Starting phenix.real_space_refine on Tue Mar 3 22:25:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xqc_67110/03_2026/9xqc_67110_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xqc_67110/03_2026/9xqc_67110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xqc_67110/03_2026/9xqc_67110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xqc_67110/03_2026/9xqc_67110.map" model { file = "/net/cci-nas-00/data/ceres_data/9xqc_67110/03_2026/9xqc_67110_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xqc_67110/03_2026/9xqc_67110_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.087 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 61 5.16 5 C 5579 2.51 5 N 1491 2.21 5 O 1637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8768 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1914 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 1 Chain: "C" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2581 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1776 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2055 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 1.93, per 1000 atoms: 0.22 Number of scatterers: 8768 At special positions: 0 Unit cell: (83.224, 121.128, 121.128, 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 61 16.00 O 1637 8.00 N 1491 7.00 C 5579 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 118 " - pdb=" SG CYS R 189 " distance=2.16 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: 0.54 Conformation dependent library (CDL) restraints added in 245.1 milliseconds 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 38.9% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.665A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.695A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.669A pdb=" N ALA A 265 " --> pdb=" O GLN A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.017A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 298 through 318 removed outlier: 3.847A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'C' and resid 9 through 29 removed outlier: 3.539A pdb=" N GLU C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 52 through 55 removed outlier: 3.626A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.855A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 28 through 44 removed outlier: 3.888A pdb=" N ALA G 34 " --> pdb=" O SER G 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 67 removed outlier: 4.453A pdb=" N VAL R 43 " --> pdb=" O THR R 39 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR R 44 " --> pdb=" O ALA R 40 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU R 48 " --> pdb=" O THR R 44 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER R 57 " --> pdb=" O PHE R 53 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE R 67 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 73 removed outlier: 6.291A pdb=" N ALA R 71 " --> pdb=" O PHE R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 96 removed outlier: 3.848A pdb=" N PHE R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET R 82 " --> pdb=" O ASN R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 106 Processing helix chain 'R' and resid 107 through 112 Processing helix chain 'R' and resid 114 through 149 Processing helix chain 'R' and resid 157 through 181 Processing helix chain 'R' and resid 182 through 184 No H-bonds generated for 'chain 'R' and resid 182 through 184' Processing helix chain 'R' and resid 200 through 228 removed outlier: 3.894A pdb=" N LEU R 206 " --> pdb=" O ALA R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 347 Proline residue: R 336 - end of helix removed outlier: 3.855A pdb=" N SER R 340 " --> pdb=" O PRO R 336 " (cutoff:3.500A) Processing helix chain 'R' and resid 351 through 376 removed outlier: 4.020A pdb=" N PHE R 357 " --> pdb=" O ILE R 353 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU R 358 " --> pdb=" O LEU R 354 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU R 359 " --> pdb=" O TYR R 355 " (cutoff:3.500A) Proline residue: R 373 - end of helix Processing helix chain 'R' and resid 382 through 390 removed outlier: 4.598A pdb=" N LEU R 388 " --> pdb=" O ARG R 384 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.238A pdb=" N LEU A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N PHE A 199 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N VAL A 201 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N LEU A 38 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 51 through 57 removed outlier: 5.947A pdb=" N THR C 52 " --> pdb=" O ASN C 345 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN C 345 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE C 340 " --> pdb=" O SER C 336 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS C 322 " --> pdb=" O GLY C 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 63 through 68 removed outlier: 3.643A pdb=" N ALA C 65 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU C 84 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA C 97 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE C 86 " --> pdb=" O VAL C 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 105 through 110 removed outlier: 6.732A pdb=" N GLY C 120 " --> pdb=" O MET C 106 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N CYS C 108 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA C 118 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TYR C 110 " --> pdb=" O TYR C 116 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N TYR C 116 " --> pdb=" O TYR C 110 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY C 121 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE C 125 " --> pdb=" O GLY C 121 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG C 142 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASN C 130 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL C 140 " --> pdb=" O ASN C 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 151 through 158 removed outlier: 3.719A pdb=" N CYS C 153 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASP C 175 " --> pdb=" O GLN C 181 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N GLN C 181 " --> pdb=" O ASP C 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 192 through 197 removed outlier: 6.863A pdb=" N GLY C 207 " --> pdb=" O MET C 193 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU C 195 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL C 205 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LEU C 197 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU C 203 " --> pdb=" O LEU C 197 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN C 225 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ASP C 217 " --> pdb=" O CYS C 223 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N CYS C 223 " --> pdb=" O ASP C 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 234 through 239 removed outlier: 6.198A pdb=" N ASP C 259 " --> pdb=" O GLU C 265 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLU C 265 " --> pdb=" O ASP C 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 278 through 283 removed outlier: 3.661A pdb=" N SER C 280 " --> pdb=" O GLY C 293 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS C 299 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ASP C 303 " --> pdb=" O ARG C 309 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ARG C 309 " --> pdb=" O ASP C 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.765A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 11 removed outlier: 4.448A pdb=" N PHE E 109 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.487A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1254 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: 1.37 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1560 1.31 - 1.44: 2318 1.44 - 1.56: 4975 1.56 - 1.69: 0 1.69 - 1.82: 86 Bond restraints: 8939 Sorted by residual: bond pdb=" CA LYS E 64 " pdb=" C LYS E 64 " ideal model delta sigma weight residual 1.525 1.442 0.083 1.32e-02 5.74e+03 3.95e+01 bond pdb=" CA LEU E 85 " pdb=" C LEU E 85 " ideal model delta sigma weight residual 1.525 1.448 0.077 1.32e-02 5.74e+03 3.39e+01 bond pdb=" C ILE A 221 " pdb=" O ILE A 221 " ideal model delta sigma weight residual 1.238 1.179 0.059 1.10e-02 8.26e+03 2.83e+01 bond pdb=" CA THR E 68 " pdb=" C THR E 68 " ideal model delta sigma weight residual 1.520 1.463 0.057 1.16e-02 7.43e+03 2.43e+01 bond pdb=" CA ASN G 23 " pdb=" C ASN G 23 " ideal model delta sigma weight residual 1.528 1.473 0.055 1.11e-02 8.12e+03 2.42e+01 ... (remaining 8934 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 9281 2.06 - 4.12: 2469 4.12 - 6.19: 317 6.19 - 8.25: 35 8.25 - 10.31: 4 Bond angle restraints: 12106 Sorted by residual: angle pdb=" N SER G 7 " pdb=" CA SER G 7 " pdb=" C SER G 7 " ideal model delta sigma weight residual 111.28 101.22 10.06 1.09e+00 8.42e-01 8.52e+01 angle pdb=" CA PHE C 297 " pdb=" CB PHE C 297 " pdb=" CG PHE C 297 " ideal model delta sigma weight residual 113.80 121.21 -7.41 1.00e+00 1.00e+00 5.48e+01 angle pdb=" CA PHE E 67 " pdb=" CB PHE E 67 " pdb=" CG PHE E 67 " ideal model delta sigma weight residual 113.80 121.03 -7.23 1.00e+00 1.00e+00 5.23e+01 angle pdb=" N SER A 228 " pdb=" CA SER A 228 " pdb=" C SER A 228 " ideal model delta sigma weight residual 111.14 118.86 -7.72 1.08e+00 8.57e-01 5.11e+01 angle pdb=" N LEU C 9 " pdb=" CA LEU C 9 " pdb=" C LEU C 9 " ideal model delta sigma weight residual 111.28 103.51 7.77 1.09e+00 8.42e-01 5.08e+01 ... (remaining 12101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 4914 17.85 - 35.70: 320 35.70 - 53.54: 51 53.54 - 71.39: 16 71.39 - 89.24: 7 Dihedral angle restraints: 5308 sinusoidal: 2052 harmonic: 3256 Sorted by residual: dihedral pdb=" CB CYS R 118 " pdb=" SG CYS R 118 " pdb=" SG CYS R 189 " pdb=" CB CYS R 189 " ideal model delta sinusoidal sigma weight residual 93.00 147.39 -54.39 1 1.00e+01 1.00e-02 4.01e+01 dihedral pdb=" CA LYS C 83 " pdb=" C LYS C 83 " pdb=" N LEU C 84 " pdb=" CA LEU C 84 " ideal model delta harmonic sigma weight residual 180.00 152.14 27.86 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA ASP A 217 " pdb=" C ASP A 217 " pdb=" N VAL A 218 " pdb=" CA VAL A 218 " ideal model delta harmonic sigma weight residual 180.00 152.82 27.18 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 5305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 949 0.090 - 0.179: 353 0.179 - 0.269: 74 0.269 - 0.358: 10 0.358 - 0.448: 5 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CA THR R 180 " pdb=" N THR R 180 " pdb=" C THR R 180 " pdb=" CB THR R 180 " both_signs ideal model delta sigma weight residual False 2.53 2.08 0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" CA THR C 92 " pdb=" N THR C 92 " pdb=" C THR C 92 " pdb=" CB THR C 92 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" CA ASP A 217 " pdb=" N ASP A 217 " pdb=" C ASP A 217 " pdb=" CB ASP A 217 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 1388 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 337 " 0.115 2.00e-02 2.50e+03 6.28e-02 9.86e+01 pdb=" CG TRP C 337 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP C 337 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP C 337 " -0.045 2.00e-02 2.50e+03 pdb=" NE1 TRP C 337 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TRP C 337 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 337 " -0.080 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 337 " 0.081 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 337 " -0.046 2.00e-02 2.50e+03 pdb=" CH2 TRP C 337 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 68 " -0.095 2.00e-02 2.50e+03 5.16e-02 6.66e+01 pdb=" CG TRP C 68 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP C 68 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP C 68 " 0.073 2.00e-02 2.50e+03 pdb=" NE1 TRP C 68 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TRP C 68 " 0.030 2.00e-02 2.50e+03 pdb=" CE3 TRP C 68 " 0.065 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 68 " -0.045 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 68 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 68 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 257 " 0.094 2.00e-02 2.50e+03 6.10e-02 6.52e+01 pdb=" CG PHE A 257 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE A 257 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 PHE A 257 " -0.069 2.00e-02 2.50e+03 pdb=" CE1 PHE A 257 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 257 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 257 " 0.079 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 943 2.78 - 3.31: 9057 3.31 - 3.84: 14442 3.84 - 4.37: 18385 4.37 - 4.90: 30462 Nonbonded interactions: 73289 Sorted by model distance: nonbonded pdb=" CD1 ILE R 113 " pdb=" SG CYS R 189 " model vdw 2.247 3.820 nonbonded pdb=" O LEU R 190 " pdb=" N MET R 192 " model vdw 2.426 3.120 nonbonded pdb=" O LYS R 201 " pdb=" C ALA R 202 " model vdw 2.460 3.270 nonbonded pdb=" O PRO G 54 " pdb=" OD1 ASN G 58 " model vdw 2.471 3.040 nonbonded pdb=" N GLY C 315 " pdb=" O GLY C 315 " model vdw 2.481 2.496 ... (remaining 73284 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: 2.500 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: 0.030 Set scattering table: 0.040 Process input model: 9.020 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 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 : 0.012 0.131 8940 Z= 0.778 Angle : 1.801 11.442 12108 Z= 1.217 Chirality : 0.095 0.448 1391 Planarity : 0.015 0.159 1530 Dihedral : 13.206 89.236 3199 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.80 % Favored : 96.11 % Rotamer: Outliers : 1.14 % Allowed : 5.60 % Favored : 93.26 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.24), residues: 1106 helix: -0.64 (0.24), residues: 356 sheet: 0.68 (0.33), residues: 248 loop : -0.17 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 37 TYR 0.090 0.018 TYR E 175 PHE 0.094 0.013 PHE A 257 TRP 0.115 0.022 TRP C 337 HIS 0.016 0.003 HIS R 122 Details of bonding type rmsd covalent geometry : bond 0.01216 ( 8939) covalent geometry : angle 1.79798 (12106) SS BOND : bond 0.13118 ( 1) SS BOND : angle 8.64411 ( 2) hydrogen bonds : bond 0.18786 ( 442) hydrogen bonds : angle 7.12353 ( 1254) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 284 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7843 (mttp) cc_final: 0.7578 (mtpt) REVERT: A 186 GLU cc_start: 0.7429 (tt0) cc_final: 0.6982 (tt0) REVERT: A 345 ASP cc_start: 0.8371 (m-30) cc_final: 0.8027 (m-30) REVERT: C 15 GLU cc_start: 0.8169 (tp30) cc_final: 0.7931 (tt0) REVERT: C 18 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7750 (tm-30) REVERT: C 24 ARG cc_start: 0.7778 (ttp-170) cc_final: 0.7429 (ttp-170) REVERT: C 25 ASP cc_start: 0.7549 (m-30) cc_final: 0.6943 (m-30) REVERT: C 64 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.7622 (m-80) REVERT: C 330 MET cc_start: 0.8378 (mmt) cc_final: 0.8145 (mmm) REVERT: G 28 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8291 (mptp) outliers start: 11 outliers final: 2 residues processed: 290 average time/residue: 0.5502 time to fit residues: 169.3138 Evaluate side-chains 193 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 189 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 64 TYR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain R residue 77 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 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 238 ASN A 261 GLN A 359 ASN E 2 GLN E 76 ASN E 171 ASN R 85 ASN ** R 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 349 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.151932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124769 restraints weight = 12307.707| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.23 r_work: 0.3172 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8940 Z= 0.154 Angle : 0.648 8.141 12108 Z= 0.341 Chirality : 0.045 0.234 1391 Planarity : 0.004 0.045 1530 Dihedral : 6.109 88.253 1220 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.05 % Allowed : 15.66 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.25), residues: 1106 helix: 1.36 (0.26), residues: 374 sheet: 0.66 (0.30), residues: 296 loop : 0.49 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 202 TYR 0.015 0.001 TYR A 306 PHE 0.020 0.002 PHE R 357 TRP 0.021 0.002 TRP A 211 HIS 0.007 0.001 HIS G 43 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8939) covalent geometry : angle 0.64752 (12106) SS BOND : bond 0.01280 ( 1) SS BOND : angle 2.17150 ( 2) hydrogen bonds : bond 0.04845 ( 442) hydrogen bonds : angle 4.83263 ( 1254) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 0.344 Fit side-chains REVERT: A 351 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8543 (mp) REVERT: C 24 ARG cc_start: 0.8295 (ttp-170) cc_final: 0.7987 (ttp-170) REVERT: C 25 ASP cc_start: 0.7948 (m-30) cc_final: 0.7500 (m-30) REVERT: E 42 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8387 (mmmm) REVERT: E 89 ASP cc_start: 0.8640 (m-30) cc_final: 0.8329 (m-30) REVERT: E 115 THR cc_start: 0.9006 (t) cc_final: 0.8666 (m) REVERT: E 186 GLN cc_start: 0.8830 (tt0) cc_final: 0.8542 (tt0) REVERT: G 13 LYS cc_start: 0.8731 (mmmt) cc_final: 0.8406 (tttm) REVERT: R 72 PHE cc_start: 0.7342 (m-80) cc_final: 0.7113 (m-80) REVERT: R 189 CYS cc_start: 0.6862 (t) cc_final: 0.6651 (t) outliers start: 39 outliers final: 8 residues processed: 232 average time/residue: 0.5766 time to fit residues: 141.4881 Evaluate side-chains 183 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 173 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain R residue 146 MET Chi-restraints excluded: chain R residue 330 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 77 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS A 245 ASN C 93 ASN E 81 GLN E 142 GLN E 194 ASN R 85 ASN R 151 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.148912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.121528 restraints weight = 12196.430| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.02 r_work: 0.3147 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8940 Z= 0.165 Angle : 0.638 11.369 12108 Z= 0.329 Chirality : 0.044 0.217 1391 Planarity : 0.004 0.046 1530 Dihedral : 4.848 23.443 1214 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.25 % Allowed : 18.88 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.25), residues: 1106 helix: 1.56 (0.26), residues: 377 sheet: 0.60 (0.30), residues: 289 loop : 0.45 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 32 TYR 0.015 0.001 TYR A 306 PHE 0.017 0.002 PHE R 357 TRP 0.017 0.002 TRP A 211 HIS 0.006 0.001 HIS G 43 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 8939) covalent geometry : angle 0.63799 (12106) SS BOND : bond 0.00015 ( 1) SS BOND : angle 0.90670 ( 2) hydrogen bonds : bond 0.04664 ( 442) hydrogen bonds : angle 4.53221 ( 1254) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 183 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 306 TYR cc_start: 0.8254 (m-80) cc_final: 0.8032 (m-80) REVERT: A 351 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8353 (mp) REVERT: A 356 ARG cc_start: 0.8113 (ttm-80) cc_final: 0.7733 (mtm180) REVERT: C 24 ARG cc_start: 0.8290 (ttp-170) cc_final: 0.8042 (ttp-170) REVERT: C 25 ASP cc_start: 0.7991 (m-30) cc_final: 0.7557 (m-30) REVERT: C 202 ARG cc_start: 0.8096 (mtp85) cc_final: 0.7823 (mmm160) REVERT: C 319 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7994 (ttm170) REVERT: E 42 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8570 (mmmm) REVERT: E 89 ASP cc_start: 0.8651 (m-30) cc_final: 0.8341 (m-30) REVERT: G 13 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8549 (tttm) REVERT: G 57 GLU cc_start: 0.8202 (mp0) cc_final: 0.7926 (mp0) outliers start: 41 outliers final: 12 residues processed: 207 average time/residue: 0.6316 time to fit residues: 137.9722 Evaluate side-chains 177 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain R residue 146 MET Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 330 VAL Chi-restraints excluded: chain R residue 333 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 57 optimal weight: 0.4980 chunk 109 optimal weight: 0.0980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN C 80 GLN R 85 ASN R 356 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.150523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.123213 restraints weight = 12357.633| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.28 r_work: 0.3153 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8940 Z= 0.135 Angle : 0.591 10.019 12108 Z= 0.303 Chirality : 0.043 0.254 1391 Planarity : 0.004 0.048 1530 Dihedral : 4.465 18.293 1213 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.98 % Allowed : 19.29 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.25), residues: 1106 helix: 1.76 (0.26), residues: 375 sheet: 0.56 (0.31), residues: 276 loop : 0.35 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 31 TYR 0.014 0.001 TYR A 306 PHE 0.015 0.001 PHE R 61 TRP 0.016 0.002 TRP A 211 HIS 0.005 0.001 HIS G 43 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8939) covalent geometry : angle 0.59108 (12106) SS BOND : bond 0.00157 ( 1) SS BOND : angle 1.30604 ( 2) hydrogen bonds : bond 0.04160 ( 442) hydrogen bonds : angle 4.32159 ( 1254) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 176 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 306 TYR cc_start: 0.8218 (m-80) cc_final: 0.7817 (m-80) REVERT: A 351 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8394 (mp) REVERT: C 24 ARG cc_start: 0.8270 (ttp-170) cc_final: 0.8049 (ttp-170) REVERT: C 25 ASP cc_start: 0.8055 (m-30) cc_final: 0.7677 (m-30) REVERT: C 57 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8569 (mtt-85) REVERT: C 151 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8720 (mm) REVERT: C 220 GLU cc_start: 0.7489 (pt0) cc_final: 0.7225 (pt0) REVERT: C 285 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8398 (tttt) REVERT: C 319 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8085 (ttm170) REVERT: E 42 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8589 (mmmm) REVERT: E 86 ARG cc_start: 0.7778 (mtm-85) cc_final: 0.7321 (mtt180) REVERT: E 89 ASP cc_start: 0.8650 (m-30) cc_final: 0.8312 (m-30) REVERT: E 186 GLN cc_start: 0.8797 (tt0) cc_final: 0.8561 (tt0) REVERT: G 8 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7623 (mp) REVERT: G 19 LYS cc_start: 0.8896 (mtmt) cc_final: 0.8599 (mtmm) REVERT: R 53 PHE cc_start: 0.8186 (t80) cc_final: 0.7928 (t80) REVERT: R 61 PHE cc_start: 0.8357 (t80) cc_final: 0.8155 (t80) REVERT: R 92 PHE cc_start: 0.8686 (t80) cc_final: 0.8482 (t80) REVERT: R 204 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7325 (tp) REVERT: R 369 SER cc_start: 0.9091 (m) cc_final: 0.8822 (t) outliers start: 48 outliers final: 19 residues processed: 206 average time/residue: 0.6298 time to fit residues: 137.1247 Evaluate side-chains 183 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 330 VAL Chi-restraints excluded: chain R residue 333 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 48 optimal weight: 0.0770 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN E 142 GLN R 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.149110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.122274 restraints weight = 12306.691| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.18 r_work: 0.3145 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8940 Z= 0.135 Angle : 0.590 10.710 12108 Z= 0.300 Chirality : 0.042 0.202 1391 Planarity : 0.004 0.048 1530 Dihedral : 4.383 18.025 1213 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.36 % Allowed : 21.16 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.26), residues: 1106 helix: 1.88 (0.26), residues: 374 sheet: 0.46 (0.31), residues: 287 loop : 0.38 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 309 TYR 0.016 0.001 TYR A 306 PHE 0.014 0.001 PHE A 189 TRP 0.015 0.002 TRP A 211 HIS 0.005 0.001 HIS G 43 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8939) covalent geometry : angle 0.59035 (12106) SS BOND : bond 0.00000 ( 1) SS BOND : angle 0.89360 ( 2) hydrogen bonds : bond 0.04095 ( 442) hydrogen bonds : angle 4.29277 ( 1254) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8440 (mtmm) REVERT: A 351 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8507 (mp) REVERT: C 24 ARG cc_start: 0.8216 (ttp-170) cc_final: 0.7987 (ttp-170) REVERT: C 25 ASP cc_start: 0.8040 (m-30) cc_final: 0.7669 (m-30) REVERT: C 28 LYS cc_start: 0.8515 (mmmm) cc_final: 0.8158 (tppp) REVERT: C 151 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8697 (mm) REVERT: C 202 ARG cc_start: 0.7979 (mtp85) cc_final: 0.7750 (mmm160) REVERT: C 285 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8441 (tttt) REVERT: C 319 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8125 (ttm170) REVERT: E 12 GLN cc_start: 0.8574 (mm110) cc_final: 0.7687 (pp30) REVERT: E 42 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8638 (mmmm) REVERT: E 86 ARG cc_start: 0.7736 (mtm-85) cc_final: 0.7304 (mtt180) REVERT: E 89 ASP cc_start: 0.8651 (m-30) cc_final: 0.8337 (m-30) REVERT: E 144 THR cc_start: 0.7273 (p) cc_final: 0.6954 (t) REVERT: E 186 GLN cc_start: 0.8770 (tt0) cc_final: 0.8554 (tt0) REVERT: G 8 ILE cc_start: 0.7894 (OUTLIER) cc_final: 0.7680 (mp) REVERT: G 46 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7918 (mt-10) REVERT: G 57 GLU cc_start: 0.8312 (mp0) cc_final: 0.8094 (mp0) REVERT: R 154 ARG cc_start: 0.4486 (OUTLIER) cc_final: 0.3672 (ppt170) REVERT: R 204 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7262 (tp) REVERT: R 369 SER cc_start: 0.9018 (m) cc_final: 0.8804 (t) outliers start: 42 outliers final: 20 residues processed: 195 average time/residue: 0.6384 time to fit residues: 131.6655 Evaluate side-chains 184 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain R residue 154 ARG Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 330 VAL Chi-restraints excluded: chain R residue 333 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 0.0670 chunk 57 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 0.0570 chunk 1 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN E 76 ASN E 142 GLN R 85 ASN ** R 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.150744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.124233 restraints weight = 12298.383| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.43 r_work: 0.3137 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8940 Z= 0.124 Angle : 0.568 10.194 12108 Z= 0.290 Chirality : 0.042 0.237 1391 Planarity : 0.004 0.048 1530 Dihedral : 4.283 19.537 1213 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.46 % Allowed : 21.37 % Favored : 74.17 % 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 are not related in a simple way. whole: 1.35 (0.26), residues: 1106 helix: 1.96 (0.26), residues: 371 sheet: 0.57 (0.31), residues: 274 loop : 0.34 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 309 TYR 0.015 0.001 TYR R 222 PHE 0.019 0.001 PHE R 128 TRP 0.014 0.001 TRP A 211 HIS 0.004 0.001 HIS G 43 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8939) covalent geometry : angle 0.56787 (12106) SS BOND : bond 0.00032 ( 1) SS BOND : angle 0.73332 ( 2) hydrogen bonds : bond 0.03967 ( 442) hydrogen bonds : angle 4.17003 ( 1254) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 173 time to evaluate : 0.332 Fit side-chains REVERT: A 10 LYS cc_start: 0.8860 (mtpt) cc_final: 0.8398 (mtmm) REVERT: A 213 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8290 (mt0) REVERT: A 351 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8480 (mp) REVERT: C 24 ARG cc_start: 0.8288 (ttp-170) cc_final: 0.7851 (ttp-170) REVERT: C 25 ASP cc_start: 0.8086 (m-30) cc_final: 0.7415 (m-30) REVERT: C 28 LYS cc_start: 0.8531 (mmmm) cc_final: 0.8189 (tppp) REVERT: C 151 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8702 (mm) REVERT: C 202 ARG cc_start: 0.7999 (mtp85) cc_final: 0.7723 (mmm160) REVERT: C 285 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8466 (tttt) REVERT: C 296 ASP cc_start: 0.7893 (t0) cc_final: 0.7504 (t0) REVERT: C 309 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8236 (ttp-110) REVERT: E 12 GLN cc_start: 0.8575 (mm110) cc_final: 0.7675 (pp30) REVERT: E 42 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8653 (mmmm) REVERT: E 86 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.7266 (mtt180) REVERT: E 89 ASP cc_start: 0.8664 (m-30) cc_final: 0.8325 (m-30) REVERT: E 144 THR cc_start: 0.7191 (p) cc_final: 0.6899 (t) REVERT: G 46 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7925 (mt-10) REVERT: R 154 ARG cc_start: 0.4526 (OUTLIER) cc_final: 0.3722 (ppt170) REVERT: R 199 LYS cc_start: 0.5539 (OUTLIER) cc_final: 0.5254 (pptt) REVERT: R 204 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7322 (tp) outliers start: 43 outliers final: 21 residues processed: 201 average time/residue: 0.6555 time to fit residues: 139.0312 Evaluate side-chains 186 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 154 ARG Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 199 LYS Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 330 VAL Chi-restraints excluded: chain R residue 333 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 79 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN E 76 ASN E 142 GLN E 194 ASN R 85 ASN ** R 151 GLN ** 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 = 0.3725 r_free = 0.3725 target = 0.145731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.111293 restraints weight = 12394.941| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.24 r_work: 0.3126 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8940 Z= 0.221 Angle : 0.649 10.104 12108 Z= 0.335 Chirality : 0.046 0.361 1391 Planarity : 0.004 0.049 1530 Dihedral : 4.706 19.923 1213 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.25 % Allowed : 22.61 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.26), residues: 1106 helix: 1.75 (0.27), residues: 374 sheet: 0.47 (0.31), residues: 292 loop : 0.39 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 309 TYR 0.014 0.002 TYR R 222 PHE 0.029 0.002 PHE R 92 TRP 0.015 0.002 TRP A 211 HIS 0.008 0.001 HIS G 43 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 8939) covalent geometry : angle 0.64943 (12106) SS BOND : bond 0.00177 ( 1) SS BOND : angle 0.86234 ( 2) hydrogen bonds : bond 0.04724 ( 442) hydrogen bonds : angle 4.54566 ( 1254) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 213 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8444 (mt0) REVERT: A 323 ARG cc_start: 0.7667 (mtm-85) cc_final: 0.7439 (mtm-85) REVERT: A 351 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8529 (mp) REVERT: C 24 ARG cc_start: 0.8344 (ttp-170) cc_final: 0.8103 (ttp-170) REVERT: C 25 ASP cc_start: 0.8155 (m-30) cc_final: 0.7770 (m-30) REVERT: C 151 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8788 (mm) REVERT: C 202 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7846 (mmm160) REVERT: C 285 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8497 (tttt) REVERT: C 296 ASP cc_start: 0.8146 (t0) cc_final: 0.7803 (t0) REVERT: C 309 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8323 (ttp-110) REVERT: E 86 ARG cc_start: 0.7794 (mtm-85) cc_final: 0.7429 (mtt180) REVERT: E 144 THR cc_start: 0.7463 (p) cc_final: 0.7068 (t) REVERT: R 154 ARG cc_start: 0.4398 (OUTLIER) cc_final: 0.3685 (ppt170) REVERT: R 199 LYS cc_start: 0.5606 (OUTLIER) cc_final: 0.5216 (pptt) REVERT: R 204 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7487 (tp) outliers start: 41 outliers final: 22 residues processed: 198 average time/residue: 0.6537 time to fit residues: 136.5360 Evaluate side-chains 191 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 159 CYS Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain R residue 154 ARG Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 199 LYS Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 330 VAL Chi-restraints excluded: chain R residue 333 CYS Chi-restraints excluded: chain R residue 334 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.0370 chunk 58 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 57 optimal weight: 0.0980 chunk 28 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 76 ASN E 142 GLN ** R 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 ASN ** R 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.151072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.124479 restraints weight = 12340.364| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.90 r_work: 0.3191 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8940 Z= 0.117 Angle : 0.602 11.733 12108 Z= 0.302 Chirality : 0.042 0.318 1391 Planarity : 0.004 0.048 1530 Dihedral : 4.251 17.676 1213 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.90 % Allowed : 24.17 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.26), residues: 1106 helix: 2.04 (0.27), residues: 372 sheet: 0.58 (0.31), residues: 282 loop : 0.45 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 309 TYR 0.011 0.001 TYR R 222 PHE 0.018 0.001 PHE R 92 TRP 0.015 0.002 TRP C 174 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 8939) covalent geometry : angle 0.60146 (12106) SS BOND : bond 0.00191 ( 1) SS BOND : angle 0.92750 ( 2) hydrogen bonds : bond 0.03777 ( 442) hydrogen bonds : angle 4.19406 ( 1254) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.369 Fit side-chains REVERT: A 10 LYS cc_start: 0.8753 (mtpt) cc_final: 0.8279 (mtmm) REVERT: A 351 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8438 (mp) REVERT: C 24 ARG cc_start: 0.8230 (ttp-170) cc_final: 0.7981 (ttp-110) REVERT: C 25 ASP cc_start: 0.8113 (m-30) cc_final: 0.7726 (m-30) REVERT: C 62 LYS cc_start: 0.8811 (mtpt) cc_final: 0.8541 (mttp) REVERT: C 151 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8677 (mm) REVERT: C 202 ARG cc_start: 0.7894 (mtp85) cc_final: 0.7590 (mmm160) REVERT: C 285 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8382 (tttt) REVERT: C 296 ASP cc_start: 0.7693 (t0) cc_final: 0.7486 (t0) REVERT: C 309 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8224 (ttp-110) REVERT: E 42 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8661 (mmmm) REVERT: E 89 ASP cc_start: 0.8516 (m-30) cc_final: 0.8281 (m-30) REVERT: E 144 THR cc_start: 0.7318 (p) cc_final: 0.6997 (t) REVERT: E 218 ARG cc_start: 0.7678 (ptm-80) cc_final: 0.7452 (ptp90) REVERT: G 21 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8079 (mp0) REVERT: G 37 MET cc_start: 0.8454 (ttp) cc_final: 0.8233 (mtm) REVERT: R 154 ARG cc_start: 0.4558 (OUTLIER) cc_final: 0.3907 (ppt170) REVERT: R 204 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7429 (tp) outliers start: 28 outliers final: 10 residues processed: 186 average time/residue: 0.6483 time to fit residues: 127.3381 Evaluate side-chains 175 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain R residue 154 ARG Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 228 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 71 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN E 76 ASN ** R 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.149491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.123032 restraints weight = 12291.909| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.88 r_work: 0.3167 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8940 Z= 0.140 Angle : 0.629 11.980 12108 Z= 0.319 Chirality : 0.043 0.294 1391 Planarity : 0.004 0.048 1530 Dihedral : 4.309 17.683 1213 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.70 % Allowed : 24.38 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.26), residues: 1106 helix: 1.99 (0.27), residues: 373 sheet: 0.54 (0.31), residues: 283 loop : 0.47 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 309 TYR 0.010 0.001 TYR E 190 PHE 0.022 0.001 PHE R 92 TRP 0.014 0.002 TRP A 211 HIS 0.005 0.001 HIS G 43 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8939) covalent geometry : angle 0.62920 (12106) SS BOND : bond 0.00035 ( 1) SS BOND : angle 0.89294 ( 2) hydrogen bonds : bond 0.03975 ( 442) hydrogen bonds : angle 4.24156 ( 1254) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.334 Fit side-chains REVERT: A 10 LYS cc_start: 0.8869 (mtpt) cc_final: 0.8402 (mtmm) REVERT: A 351 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8451 (mp) REVERT: C 24 ARG cc_start: 0.8253 (ttp-170) cc_final: 0.7992 (ttp-110) REVERT: C 25 ASP cc_start: 0.8056 (m-30) cc_final: 0.7671 (m-30) REVERT: C 151 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8705 (mm) REVERT: C 202 ARG cc_start: 0.7930 (mtp85) cc_final: 0.7697 (mmm160) REVERT: C 285 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8418 (tttt) REVERT: E 12 GLN cc_start: 0.8567 (mm110) cc_final: 0.7680 (pp30) REVERT: E 42 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8647 (mmmm) REVERT: E 89 ASP cc_start: 0.8581 (m-30) cc_final: 0.8354 (m-30) REVERT: E 144 THR cc_start: 0.7460 (p) cc_final: 0.7081 (t) REVERT: E 218 ARG cc_start: 0.7694 (ptm-80) cc_final: 0.7453 (ptp90) REVERT: G 21 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8133 (mp0) REVERT: R 154 ARG cc_start: 0.4546 (OUTLIER) cc_final: 0.3778 (ppt170) REVERT: R 357 PHE cc_start: 0.7465 (m-80) cc_final: 0.7125 (m-80) outliers start: 26 outliers final: 13 residues processed: 177 average time/residue: 0.6843 time to fit residues: 127.7868 Evaluate side-chains 173 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain R residue 154 ARG Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 334 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN E 76 ASN ** R 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.149479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.122876 restraints weight = 12273.983| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.88 r_work: 0.3164 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8940 Z= 0.143 Angle : 0.653 12.928 12108 Z= 0.332 Chirality : 0.043 0.322 1391 Planarity : 0.004 0.049 1530 Dihedral : 4.337 17.908 1213 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.80 % Allowed : 24.38 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.26), residues: 1106 helix: 1.86 (0.26), residues: 373 sheet: 0.52 (0.32), residues: 276 loop : 0.51 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 309 TYR 0.014 0.001 TYR R 222 PHE 0.021 0.001 PHE R 92 TRP 0.014 0.002 TRP A 211 HIS 0.005 0.001 HIS G 43 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8939) covalent geometry : angle 0.65281 (12106) SS BOND : bond 0.00058 ( 1) SS BOND : angle 0.82740 ( 2) hydrogen bonds : bond 0.04027 ( 442) hydrogen bonds : angle 4.34103 ( 1254) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8841 (mtpt) cc_final: 0.8400 (mtmm) REVERT: A 247 ARG cc_start: 0.8362 (mtm110) cc_final: 0.8083 (ptt-90) REVERT: A 351 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8487 (mp) REVERT: C 13 ARG cc_start: 0.7814 (ptt90) cc_final: 0.7445 (mtm110) REVERT: C 24 ARG cc_start: 0.8273 (ttp-170) cc_final: 0.8009 (ttp-110) REVERT: C 25 ASP cc_start: 0.8100 (m-30) cc_final: 0.7711 (m-30) REVERT: C 62 LYS cc_start: 0.8822 (mtpt) cc_final: 0.8557 (mttp) REVERT: C 151 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8699 (mm) REVERT: C 202 ARG cc_start: 0.7924 (mtp85) cc_final: 0.7693 (mmm160) REVERT: C 285 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8399 (tttt) REVERT: C 309 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8195 (ttp-110) REVERT: E 42 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8639 (mmmm) REVERT: E 89 ASP cc_start: 0.8579 (m-30) cc_final: 0.8320 (m-30) REVERT: E 144 THR cc_start: 0.7488 (p) cc_final: 0.7116 (t) REVERT: E 218 ARG cc_start: 0.7698 (ptm-80) cc_final: 0.7430 (ptp90) REVERT: G 21 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: R 154 ARG cc_start: 0.4538 (OUTLIER) cc_final: 0.3787 (ppt170) REVERT: R 184 SER cc_start: 0.5337 (t) cc_final: 0.5134 (p) REVERT: R 357 PHE cc_start: 0.7513 (m-80) cc_final: 0.7268 (m-80) outliers start: 27 outliers final: 13 residues processed: 174 average time/residue: 0.7010 time to fit residues: 128.6585 Evaluate side-chains 176 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain R residue 154 ARG Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 334 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 0.0770 chunk 60 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN C 93 ASN E 38 GLN E 76 ASN E 142 GLN ** R 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.146122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.113935 restraints weight = 12126.226| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.13 r_work: 0.3126 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8940 Z= 0.220 Angle : 0.691 12.263 12108 Z= 0.357 Chirality : 0.046 0.321 1391 Planarity : 0.005 0.049 1530 Dihedral : 4.690 20.796 1213 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.49 % Allowed : 24.90 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.26), residues: 1106 helix: 1.55 (0.26), residues: 372 sheet: 0.38 (0.31), residues: 286 loop : 0.37 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 309 TYR 0.017 0.002 TYR R 222 PHE 0.028 0.002 PHE R 92 TRP 0.026 0.002 TRP R 169 HIS 0.008 0.001 HIS G 43 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 8939) covalent geometry : angle 0.69125 (12106) SS BOND : bond 0.00125 ( 1) SS BOND : angle 0.89042 ( 2) hydrogen bonds : bond 0.04672 ( 442) hydrogen bonds : angle 4.59364 ( 1254) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3584.52 seconds wall clock time: 61 minutes 47.30 seconds (3707.30 seconds total)