 298 " pdb=" CB ILE A 298 " ideal model delta sigma weight residual 112.16 108.19 3.97 1.55e+00 4.16e-01 6.58e+00 angle pdb=" CA GLY B 330 " pdb=" C GLY B 330 " pdb=" N SER B 331 " ideal model delta sigma weight residual 114.74 117.36 -2.62 1.13e+00 7.83e-01 5.38e+00 angle pdb=" N GLY B 224 " pdb=" CA GLY B 224 " pdb=" C GLY B 224 " ideal model delta sigma weight residual 113.18 107.72 5.46 2.37e+00 1.78e-01 5.31e+00 angle pdb=" N ALA N 92 " pdb=" CA ALA N 92 " pdb=" C ALA N 92 " ideal model delta sigma weight residual 107.88 110.86 -2.98 1.41e+00 5.03e-01 4.47e+00 ... (remaining 11198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 4450 17.72 - 35.44: 365 35.44 - 53.15: 89 53.15 - 70.87: 21 70.87 - 88.59: 6 Dihedral angle restraints: 4931 sinusoidal: 1961 harmonic: 2970 Sorted by residual: dihedral pdb=" CA LEU A 281 " pdb=" C LEU A 281 " pdb=" N ASN A 282 " pdb=" CA ASN A 282 " ideal model delta harmonic sigma weight residual 180.00 -152.47 -27.53 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CB CYS R 441 " pdb=" SG CYS R 441 " pdb=" SG CYS R 444 " pdb=" CB CYS R 444 " ideal model delta sinusoidal sigma weight residual -86.00 -127.09 41.09 1 1.00e+01 1.00e-02 2.36e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual -86.00 -57.67 -28.33 1 1.00e+01 1.00e-02 1.15e+01 ... (remaining 4928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 766 0.027 - 0.053: 305 0.053 - 0.080: 99 0.080 - 0.106: 52 0.106 - 0.133: 25 Chirality restraints: 1247 Sorted by residual: chirality pdb=" CA VAL B 112 " pdb=" N VAL B 112 " pdb=" C VAL B 112 " pdb=" CB VAL B 112 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA ILE A 244 " pdb=" N ILE A 244 " pdb=" C ILE A 244 " pdb=" CB ILE A 244 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA ILE B 229 " pdb=" N ILE B 229 " pdb=" C ILE B 229 " pdb=" CB ILE B 229 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 1244 not shown) Planarity restraints: 1426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 464 " 0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO R 465 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO R 465 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 465 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.021 5.00e-02 4.00e+02 3.11e-02 1.55e+00 pdb=" N PRO B 236 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 143 " 0.004 2.00e-02 2.50e+03 8.45e-03 7.14e-01 pdb=" C THR B 143 " -0.015 2.00e-02 2.50e+03 pdb=" O THR B 143 " 0.006 2.00e-02 2.50e+03 pdb=" N GLY B 144 " 0.005 2.00e-02 2.50e+03 ... (remaining 1423 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1504 2.77 - 3.31: 7694 3.31 - 3.84: 13309 3.84 - 4.37: 16508 4.37 - 4.90: 28407 Nonbonded interactions: 67422 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.243 3.040 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.263 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.268 3.040 nonbonded pdb=" O VAL R 109 " pdb=" OG SER R 155 " model vdw 2.295 3.040 nonbonded pdb=" OG1 THR N 28 " pdb=" OD1 ASN N 31 " model vdw 2.307 3.040 ... (remaining 67417 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.090 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 0.033 8279 Z= 0.116 Angle : 0.473 6.851 11211 Z= 0.268 Chirality : 0.038 0.133 1247 Planarity : 0.002 0.032 1426 Dihedral : 14.226 88.587 2997 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.91 % Allowed : 8.23 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.27), residues: 1002 helix: 2.54 (0.28), residues: 382 sheet: 0.08 (0.34), residues: 216 loop : -0.60 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 228 TYR 0.013 0.001 TYR R 431 PHE 0.014 0.001 PHE R 435 TRP 0.011 0.001 TRP A 234 HIS 0.002 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 8275) covalent geometry : angle 0.47303 (11203) SS BOND : bond 0.00171 ( 4) SS BOND : angle 0.74839 ( 8) hydrogen bonds : bond 0.18479 ( 413) hydrogen bonds : angle 6.20736 ( 1179) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 185 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 THR cc_start: 0.7893 (m) cc_final: 0.7539 (p) REVERT: A 258 GLU cc_start: 0.8523 (tt0) cc_final: 0.8063 (tt0) REVERT: A 274 THR cc_start: 0.8655 (m) cc_final: 0.8264 (p) REVERT: A 323 ARG cc_start: 0.6525 (mtm180) cc_final: 0.5833 (mmm160) REVERT: B 46 ARG cc_start: 0.8125 (mtt90) cc_final: 0.7848 (mmt-90) REVERT: B 323 ASP cc_start: 0.7477 (p0) cc_final: 0.7215 (p0) REVERT: N 46 GLU cc_start: 0.8210 (pt0) cc_final: 0.7836 (pt0) REVERT: R 106 MET cc_start: 0.7764 (mmp) cc_final: 0.7412 (tpp) REVERT: R 134 ARG cc_start: 0.7730 (mpp-170) cc_final: 0.7247 (mtm180) outliers start: 8 outliers final: 8 residues processed: 193 average time/residue: 0.6362 time to fit residues: 129.6558 Evaluate side-chains 134 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 444 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 GLN A 347 HIS ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN N 3 GLN N 13 GLN N 35 ASN ** R 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 460 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.173994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.137631 restraints weight = 8593.333| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.69 r_work: 0.3335 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8279 Z= 0.171 Angle : 0.592 8.189 11211 Z= 0.318 Chirality : 0.044 0.174 1247 Planarity : 0.004 0.046 1426 Dihedral : 6.256 58.869 1130 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.23 % Allowed : 13.60 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.26), residues: 1002 helix: 2.60 (0.27), residues: 376 sheet: 0.09 (0.33), residues: 212 loop : -0.71 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 307 TYR 0.017 0.002 TYR A 329 PHE 0.021 0.002 PHE R 435 TRP 0.022 0.002 TRP B 82 HIS 0.006 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8275) covalent geometry : angle 0.59030 (11203) SS BOND : bond 0.00186 ( 4) SS BOND : angle 1.87140 ( 8) hydrogen bonds : bond 0.05461 ( 413) hydrogen bonds : angle 4.67251 ( 1179) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7527 (ttt180) REVERT: A 274 THR cc_start: 0.8526 (m) cc_final: 0.8202 (p) REVERT: A 304 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7043 (mt-10) REVERT: B 46 ARG cc_start: 0.8501 (mtt90) cc_final: 0.8044 (mmt-90) REVERT: B 186 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7483 (m-30) REVERT: N 65 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7949 (ttpt) REVERT: N 83 MET cc_start: 0.7922 (mtm) cc_final: 0.7655 (mtm) REVERT: R 92 LYS cc_start: 0.8116 (ptpt) cc_final: 0.7655 (pttm) REVERT: R 106 MET cc_start: 0.7756 (mmp) cc_final: 0.7422 (tpp) REVERT: R 470 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8540 (mp) outliers start: 37 outliers final: 18 residues processed: 140 average time/residue: 0.6388 time to fit residues: 94.6343 Evaluate side-chains 133 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 444 CYS Chi-restraints excluded: chain R residue 470 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 60 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 30 optimal weight: 0.0770 chunk 31 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN A 347 HIS B 268 ASN N 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.178184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.141752 restraints weight = 8472.601| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.59 r_work: 0.3412 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8279 Z= 0.116 Angle : 0.511 7.022 11211 Z= 0.274 Chirality : 0.041 0.169 1247 Planarity : 0.003 0.049 1426 Dihedral : 5.741 53.302 1129 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.89 % Allowed : 14.40 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.26), residues: 1002 helix: 2.72 (0.27), residues: 377 sheet: 0.30 (0.33), residues: 221 loop : -0.69 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 307 TYR 0.013 0.001 TYR A 329 PHE 0.016 0.001 PHE R 435 TRP 0.021 0.002 TRP B 82 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8275) covalent geometry : angle 0.51013 (11203) SS BOND : bond 0.00174 ( 4) SS BOND : angle 1.37013 ( 8) hydrogen bonds : bond 0.04439 ( 413) hydrogen bonds : angle 4.31004 ( 1179) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 THR cc_start: 0.8418 (m) cc_final: 0.8149 (p) REVERT: A 307 ARG cc_start: 0.7471 (mtm110) cc_final: 0.7208 (mtm-85) REVERT: B 46 ARG cc_start: 0.8426 (mtt90) cc_final: 0.8079 (mmt-90) REVERT: B 127 LYS cc_start: 0.8262 (mmtt) cc_final: 0.7697 (mptt) REVERT: B 186 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7223 (m-30) REVERT: N 65 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8017 (ttpt) REVERT: R 50 TYR cc_start: 0.7287 (t80) cc_final: 0.7040 (t80) REVERT: R 92 LYS cc_start: 0.8236 (ptpt) cc_final: 0.7761 (pttm) REVERT: R 106 MET cc_start: 0.7741 (mmp) cc_final: 0.7536 (tpp) outliers start: 34 outliers final: 16 residues processed: 138 average time/residue: 0.6261 time to fit residues: 91.5912 Evaluate side-chains 127 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 198 ASN Chi-restraints excluded: chain R residue 444 CYS Chi-restraints excluded: chain R residue 466 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 347 HIS B 268 ASN B 340 ASN N 31 ASN R 472 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.176475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.141519 restraints weight = 8709.009| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.50 r_work: 0.3388 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8279 Z= 0.134 Angle : 0.530 7.133 11211 Z= 0.281 Chirality : 0.041 0.166 1247 Planarity : 0.004 0.050 1426 Dihedral : 5.383 52.711 1123 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.54 % Allowed : 16.91 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.27), residues: 1002 helix: 2.70 (0.27), residues: 378 sheet: 0.30 (0.33), residues: 221 loop : -0.69 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 134 TYR 0.016 0.001 TYR N 80 PHE 0.017 0.001 PHE R 435 TRP 0.021 0.002 TRP B 82 HIS 0.005 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8275) covalent geometry : angle 0.52876 (11203) SS BOND : bond 0.00232 ( 4) SS BOND : angle 1.22806 ( 8) hydrogen bonds : bond 0.04541 ( 413) hydrogen bonds : angle 4.27697 ( 1179) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 THR cc_start: 0.8407 (m) cc_final: 0.8174 (p) REVERT: B 46 ARG cc_start: 0.8364 (mtt90) cc_final: 0.8019 (mmt-90) REVERT: B 127 LYS cc_start: 0.8209 (mmtt) cc_final: 0.7626 (mptt) REVERT: B 186 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.7319 (m-30) REVERT: B 243 THR cc_start: 0.8803 (p) cc_final: 0.8529 (p) REVERT: B 322 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7381 (m-30) REVERT: B 323 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7925 (OUTLIER) REVERT: N 65 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7971 (ttpt) REVERT: R 50 TYR cc_start: 0.7318 (t80) cc_final: 0.7057 (t80) REVERT: R 470 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8552 (mp) outliers start: 31 outliers final: 18 residues processed: 130 average time/residue: 0.6700 time to fit residues: 91.9048 Evaluate side-chains 129 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 122 CYS Chi-restraints excluded: chain R residue 197 ILE Chi-restraints excluded: chain R residue 198 ASN Chi-restraints excluded: chain R residue 444 CYS Chi-restraints excluded: chain R residue 470 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 90 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 23 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 HIS B 268 ASN R 131 GLN R 416 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.175467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.138234 restraints weight = 8631.857| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.63 r_work: 0.3370 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8279 Z= 0.159 Angle : 0.569 10.854 11211 Z= 0.298 Chirality : 0.042 0.165 1247 Planarity : 0.004 0.050 1426 Dihedral : 5.644 57.605 1123 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.66 % Allowed : 17.60 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.27), residues: 1002 helix: 2.61 (0.27), residues: 378 sheet: 0.22 (0.33), residues: 223 loop : -0.68 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 307 TYR 0.017 0.002 TYR N 80 PHE 0.017 0.002 PHE R 435 TRP 0.021 0.002 TRP B 82 HIS 0.005 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8275) covalent geometry : angle 0.56859 (11203) SS BOND : bond 0.00277 ( 4) SS BOND : angle 1.29556 ( 8) hydrogen bonds : bond 0.04797 ( 413) hydrogen bonds : angle 4.33688 ( 1179) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 THR cc_start: 0.8435 (m) cc_final: 0.8223 (p) REVERT: A 307 ARG cc_start: 0.7480 (mtm110) cc_final: 0.7134 (mtm-85) REVERT: B 46 ARG cc_start: 0.8416 (mtt90) cc_final: 0.8063 (mmt-90) REVERT: B 127 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7620 (mptt) REVERT: B 186 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7391 (m-30) REVERT: B 198 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7740 (mt) REVERT: B 243 THR cc_start: 0.8822 (p) cc_final: 0.8539 (p) REVERT: B 322 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7359 (m-30) REVERT: B 323 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7941 (OUTLIER) REVERT: N 65 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7963 (ttpt) REVERT: R 50 TYR cc_start: 0.7366 (t80) cc_final: 0.7130 (t80) REVERT: R 92 LYS cc_start: 0.8137 (ptmt) cc_final: 0.7759 (pttm) REVERT: R 465 PRO cc_start: 0.8233 (Cg_exo) cc_final: 0.7992 (Cg_endo) REVERT: R 470 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8527 (mp) outliers start: 32 outliers final: 20 residues processed: 130 average time/residue: 0.6311 time to fit residues: 86.7436 Evaluate side-chains 133 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 122 CYS Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 198 ASN Chi-restraints excluded: chain R residue 444 CYS Chi-restraints excluded: chain R residue 470 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 93 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 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 347 HIS B 268 ASN R 472 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.177428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.141061 restraints weight = 8527.102| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.57 r_work: 0.3378 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8279 Z= 0.113 Angle : 0.509 9.200 11211 Z= 0.268 Chirality : 0.041 0.165 1247 Planarity : 0.003 0.052 1426 Dihedral : 5.068 49.585 1121 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.20 % Allowed : 18.86 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.27), residues: 1002 helix: 2.77 (0.27), residues: 378 sheet: 0.27 (0.33), residues: 217 loop : -0.60 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 307 TYR 0.014 0.001 TYR A 329 PHE 0.014 0.001 PHE R 435 TRP 0.020 0.001 TRP B 82 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 8275) covalent geometry : angle 0.50841 (11203) SS BOND : bond 0.00201 ( 4) SS BOND : angle 1.03048 ( 8) hydrogen bonds : bond 0.04142 ( 413) hydrogen bonds : angle 4.15157 ( 1179) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 GLU cc_start: 0.8751 (tt0) cc_final: 0.8313 (tt0) REVERT: A 274 THR cc_start: 0.8402 (m) cc_final: 0.8175 (p) REVERT: A 307 ARG cc_start: 0.7436 (mtm110) cc_final: 0.7208 (mtm-85) REVERT: A 333 ASP cc_start: 0.6953 (OUTLIER) cc_final: 0.6421 (m-30) REVERT: B 46 ARG cc_start: 0.8348 (mtt90) cc_final: 0.8022 (mmt-90) REVERT: B 186 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7210 (m-30) REVERT: B 198 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7660 (mt) REVERT: B 243 THR cc_start: 0.8771 (p) cc_final: 0.8469 (p) REVERT: B 322 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7343 (m-30) REVERT: G 21 MET cc_start: 0.7060 (ttt) cc_final: 0.6775 (ttt) REVERT: N 65 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7969 (ttpt) REVERT: R 50 TYR cc_start: 0.7313 (t80) cc_final: 0.7015 (t80) REVERT: R 92 LYS cc_start: 0.8143 (ptmt) cc_final: 0.7752 (pttm) REVERT: R 465 PRO cc_start: 0.8178 (Cg_exo) cc_final: 0.7940 (Cg_endo) REVERT: R 470 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8535 (mp) outliers start: 28 outliers final: 18 residues processed: 134 average time/residue: 0.6559 time to fit residues: 92.8551 Evaluate side-chains 136 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 122 CYS Chi-restraints excluded: chain R residue 198 ASN Chi-restraints excluded: chain R residue 444 CYS Chi-restraints excluded: chain R residue 470 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 67 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 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 347 HIS ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.176652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.140042 restraints weight = 8594.890| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.57 r_work: 0.3366 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8279 Z= 0.129 Angle : 0.527 9.280 11211 Z= 0.277 Chirality : 0.041 0.164 1247 Planarity : 0.003 0.053 1426 Dihedral : 5.145 51.363 1121 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.77 % Allowed : 18.40 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.27), residues: 1002 helix: 2.75 (0.27), residues: 378 sheet: 0.30 (0.33), residues: 225 loop : -0.62 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 307 TYR 0.016 0.001 TYR N 80 PHE 0.016 0.001 PHE R 435 TRP 0.020 0.002 TRP B 82 HIS 0.007 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8275) covalent geometry : angle 0.52587 (11203) SS BOND : bond 0.00248 ( 4) SS BOND : angle 1.10781 ( 8) hydrogen bonds : bond 0.04342 ( 413) hydrogen bonds : angle 4.18126 ( 1179) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 THR cc_start: 0.8064 (m) cc_final: 0.7567 (p) REVERT: A 274 THR cc_start: 0.8426 (m) cc_final: 0.8191 (p) REVERT: A 307 ARG cc_start: 0.7458 (mtm110) cc_final: 0.7236 (mtm-85) REVERT: B 46 ARG cc_start: 0.8362 (mtt90) cc_final: 0.7991 (mmt-90) REVERT: B 186 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7263 (m-30) REVERT: B 198 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7714 (mt) REVERT: B 243 THR cc_start: 0.8780 (p) cc_final: 0.8480 (p) REVERT: B 322 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7351 (m-30) REVERT: G 21 MET cc_start: 0.7212 (ttt) cc_final: 0.6899 (ttt) REVERT: N 65 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7963 (ttpt) REVERT: R 50 TYR cc_start: 0.7347 (t80) cc_final: 0.7047 (t80) REVERT: R 92 LYS cc_start: 0.8172 (ptmt) cc_final: 0.7778 (pttm) REVERT: R 465 PRO cc_start: 0.8204 (Cg_exo) cc_final: 0.7982 (Cg_endo) REVERT: R 470 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8545 (mp) outliers start: 33 outliers final: 20 residues processed: 137 average time/residue: 0.6469 time to fit residues: 93.5870 Evaluate side-chains 140 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 122 CYS Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 198 ASN Chi-restraints excluded: chain R residue 444 CYS Chi-restraints excluded: chain R residue 470 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 HIS ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN N 3 GLN R 472 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.176487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.140565 restraints weight = 8545.518| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.53 r_work: 0.3381 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8279 Z= 0.127 Angle : 0.527 8.951 11211 Z= 0.276 Chirality : 0.041 0.165 1247 Planarity : 0.003 0.055 1426 Dihedral : 5.046 51.169 1121 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.54 % Allowed : 18.51 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.27), residues: 1002 helix: 2.72 (0.27), residues: 378 sheet: 0.25 (0.33), residues: 217 loop : -0.57 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 307 TYR 0.015 0.001 TYR N 80 PHE 0.015 0.001 PHE R 435 TRP 0.020 0.002 TRP B 82 HIS 0.006 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8275) covalent geometry : angle 0.52628 (11203) SS BOND : bond 0.00224 ( 4) SS BOND : angle 1.18112 ( 8) hydrogen bonds : bond 0.04318 ( 413) hydrogen bonds : angle 4.19436 ( 1179) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8535 (mt) REVERT: A 55 THR cc_start: 0.8125 (m) cc_final: 0.7657 (p) REVERT: A 258 GLU cc_start: 0.8760 (tt0) cc_final: 0.8331 (tt0) REVERT: A 274 THR cc_start: 0.8417 (m) cc_final: 0.8199 (p) REVERT: A 333 ASP cc_start: 0.6993 (OUTLIER) cc_final: 0.6500 (m-30) REVERT: B 46 ARG cc_start: 0.8360 (mtt90) cc_final: 0.7993 (mmt-90) REVERT: B 186 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7260 (m-30) REVERT: B 198 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7716 (mt) REVERT: B 243 THR cc_start: 0.8775 (p) cc_final: 0.8465 (p) REVERT: B 322 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7308 (m-30) REVERT: B 323 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.8037 (OUTLIER) REVERT: G 21 MET cc_start: 0.7299 (ttt) cc_final: 0.6855 (ttt) REVERT: N 65 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7955 (ttpt) REVERT: R 92 LYS cc_start: 0.8327 (ptmt) cc_final: 0.7900 (pttm) REVERT: R 179 LYS cc_start: 0.8324 (mmmm) cc_final: 0.8086 (mmtm) outliers start: 31 outliers final: 18 residues processed: 135 average time/residue: 0.6514 time to fit residues: 93.0050 Evaluate side-chains 136 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 122 CYS Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 198 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 62 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 74 optimal weight: 0.2980 chunk 64 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 chunk 80 optimal weight: 0.8980 chunk 12 optimal weight: 0.0770 chunk 20 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 HIS ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.177960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.139915 restraints weight = 8535.795| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.59 r_work: 0.3379 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8279 Z= 0.104 Angle : 0.492 8.813 11211 Z= 0.259 Chirality : 0.040 0.164 1247 Planarity : 0.003 0.054 1426 Dihedral : 4.658 44.239 1120 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.74 % Allowed : 19.31 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.27), residues: 1002 helix: 2.84 (0.27), residues: 378 sheet: 0.40 (0.33), residues: 223 loop : -0.59 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 134 TYR 0.013 0.001 TYR N 80 PHE 0.014 0.001 PHE R 435 TRP 0.020 0.001 TRP B 82 HIS 0.006 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 8275) covalent geometry : angle 0.49169 (11203) SS BOND : bond 0.00163 ( 4) SS BOND : angle 0.97473 ( 8) hydrogen bonds : bond 0.03894 ( 413) hydrogen bonds : angle 4.05156 ( 1179) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8509 (mt) REVERT: A 55 THR cc_start: 0.8001 (m) cc_final: 0.7572 (p) REVERT: A 258 GLU cc_start: 0.8732 (tt0) cc_final: 0.8289 (tt0) REVERT: A 274 THR cc_start: 0.8340 (m) cc_final: 0.8097 (p) REVERT: A 333 ASP cc_start: 0.7008 (OUTLIER) cc_final: 0.6464 (m-30) REVERT: B 46 ARG cc_start: 0.8416 (mtt90) cc_final: 0.8028 (mmt-90) REVERT: B 186 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7140 (m-30) REVERT: B 198 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7632 (mt) REVERT: B 243 THR cc_start: 0.8756 (p) cc_final: 0.8439 (p) REVERT: B 322 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7435 (m-30) REVERT: B 323 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.8010 (OUTLIER) REVERT: G 21 MET cc_start: 0.7301 (ttt) cc_final: 0.6862 (ttt) REVERT: R 92 LYS cc_start: 0.8342 (ptmt) cc_final: 0.7886 (pttm) outliers start: 24 outliers final: 16 residues processed: 132 average time/residue: 0.6636 time to fit residues: 92.5577 Evaluate side-chains 133 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 122 CYS Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 198 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 0.0970 chunk 38 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 HIS ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN R 472 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.176848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.140446 restraints weight = 8501.723| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.54 r_work: 0.3379 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8279 Z= 0.130 Angle : 0.535 8.890 11211 Z= 0.280 Chirality : 0.041 0.163 1247 Planarity : 0.004 0.055 1426 Dihedral : 4.993 51.722 1120 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.97 % Allowed : 19.54 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.27), residues: 1002 helix: 2.79 (0.27), residues: 378 sheet: 0.35 (0.34), residues: 215 loop : -0.61 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 307 TYR 0.017 0.001 TYR N 80 PHE 0.016 0.001 PHE R 435 TRP 0.020 0.002 TRP B 82 HIS 0.008 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8275) covalent geometry : angle 0.53436 (11203) SS BOND : bond 0.00216 ( 4) SS BOND : angle 1.13715 ( 8) hydrogen bonds : bond 0.04300 ( 413) hydrogen bonds : angle 4.16380 ( 1179) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8571 (mt) REVERT: A 55 THR cc_start: 0.8044 (m) cc_final: 0.7605 (p) REVERT: A 258 GLU cc_start: 0.8762 (tt0) cc_final: 0.8323 (tt0) REVERT: A 307 ARG cc_start: 0.7512 (mtm110) cc_final: 0.7188 (mtm-85) REVERT: A 333 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6414 (m-30) REVERT: B 46 ARG cc_start: 0.8335 (mtt90) cc_final: 0.8024 (mmt-90) REVERT: B 186 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7241 (m-30) REVERT: B 198 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7722 (mt) REVERT: B 243 THR cc_start: 0.8763 (p) cc_final: 0.8508 (p) REVERT: B 322 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7328 (m-30) REVERT: B 323 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.8051 (OUTLIER) REVERT: G 21 MET cc_start: 0.7340 (ttt) cc_final: 0.6885 (ttt) REVERT: R 38 CYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7746 (t) REVERT: R 92 LYS cc_start: 0.8389 (ptmt) cc_final: 0.7949 (pttm) outliers start: 26 outliers final: 19 residues processed: 130 average time/residue: 0.6359 time to fit residues: 87.1345 Evaluate side-chains 133 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 38 CYS Chi-restraints excluded: chain R residue 122 CYS Chi-restraints excluded: chain R residue 188 THR Chi-restraints excluded: chain R residue 466 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 35 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 HIS ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.176849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.140319 restraints weight = 8633.149| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.55 r_work: 0.3371 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8279 Z= 0.128 Angle : 0.532 8.944 11211 Z= 0.278 Chirality : 0.041 0.164 1247 Planarity : 0.004 0.055 1426 Dihedral : 5.009 51.654 1120 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.09 % Allowed : 19.31 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.27), residues: 1002 helix: 2.78 (0.27), residues: 378 sheet: 0.28 (0.33), residues: 217 loop : -0.61 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 307 TYR 0.016 0.001 TYR N 80 PHE 0.014 0.001 PHE R 435 TRP 0.020 0.002 TRP B 82 HIS 0.009 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8275) covalent geometry : angle 0.53125 (11203) SS BOND : bond 0.00214 ( 4) SS BOND : angle 1.10869 ( 8) hydrogen bonds : bond 0.04287 ( 413) hydrogen bonds : angle 4.16778 ( 1179) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3443.48 seconds wall clock time: 59 minutes 26.05 seconds (3566.05 seconds total)