Starting phenix.real_space_refine on Sat Aug 23 01:01:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hcq_34663/08_2025/8hcq_34663_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hcq_34663/08_2025/8hcq_34663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hcq_34663/08_2025/8hcq_34663.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hcq_34663/08_2025/8hcq_34663.map" model { file = "/net/cci-nas-00/data/ceres_data/8hcq_34663/08_2025/8hcq_34663_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hcq_34663/08_2025/8hcq_34663_neut.cif" } resolution = 3.01 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= 0.002 sd= 0.032 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 67 5.16 5 C 5725 2.51 5 N 1526 2.21 5 O 1673 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8991 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1687 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 199} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2591 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1769 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 410 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "L" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 171 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "R" Number of atoms: 2363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2363 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 11, 'TRANS': 291} Chain breaks: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4, 'ASP:plan': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 45 Time building chain proxies: 1.67, per 1000 atoms: 0.19 Number of scatterers: 8991 At special positions: 0 Unit cell: (107.944, 112.888, 126.072, 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 67 16.00 O 1673 8.00 N 1526 7.00 C 5725 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 15 " distance=2.03 Simple disulfide: pdb=" SG CYS L 3 " - pdb=" SG CYS L 11 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 202.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 14 sheets defined 36.0% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 8 through 27 removed outlier: 3.560A pdb=" N ASP A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 230 through 243 removed outlier: 3.539A pdb=" N ALA A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 268 Processing helix chain 'A' and resid 296 through 316 removed outlier: 3.989A pdb=" N THR A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A 301 " --> pdb=" O PRO A 297 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA A 302 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 357 removed outlier: 3.558A pdb=" N LEU A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 354 " --> pdb=" O GLN A 350 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU A 355 " --> pdb=" O MET A 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 12 Processing helix chain 'B' and resid 13 through 31 removed outlier: 3.521A pdb=" N GLU B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 40 Processing helix chain 'E' and resid 52 through 55 removed outlier: 3.997A 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 220 through 224 Processing helix chain 'G' and resid 7 through 25 removed outlier: 4.406A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.610A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 18 removed outlier: 3.726A pdb=" N VAL L 12 " --> pdb=" O ASP L 8 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 109 removed outlier: 3.529A pdb=" N TYR R 81 " --> pdb=" O SER R 77 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR R 84 " --> pdb=" O LYS R 80 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE R 86 " --> pdb=" O ILE R 82 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL R 96 " --> pdb=" O ILE R 92 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS R 109 " --> pdb=" O ILE R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 143 Proline residue: R 135 - end of helix removed outlier: 3.516A pdb=" N PHE R 139 " --> pdb=" O PRO R 135 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 159 removed outlier: 3.806A pdb=" N VAL R 155 " --> pdb=" O ASN R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 189 Processing helix chain 'R' and resid 199 through 222 removed outlier: 3.678A pdb=" N VAL R 207 " --> pdb=" O ALA R 203 " (cutoff:3.500A) Proline residue: R 219 - end of helix removed outlier: 3.971A pdb=" N ILE R 222 " --> pdb=" O ILE R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 253 Processing helix chain 'R' and resid 254 through 264 Processing helix chain 'R' and resid 264 through 283 removed outlier: 3.836A pdb=" N VAL R 269 " --> pdb=" O CYS R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 297 through 330 Proline residue: R 321 - end of helix removed outlier: 3.783A pdb=" N ARG R 326 " --> pdb=" O LEU R 322 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS R 330 " --> pdb=" O ARG R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 339 through 373 removed outlier: 3.812A pdb=" N LEU R 343 " --> pdb=" O ASN R 339 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU R 344 " --> pdb=" O ARG R 340 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE R 346 " --> pdb=" O GLU R 342 " (cutoff:3.500A) Proline residue: R 366 - end of helix removed outlier: 3.792A pdb=" N LEU R 369 " --> pdb=" O ASN R 365 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 189 removed outlier: 4.525A pdb=" N PHE A 187 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ARG A 35 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ILE A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU A 37 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL A 222 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU A 39 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE A 219 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE A 255 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE A 221 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL A 252 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N HIS A 327 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU A 254 " --> pdb=" O HIS A 327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 56 removed outlier: 6.717A pdb=" N ILE B 343 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N THR B 55 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU B 341 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.930A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN B 93 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.924A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N CYS B 126 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU B 143 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG B 139 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.970A pdb=" N THR B 183 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 3.776A pdb=" N ALA B 236 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 257 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 281 through 283 removed outlier: 3.579A pdb=" N ALA B 292 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN B 300 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 311 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 5 removed outlier: 3.860A pdb=" N THR E 68 " --> pdb=" O GLN E 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 5.869A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR E 93 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11 removed outlier: 5.869A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR E 93 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG E 97 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 4.294A 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 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.076A pdb=" N VAL E 147 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 230 through 231 removed outlier: 4.079A pdb=" N TYR R 231 " --> pdb=" O GLU R 234 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU R 234 " --> pdb=" O TYR R 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 402 hydrogen bonds defined for protein. 1140 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: 1.07 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2904 1.34 - 1.46: 2087 1.46 - 1.58: 4095 1.58 - 1.70: 0 1.70 - 1.82: 94 Bond restraints: 9180 Sorted by residual: bond pdb=" N GLU A 205 " pdb=" CA GLU A 205 " ideal model delta sigma weight residual 1.457 1.506 -0.048 1.29e-02 6.01e+03 1.41e+01 bond pdb=" N LYS R 377 " pdb=" CA LYS R 377 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.22e-02 6.72e+03 6.33e+00 bond pdb=" C MET R 266 " pdb=" N PRO R 267 " ideal model delta sigma weight residual 1.336 1.362 -0.026 1.20e-02 6.94e+03 4.79e+00 bond pdb=" N MET E 92 " pdb=" CA MET E 92 " ideal model delta sigma weight residual 1.456 1.479 -0.023 1.29e-02 6.01e+03 3.22e+00 bond pdb=" C MET E 92 " pdb=" N TYR E 93 " ideal model delta sigma weight residual 1.330 1.310 0.019 1.32e-02 5.74e+03 2.17e+00 ... (remaining 9175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 12282 2.57 - 5.14: 149 5.14 - 7.71: 17 7.71 - 10.28: 1 10.28 - 12.85: 1 Bond angle restraints: 12450 Sorted by residual: angle pdb=" C ARG R 340 " pdb=" CA ARG R 340 " pdb=" CB ARG R 340 " ideal model delta sigma weight residual 116.34 110.69 5.65 1.40e+00 5.10e-01 1.63e+01 angle pdb=" C SER L 4 " pdb=" N SER L 5 " pdb=" CA SER L 5 " ideal model delta sigma weight residual 121.54 128.78 -7.24 1.91e+00 2.74e-01 1.44e+01 angle pdb=" CA MET R 266 " pdb=" CB MET R 266 " pdb=" CG MET R 266 " ideal model delta sigma weight residual 114.10 121.60 -7.50 2.00e+00 2.50e-01 1.41e+01 angle pdb=" CA LEU G 15 " pdb=" CB LEU G 15 " pdb=" CG LEU G 15 " ideal model delta sigma weight residual 116.30 129.15 -12.85 3.50e+00 8.16e-02 1.35e+01 angle pdb=" O ASP A 204 " pdb=" C ASP A 204 " pdb=" N GLU A 205 " ideal model delta sigma weight residual 123.29 119.66 3.63 1.00e+00 1.00e+00 1.32e+01 ... (remaining 12445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 4651 16.30 - 32.59: 554 32.59 - 48.89: 178 48.89 - 65.19: 37 65.19 - 81.49: 8 Dihedral angle restraints: 5428 sinusoidal: 2071 harmonic: 3357 Sorted by residual: dihedral pdb=" CB CYS L 1 " pdb=" SG CYS L 1 " pdb=" SG CYS L 15 " pdb=" CB CYS L 15 " ideal model delta sinusoidal sigma weight residual -86.00 -127.39 41.39 1 1.00e+01 1.00e-02 2.40e+01 dihedral pdb=" CG ARG A 230 " pdb=" CD ARG A 230 " pdb=" NE ARG A 230 " pdb=" CZ ARG A 230 " ideal model delta sinusoidal sigma weight residual 90.00 41.36 48.64 2 1.50e+01 4.44e-03 1.20e+01 dihedral pdb=" CA GLN B 264 " pdb=" C GLN B 264 " pdb=" N GLU B 265 " pdb=" CA GLU B 265 " ideal model delta harmonic sigma weight residual 180.00 162.92 17.08 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 5425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 910 0.029 - 0.059: 324 0.059 - 0.088: 105 0.088 - 0.118: 66 0.118 - 0.147: 11 Chirality restraints: 1416 Sorted by residual: chirality pdb=" CA MET E 92 " pdb=" N MET E 92 " pdb=" C MET E 92 " pdb=" CB MET E 92 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA ASN E 76 " pdb=" N ASN E 76 " pdb=" C ASN E 76 " pdb=" CB ASN E 76 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA ILE R 196 " pdb=" N ILE R 196 " pdb=" C ILE R 196 " pdb=" CB ILE R 196 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 1413 not shown) Planarity restraints: 1580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN R 339 " -0.017 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C ASN R 339 " 0.062 2.00e-02 2.50e+03 pdb=" O ASN R 339 " -0.024 2.00e-02 2.50e+03 pdb=" N ARG R 340 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 198 " -0.051 5.00e-02 4.00e+02 7.75e-02 9.60e+00 pdb=" N PRO R 199 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO R 199 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO R 199 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 204 " -0.015 2.00e-02 2.50e+03 2.87e-02 8.21e+00 pdb=" C ASP A 204 " 0.050 2.00e-02 2.50e+03 pdb=" O ASP A 204 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU A 205 " -0.016 2.00e-02 2.50e+03 ... (remaining 1577 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 10 2.27 - 2.93: 3874 2.93 - 3.58: 12956 3.58 - 4.24: 19861 4.24 - 4.90: 33518 Nonbonded interactions: 70219 Sorted by model distance: nonbonded pdb=" CE1 HIS A 195 " pdb=" CE1 PHE A 197 " model vdw 1.609 3.560 nonbonded pdb=" ND1 HIS A 195 " pdb=" CE1 PHE A 197 " model vdw 2.019 3.420 nonbonded pdb=" OD2 ASP B 32 " pdb=" OG SER G 31 " model vdw 2.191 3.040 nonbonded pdb=" OG SER B 336 " pdb=" OD1 ASP B 338 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR B 70 " pdb=" O PRO B 112 " model vdw 2.204 3.040 ... (remaining 70214 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: 1.010 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.810 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 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 : 0.003 0.060 9182 Z= 0.137 Angle : 0.662 12.855 12454 Z= 0.353 Chirality : 0.039 0.147 1416 Planarity : 0.005 0.077 1580 Dihedral : 16.120 81.487 3250 Min Nonbonded Distance : 1.609 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.71 % Favored : 96.11 % Rotamer: Outliers : 0.21 % Allowed : 29.47 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.25), residues: 1131 helix: 1.42 (0.28), residues: 371 sheet: 0.87 (0.33), residues: 268 loop : -0.94 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 24 TYR 0.012 0.001 TYR E 235 PHE 0.020 0.001 PHE E 212 TRP 0.006 0.001 TRP B 68 HIS 0.013 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9180) covalent geometry : angle 0.66221 (12450) SS BOND : bond 0.00271 ( 2) SS BOND : angle 0.69877 ( 4) hydrogen bonds : bond 0.22926 ( 401) hydrogen bonds : angle 6.86824 ( 1140) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 164 time to evaluate : 0.284 Fit side-chains REVERT: A 35 ARG cc_start: 0.7423 (mtm-85) cc_final: 0.7138 (mtm180) REVERT: B 13 ARG cc_start: 0.6661 (mpp80) cc_final: 0.6292 (mpp80) REVERT: B 175 ASP cc_start: 0.7093 (m-30) cc_final: 0.6882 (m-30) REVERT: B 202 ARG cc_start: 0.7003 (tpp-160) cc_final: 0.6266 (tpt170) REVERT: B 334 THR cc_start: 0.8198 (t) cc_final: 0.7796 (p) REVERT: R 181 VAL cc_start: 0.7129 (t) cc_final: 0.6865 (t) REVERT: R 212 LEU cc_start: 0.7808 (tm) cc_final: 0.7589 (tp) REVERT: R 224 PHE cc_start: 0.6646 (t80) cc_final: 0.5107 (t80) outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.0852 time to fit residues: 19.5288 Evaluate side-chains 147 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.0170 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 342 ASN A 352 ASN B 93 ASN B 160 ASN B 181 GLN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** R 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 165 GLN R 175 ASN ** R 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.153749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.136144 restraints weight = 13031.432| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.33 r_work: 0.3689 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9182 Z= 0.185 Angle : 0.654 8.952 12454 Z= 0.341 Chirality : 0.045 0.182 1416 Planarity : 0.005 0.060 1580 Dihedral : 4.314 17.209 1244 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.98 % Favored : 95.84 % Rotamer: Outliers : 5.89 % Allowed : 23.16 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.25), residues: 1131 helix: 1.20 (0.27), residues: 384 sheet: 0.65 (0.33), residues: 262 loop : -0.88 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 24 TYR 0.018 0.002 TYR E 175 PHE 0.029 0.002 PHE L 14 TRP 0.012 0.002 TRP B 216 HIS 0.007 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 9180) covalent geometry : angle 0.65354 (12450) SS BOND : bond 0.00417 ( 2) SS BOND : angle 1.09730 ( 4) hydrogen bonds : bond 0.04682 ( 401) hydrogen bonds : angle 4.54118 ( 1140) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 196 time to evaluate : 0.334 Fit side-chains REVERT: A 35 ARG cc_start: 0.8157 (mtm-85) cc_final: 0.7942 (mtm180) REVERT: A 262 LEU cc_start: 0.6442 (tt) cc_final: 0.6151 (tp) REVERT: B 13 ARG cc_start: 0.6906 (mpp80) cc_final: 0.6320 (mpp80) REVERT: B 173 LEU cc_start: 0.8227 (tt) cc_final: 0.7892 (tp) REVERT: B 188 HIS cc_start: 0.8490 (OUTLIER) cc_final: 0.8011 (m-70) REVERT: B 215 LEU cc_start: 0.7773 (tp) cc_final: 0.7472 (tp) REVERT: B 217 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7410 (t0) REVERT: B 334 THR cc_start: 0.8350 (t) cc_final: 0.8056 (p) REVERT: E 28 PHE cc_start: 0.7997 (t80) cc_final: 0.7738 (t80) REVERT: E 36 VAL cc_start: 0.8518 (t) cc_final: 0.8245 (t) REVERT: E 66 ARG cc_start: 0.7674 (ttp80) cc_final: 0.7179 (ttp80) REVERT: E 82 MET cc_start: 0.7786 (mmt) cc_final: 0.7474 (mmt) REVERT: E 86 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6718 (mtt180) REVERT: E 212 PHE cc_start: 0.7762 (m-80) cc_final: 0.7507 (m-80) REVERT: L 7 MET cc_start: 0.5111 (tpp) cc_final: 0.4766 (tpp) REVERT: R 102 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7738 (mt) REVERT: R 108 ASN cc_start: 0.7457 (t0) cc_final: 0.7119 (t0) REVERT: R 181 VAL cc_start: 0.7637 (t) cc_final: 0.7378 (t) REVERT: R 212 LEU cc_start: 0.8271 (tm) cc_final: 0.7941 (tp) REVERT: R 224 PHE cc_start: 0.7390 (t80) cc_final: 0.6129 (t80) REVERT: R 255 LYS cc_start: 0.6919 (OUTLIER) cc_final: 0.6634 (tttm) REVERT: R 278 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7539 (ttp) outliers start: 57 outliers final: 35 residues processed: 232 average time/residue: 0.0886 time to fit residues: 27.6245 Evaluate side-chains 216 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 175 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 142 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 239 PHE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 177 CYS Chi-restraints excluded: chain R residue 180 SER Chi-restraints excluded: chain R residue 255 LYS Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 278 MET Chi-restraints excluded: chain R residue 280 CYS Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 310 CYS Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 350 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 60 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 ASN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN B 300 ASN G 44 HIS R 116 ASN R 175 ASN R 356 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.151684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.134437 restraints weight = 12892.887| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.25 r_work: 0.3667 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9182 Z= 0.149 Angle : 0.578 7.886 12454 Z= 0.301 Chirality : 0.042 0.166 1416 Planarity : 0.004 0.053 1580 Dihedral : 4.142 17.809 1244 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.63 % Favored : 96.20 % Rotamer: Outliers : 6.31 % Allowed : 23.68 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.25), residues: 1131 helix: 1.40 (0.27), residues: 382 sheet: 0.61 (0.33), residues: 257 loop : -0.98 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 230 TYR 0.015 0.001 TYR E 235 PHE 0.012 0.002 PHE A 197 TRP 0.013 0.001 TRP B 216 HIS 0.024 0.002 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9180) covalent geometry : angle 0.57792 (12450) SS BOND : bond 0.00377 ( 2) SS BOND : angle 1.13248 ( 4) hydrogen bonds : bond 0.04241 ( 401) hydrogen bonds : angle 4.32702 ( 1140) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 193 time to evaluate : 0.334 Fit side-chains REVERT: A 46 LYS cc_start: 0.6983 (OUTLIER) cc_final: 0.6057 (mptm) REVERT: A 188 GLN cc_start: 0.6848 (OUTLIER) cc_final: 0.6466 (tm-30) REVERT: A 215 ASP cc_start: 0.7389 (t0) cc_final: 0.7014 (t0) REVERT: A 262 LEU cc_start: 0.6627 (tt) cc_final: 0.6350 (tp) REVERT: A 339 ARG cc_start: 0.7139 (ttt90) cc_final: 0.6834 (mtp85) REVERT: B 13 ARG cc_start: 0.6934 (mpp80) cc_final: 0.6384 (mpp80) REVERT: B 170 THR cc_start: 0.7172 (t) cc_final: 0.5726 (m) REVERT: B 188 HIS cc_start: 0.8491 (OUTLIER) cc_final: 0.7935 (m-70) REVERT: B 215 LEU cc_start: 0.7796 (tp) cc_final: 0.7511 (tp) REVERT: B 261 ARG cc_start: 0.8507 (mtm180) cc_final: 0.8300 (mtp180) REVERT: B 266 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7997 (mp) REVERT: B 334 THR cc_start: 0.8295 (t) cc_final: 0.8029 (p) REVERT: E 66 ARG cc_start: 0.7668 (ttp80) cc_final: 0.7178 (ttp80) REVERT: E 82 MET cc_start: 0.7962 (mmt) cc_final: 0.7567 (mmt) REVERT: E 86 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6654 (ptp-170) REVERT: E 102 TYR cc_start: 0.7913 (t80) cc_final: 0.7611 (t80) REVERT: L 7 MET cc_start: 0.5199 (tpp) cc_final: 0.4755 (tpp) REVERT: R 86 ILE cc_start: 0.6329 (pt) cc_final: 0.6033 (pt) REVERT: R 102 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7676 (mt) REVERT: R 108 ASN cc_start: 0.7452 (t0) cc_final: 0.7037 (t0) REVERT: R 181 VAL cc_start: 0.7605 (t) cc_final: 0.7390 (t) REVERT: R 212 LEU cc_start: 0.8241 (tm) cc_final: 0.7946 (tp) REVERT: R 255 LYS cc_start: 0.6875 (OUTLIER) cc_final: 0.6597 (tttm) REVERT: R 278 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7560 (ttp) outliers start: 61 outliers final: 37 residues processed: 230 average time/residue: 0.1037 time to fit residues: 31.0324 Evaluate side-chains 236 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 142 GLN Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 177 CYS Chi-restraints excluded: chain R residue 180 SER Chi-restraints excluded: chain R residue 241 LEU Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 255 LYS Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 278 MET Chi-restraints excluded: chain R residue 310 CYS Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 350 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 89 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 0.0070 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 chunk 30 optimal weight: 0.0050 chunk 57 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 overall best weight: 0.4212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 ASN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.152346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.134988 restraints weight = 13002.512| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.30 r_work: 0.3668 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9182 Z= 0.117 Angle : 0.544 7.475 12454 Z= 0.283 Chirality : 0.041 0.161 1416 Planarity : 0.004 0.055 1580 Dihedral : 3.969 17.359 1244 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.45 % Favored : 96.37 % Rotamer: Outliers : 6.72 % Allowed : 22.85 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.25), residues: 1131 helix: 1.55 (0.27), residues: 380 sheet: 0.69 (0.33), residues: 255 loop : -0.99 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 230 TYR 0.014 0.001 TYR E 235 PHE 0.011 0.001 PHE A 187 TRP 0.011 0.001 TRP B 216 HIS 0.007 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9180) covalent geometry : angle 0.54371 (12450) SS BOND : bond 0.00257 ( 2) SS BOND : angle 0.89325 ( 4) hydrogen bonds : bond 0.03755 ( 401) hydrogen bonds : angle 4.13602 ( 1140) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 181 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6983 (OUTLIER) cc_final: 0.5957 (mptm) REVERT: A 188 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.6517 (tm-30) REVERT: A 215 ASP cc_start: 0.7406 (t0) cc_final: 0.7035 (t0) REVERT: A 249 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8338 (p) REVERT: B 170 THR cc_start: 0.7100 (t) cc_final: 0.5563 (m) REVERT: B 173 LEU cc_start: 0.8352 (tt) cc_final: 0.8043 (tp) REVERT: B 176 ILE cc_start: 0.7442 (mm) cc_final: 0.7096 (mm) REVERT: B 188 HIS cc_start: 0.8477 (OUTLIER) cc_final: 0.7966 (m-70) REVERT: B 202 ARG cc_start: 0.7791 (tpp-160) cc_final: 0.7202 (mmm160) REVERT: B 215 LEU cc_start: 0.7761 (tp) cc_final: 0.7506 (tp) REVERT: B 261 ARG cc_start: 0.8521 (mtm180) cc_final: 0.8315 (mtp180) REVERT: B 266 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7997 (mp) REVERT: B 334 THR cc_start: 0.8262 (t) cc_final: 0.8007 (p) REVERT: E 66 ARG cc_start: 0.7610 (ttp80) cc_final: 0.7152 (ttp80) REVERT: E 82 MET cc_start: 0.7953 (mmt) cc_final: 0.7467 (mmm) REVERT: E 86 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6735 (ptp-170) REVERT: L 7 MET cc_start: 0.4975 (tpp) cc_final: 0.4540 (tpp) REVERT: R 93 VAL cc_start: 0.7772 (p) cc_final: 0.7556 (t) REVERT: R 102 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7676 (mt) REVERT: R 108 ASN cc_start: 0.7488 (t0) cc_final: 0.7017 (t0) REVERT: R 212 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7940 (tp) REVERT: R 241 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6889 (pp) REVERT: R 255 LYS cc_start: 0.6848 (OUTLIER) cc_final: 0.6595 (tttm) REVERT: R 278 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7541 (ttp) outliers start: 65 outliers final: 47 residues processed: 221 average time/residue: 0.1014 time to fit residues: 29.4605 Evaluate side-chains 241 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 183 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 307 ARG Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 142 GLN Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 177 CYS Chi-restraints excluded: chain R residue 180 SER Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 240 MET Chi-restraints excluded: chain R residue 241 LEU Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 255 LYS Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 278 MET Chi-restraints excluded: chain R residue 280 CYS Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 310 CYS Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 350 MET Chi-restraints excluded: chain R residue 373 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 111 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 49 optimal weight: 0.2980 chunk 71 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 chunk 108 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.150879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.133597 restraints weight = 12927.392| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.30 r_work: 0.3647 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9182 Z= 0.126 Angle : 0.550 8.534 12454 Z= 0.286 Chirality : 0.042 0.159 1416 Planarity : 0.004 0.055 1580 Dihedral : 3.974 17.088 1244 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.36 % Favored : 96.46 % Rotamer: Outliers : 6.83 % Allowed : 22.85 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.25), residues: 1131 helix: 1.59 (0.27), residues: 380 sheet: 0.68 (0.33), residues: 265 loop : -0.94 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 339 TYR 0.014 0.001 TYR E 235 PHE 0.011 0.001 PHE A 187 TRP 0.011 0.001 TRP B 216 HIS 0.014 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9180) covalent geometry : angle 0.55035 (12450) SS BOND : bond 0.00248 ( 2) SS BOND : angle 0.81776 ( 4) hydrogen bonds : bond 0.03704 ( 401) hydrogen bonds : angle 4.09325 ( 1140) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 193 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7117 (mtm110) cc_final: 0.6843 (mtm110) REVERT: A 46 LYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6039 (mptm) REVERT: A 188 GLN cc_start: 0.7068 (OUTLIER) cc_final: 0.6735 (tm-30) REVERT: A 215 ASP cc_start: 0.7444 (t0) cc_final: 0.7082 (t0) REVERT: A 249 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8315 (p) REVERT: A 262 LEU cc_start: 0.6741 (tt) cc_final: 0.6458 (tp) REVERT: A 347 ILE cc_start: 0.8436 (tp) cc_final: 0.8160 (mt) REVERT: B 170 THR cc_start: 0.7227 (t) cc_final: 0.5771 (m) REVERT: B 173 LEU cc_start: 0.8387 (tt) cc_final: 0.8093 (tp) REVERT: B 176 ILE cc_start: 0.7578 (mm) cc_final: 0.7150 (mm) REVERT: B 188 HIS cc_start: 0.8500 (OUTLIER) cc_final: 0.8035 (m-70) REVERT: B 215 LEU cc_start: 0.7826 (tp) cc_final: 0.7507 (tp) REVERT: B 261 ARG cc_start: 0.8502 (mtm180) cc_final: 0.8202 (mtp180) REVERT: B 266 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7995 (mt) REVERT: B 334 THR cc_start: 0.8273 (t) cc_final: 0.7994 (p) REVERT: E 66 ARG cc_start: 0.7608 (ttp80) cc_final: 0.7063 (ttp80) REVERT: E 82 MET cc_start: 0.7998 (mmt) cc_final: 0.7563 (mmm) REVERT: E 86 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.7079 (mtt180) REVERT: E 102 TYR cc_start: 0.7928 (t80) cc_final: 0.7562 (t80) REVERT: E 224 VAL cc_start: 0.8166 (t) cc_final: 0.7859 (p) REVERT: G 50 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.6591 (mt) REVERT: R 102 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7665 (mt) REVERT: R 108 ASN cc_start: 0.7532 (t0) cc_final: 0.7007 (t0) REVERT: R 137 ASN cc_start: 0.7700 (m-40) cc_final: 0.7345 (m-40) REVERT: R 212 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7923 (tp) REVERT: R 224 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.6367 (t80) REVERT: R 255 LYS cc_start: 0.6867 (OUTLIER) cc_final: 0.6615 (tttm) outliers start: 66 outliers final: 48 residues processed: 232 average time/residue: 0.1055 time to fit residues: 32.3217 Evaluate side-chains 246 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 187 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 142 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 177 CYS Chi-restraints excluded: chain R residue 180 SER Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 224 PHE Chi-restraints excluded: chain R residue 240 MET Chi-restraints excluded: chain R residue 241 LEU Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 255 LYS Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 280 CYS Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 310 CYS Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 350 MET Chi-restraints excluded: chain R residue 361 ASN Chi-restraints excluded: chain R residue 373 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 107 optimal weight: 0.3980 chunk 7 optimal weight: 0.0040 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 ASN A 357 ASN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS R 339 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.150407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.133467 restraints weight = 12828.471| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.22 r_work: 0.3653 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9182 Z= 0.119 Angle : 0.552 9.178 12454 Z= 0.284 Chirality : 0.041 0.159 1416 Planarity : 0.004 0.056 1580 Dihedral : 3.955 17.241 1244 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.36 % Favored : 96.46 % Rotamer: Outliers : 7.14 % Allowed : 22.96 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.25), residues: 1131 helix: 1.61 (0.27), residues: 380 sheet: 0.67 (0.33), residues: 265 loop : -0.95 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 142 TYR 0.014 0.001 TYR E 235 PHE 0.012 0.001 PHE A 187 TRP 0.011 0.001 TRP B 216 HIS 0.011 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9180) covalent geometry : angle 0.55176 (12450) SS BOND : bond 0.00202 ( 2) SS BOND : angle 0.73579 ( 4) hydrogen bonds : bond 0.03613 ( 401) hydrogen bonds : angle 4.03663 ( 1140) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 193 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7134 (mtm110) cc_final: 0.6875 (mtm110) REVERT: A 46 LYS cc_start: 0.7009 (OUTLIER) cc_final: 0.5984 (mptm) REVERT: A 188 GLN cc_start: 0.7120 (OUTLIER) cc_final: 0.6806 (tm-30) REVERT: A 215 ASP cc_start: 0.7425 (t0) cc_final: 0.7059 (t0) REVERT: A 249 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8274 (p) REVERT: A 262 LEU cc_start: 0.6787 (tt) cc_final: 0.6511 (tp) REVERT: A 347 ILE cc_start: 0.8398 (tp) cc_final: 0.8100 (mt) REVERT: B 73 ARG cc_start: 0.8372 (ttt180) cc_final: 0.7924 (ttt180) REVERT: B 170 THR cc_start: 0.7219 (t) cc_final: 0.5764 (m) REVERT: B 173 LEU cc_start: 0.8378 (tt) cc_final: 0.8086 (tp) REVERT: B 176 ILE cc_start: 0.7588 (mm) cc_final: 0.7239 (mm) REVERT: B 188 HIS cc_start: 0.8519 (OUTLIER) cc_final: 0.7984 (m-70) REVERT: B 215 LEU cc_start: 0.7797 (tp) cc_final: 0.7484 (tp) REVERT: B 266 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7982 (mt) REVERT: B 334 THR cc_start: 0.8253 (t) cc_final: 0.7984 (p) REVERT: E 66 ARG cc_start: 0.7565 (ttp80) cc_final: 0.7034 (ttp80) REVERT: E 82 MET cc_start: 0.8051 (mmt) cc_final: 0.7573 (mmm) REVERT: E 86 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.7160 (mtt180) REVERT: E 102 TYR cc_start: 0.7915 (t80) cc_final: 0.7146 (t80) REVERT: E 224 VAL cc_start: 0.8191 (t) cc_final: 0.7890 (p) REVERT: G 50 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6834 (mt) REVERT: R 91 PHE cc_start: 0.7879 (t80) cc_final: 0.7662 (t80) REVERT: R 102 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7638 (mt) REVERT: R 108 ASN cc_start: 0.7565 (t0) cc_final: 0.7034 (t0) REVERT: R 137 ASN cc_start: 0.7668 (m-40) cc_final: 0.7292 (m-40) REVERT: R 212 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7899 (tp) REVERT: R 224 PHE cc_start: 0.7459 (OUTLIER) cc_final: 0.6270 (t80) REVERT: R 229 PHE cc_start: 0.7119 (p90) cc_final: 0.6707 (p90) REVERT: R 241 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6801 (pp) REVERT: R 255 LYS cc_start: 0.6843 (OUTLIER) cc_final: 0.6607 (tttm) REVERT: R 262 PHE cc_start: 0.7209 (t80) cc_final: 0.7000 (t80) outliers start: 69 outliers final: 51 residues processed: 233 average time/residue: 0.1059 time to fit residues: 32.5937 Evaluate side-chains 255 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 192 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain B residue 59 HIS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 142 GLN Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 145 ARG Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 180 SER Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 224 PHE Chi-restraints excluded: chain R residue 240 MET Chi-restraints excluded: chain R residue 241 LEU Chi-restraints excluded: chain R residue 255 LYS Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 280 CYS Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 310 CYS Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 339 ASN Chi-restraints excluded: chain R residue 350 MET Chi-restraints excluded: chain R residue 361 ASN Chi-restraints excluded: chain R residue 373 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 HIS ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN G 44 HIS R 300 GLN R 339 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.142270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.125714 restraints weight = 12587.054| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.10 r_work: 0.3543 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 9182 Z= 0.282 Angle : 0.717 10.403 12454 Z= 0.371 Chirality : 0.048 0.207 1416 Planarity : 0.005 0.051 1580 Dihedral : 4.772 17.836 1244 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.51 % Favored : 95.31 % Rotamer: Outliers : 6.93 % Allowed : 24.72 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.25), residues: 1131 helix: 1.05 (0.27), residues: 378 sheet: 0.48 (0.32), residues: 265 loop : -1.03 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 339 TYR 0.023 0.002 TYR E 190 PHE 0.021 0.003 PHE L 14 TRP 0.020 0.002 TRP B 216 HIS 0.037 0.003 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00666 ( 9180) covalent geometry : angle 0.71726 (12450) SS BOND : bond 0.00527 ( 2) SS BOND : angle 1.25602 ( 4) hydrogen bonds : bond 0.04861 ( 401) hydrogen bonds : angle 4.55560 ( 1140) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 207 time to evaluate : 0.211 Fit side-chains REVERT: A 20 ASP cc_start: 0.8047 (m-30) cc_final: 0.7625 (m-30) REVERT: A 24 ARG cc_start: 0.7339 (mtm110) cc_final: 0.7080 (mtm110) REVERT: A 188 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: A 215 ASP cc_start: 0.7609 (t0) cc_final: 0.7221 (t0) REVERT: A 254 LEU cc_start: 0.8430 (mm) cc_final: 0.8219 (mt) REVERT: A 262 LEU cc_start: 0.7172 (tt) cc_final: 0.6970 (tp) REVERT: A 347 ILE cc_start: 0.8409 (tp) cc_final: 0.8153 (mt) REVERT: B 13 ARG cc_start: 0.6859 (mpp80) cc_final: 0.6406 (mpp80) REVERT: B 173 LEU cc_start: 0.8456 (tt) cc_final: 0.8159 (tp) REVERT: B 188 HIS cc_start: 0.8534 (OUTLIER) cc_final: 0.8084 (m-70) REVERT: B 256 ARG cc_start: 0.8224 (mtt90) cc_final: 0.7995 (mtt90) REVERT: B 273 ASN cc_start: 0.8016 (m-40) cc_final: 0.7738 (m-40) REVERT: B 334 THR cc_start: 0.8316 (t) cc_final: 0.8042 (p) REVERT: E 82 MET cc_start: 0.8127 (mmt) cc_final: 0.7781 (mmm) REVERT: E 102 TYR cc_start: 0.8112 (t80) cc_final: 0.7850 (t80) REVERT: R 108 ASN cc_start: 0.7606 (t0) cc_final: 0.7034 (t0) REVERT: R 137 ASN cc_start: 0.7893 (m-40) cc_final: 0.7647 (m-40) REVERT: R 212 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7872 (tp) REVERT: R 224 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.6567 (t80) REVERT: R 229 PHE cc_start: 0.7493 (p90) cc_final: 0.7241 (p90) REVERT: R 255 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6807 (tttm) REVERT: R 364 ILE cc_start: 0.6716 (mt) cc_final: 0.6027 (mt) outliers start: 67 outliers final: 49 residues processed: 249 average time/residue: 0.0930 time to fit residues: 30.4232 Evaluate side-chains 247 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 193 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 188 GLN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 238 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 180 SER Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 224 PHE Chi-restraints excluded: chain R residue 240 MET Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 255 LYS Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 280 CYS Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 310 CYS Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 339 ASN Chi-restraints excluded: chain R residue 350 MET Chi-restraints excluded: chain R residue 361 ASN Chi-restraints excluded: chain R residue 367 ILE Chi-restraints excluded: chain R residue 373 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 104 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 23 optimal weight: 0.1980 chunk 76 optimal weight: 0.1980 chunk 92 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 112 optimal weight: 0.0000 chunk 16 optimal weight: 0.6980 overall best weight: 0.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN B 147 HIS ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN G 44 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.146002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.129296 restraints weight = 12703.013| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.22 r_work: 0.3591 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9182 Z= 0.121 Angle : 0.602 11.506 12454 Z= 0.307 Chirality : 0.043 0.169 1416 Planarity : 0.004 0.054 1580 Dihedral : 4.256 17.775 1244 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.18 % Favored : 96.64 % Rotamer: Outliers : 5.48 % Allowed : 27.20 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.25), residues: 1131 helix: 1.25 (0.27), residues: 378 sheet: 0.38 (0.32), residues: 266 loop : -0.98 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 339 TYR 0.015 0.001 TYR E 235 PHE 0.014 0.001 PHE R 229 TRP 0.011 0.001 TRP E 110 HIS 0.015 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9180) covalent geometry : angle 0.60203 (12450) SS BOND : bond 0.00128 ( 2) SS BOND : angle 0.71488 ( 4) hydrogen bonds : bond 0.03968 ( 401) hydrogen bonds : angle 4.25771 ( 1140) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 190 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7232 (OUTLIER) cc_final: 0.6231 (mptm) REVERT: A 215 ASP cc_start: 0.7516 (t0) cc_final: 0.7150 (t0) REVERT: A 249 THR cc_start: 0.8514 (OUTLIER) cc_final: 0.8222 (p) REVERT: A 262 LEU cc_start: 0.7151 (tt) cc_final: 0.6905 (tp) REVERT: A 347 ILE cc_start: 0.8320 (tp) cc_final: 0.8018 (mt) REVERT: B 24 ARG cc_start: 0.7731 (ttp-110) cc_final: 0.7446 (ttp-110) REVERT: B 84 LEU cc_start: 0.8495 (mt) cc_final: 0.8250 (mt) REVERT: B 170 THR cc_start: 0.7383 (t) cc_final: 0.5970 (m) REVERT: B 173 LEU cc_start: 0.8337 (tt) cc_final: 0.8063 (tp) REVERT: B 188 HIS cc_start: 0.8545 (OUTLIER) cc_final: 0.8040 (m-70) REVERT: B 202 ARG cc_start: 0.7555 (ttm-80) cc_final: 0.7342 (ttm-80) REVERT: B 273 ASN cc_start: 0.8082 (m-40) cc_final: 0.7780 (m-40) REVERT: B 334 THR cc_start: 0.8271 (t) cc_final: 0.8012 (p) REVERT: E 82 MET cc_start: 0.8066 (mmt) cc_final: 0.7626 (mmm) REVERT: E 102 TYR cc_start: 0.8014 (t80) cc_final: 0.7748 (t80) REVERT: E 140 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7341 (mtm) REVERT: E 224 VAL cc_start: 0.8340 (t) cc_final: 0.8082 (p) REVERT: R 108 ASN cc_start: 0.7557 (t0) cc_final: 0.7012 (t0) REVERT: R 137 ASN cc_start: 0.7798 (m-40) cc_final: 0.7522 (m-40) REVERT: R 212 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7864 (tp) REVERT: R 220 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7157 (tm-30) REVERT: R 224 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.6393 (t80) REVERT: R 229 PHE cc_start: 0.7482 (p90) cc_final: 0.7203 (p90) REVERT: R 367 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7325 (mt) outliers start: 53 outliers final: 35 residues processed: 223 average time/residue: 0.1053 time to fit residues: 30.5520 Evaluate side-chains 232 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 180 SER Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 220 GLU Chi-restraints excluded: chain R residue 224 PHE Chi-restraints excluded: chain R residue 240 MET Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 310 CYS Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 350 MET Chi-restraints excluded: chain R residue 361 ASN Chi-restraints excluded: chain R residue 367 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 83 optimal weight: 0.0270 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 101 optimal weight: 0.1980 chunk 25 optimal weight: 0.2980 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.146275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.129901 restraints weight = 12698.964| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.13 r_work: 0.3607 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9182 Z= 0.123 Angle : 0.600 12.746 12454 Z= 0.303 Chirality : 0.043 0.159 1416 Planarity : 0.004 0.054 1580 Dihedral : 4.145 17.703 1244 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.36 % Favored : 96.46 % Rotamer: Outliers : 5.27 % Allowed : 27.51 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.25), residues: 1131 helix: 1.42 (0.27), residues: 371 sheet: 0.38 (0.32), residues: 266 loop : -0.93 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 339 TYR 0.020 0.001 TYR E 235 PHE 0.042 0.001 PHE R 91 TRP 0.009 0.001 TRP E 110 HIS 0.007 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9180) covalent geometry : angle 0.59990 (12450) SS BOND : bond 0.00170 ( 2) SS BOND : angle 0.65223 ( 4) hydrogen bonds : bond 0.03801 ( 401) hydrogen bonds : angle 4.19936 ( 1140) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 200 time to evaluate : 0.260 Fit side-chains REVERT: A 46 LYS cc_start: 0.7205 (OUTLIER) cc_final: 0.6215 (mptm) REVERT: A 215 ASP cc_start: 0.7487 (t0) cc_final: 0.7099 (t0) REVERT: A 262 LEU cc_start: 0.7182 (tt) cc_final: 0.6934 (tp) REVERT: B 13 ARG cc_start: 0.6854 (mpp80) cc_final: 0.6395 (mpp80) REVERT: B 24 ARG cc_start: 0.7730 (ttp-110) cc_final: 0.7439 (ttp-110) REVERT: B 84 LEU cc_start: 0.8504 (mt) cc_final: 0.8256 (mt) REVERT: B 170 THR cc_start: 0.7294 (t) cc_final: 0.5854 (m) REVERT: B 173 LEU cc_start: 0.8296 (tt) cc_final: 0.8019 (tp) REVERT: B 188 HIS cc_start: 0.8547 (OUTLIER) cc_final: 0.8031 (m-70) REVERT: B 202 ARG cc_start: 0.7669 (ttm-80) cc_final: 0.7273 (mmm160) REVERT: B 273 ASN cc_start: 0.8082 (m-40) cc_final: 0.7780 (m-40) REVERT: B 334 THR cc_start: 0.8246 (t) cc_final: 0.7997 (p) REVERT: E 82 MET cc_start: 0.8046 (mmt) cc_final: 0.7588 (mmm) REVERT: E 102 TYR cc_start: 0.7946 (t80) cc_final: 0.7678 (t80) REVERT: E 140 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7369 (mtm) REVERT: E 224 VAL cc_start: 0.8369 (t) cc_final: 0.8125 (p) REVERT: R 108 ASN cc_start: 0.7554 (t0) cc_final: 0.7001 (t0) REVERT: R 137 ASN cc_start: 0.7792 (m-40) cc_final: 0.7515 (m-40) REVERT: R 212 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7863 (tp) REVERT: R 220 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7084 (tm-30) REVERT: R 224 PHE cc_start: 0.7588 (OUTLIER) cc_final: 0.6303 (t80) REVERT: R 229 PHE cc_start: 0.7462 (p90) cc_final: 0.7205 (p90) REVERT: R 360 MET cc_start: 0.7630 (tmm) cc_final: 0.7389 (tmm) REVERT: R 367 ILE cc_start: 0.7759 (pt) cc_final: 0.7442 (mt) outliers start: 51 outliers final: 36 residues processed: 231 average time/residue: 0.0938 time to fit residues: 28.6963 Evaluate side-chains 244 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 180 SER Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 220 GLU Chi-restraints excluded: chain R residue 224 PHE Chi-restraints excluded: chain R residue 240 MET Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 280 CYS Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 310 CYS Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 350 MET Chi-restraints excluded: chain R residue 361 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 107 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 62 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.143518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.126888 restraints weight = 12687.553| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.21 r_work: 0.3556 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9182 Z= 0.184 Angle : 0.642 12.203 12454 Z= 0.326 Chirality : 0.045 0.166 1416 Planarity : 0.004 0.053 1580 Dihedral : 4.351 17.513 1244 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.80 % Favored : 96.02 % Rotamer: Outliers : 4.86 % Allowed : 28.13 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.25), residues: 1131 helix: 1.16 (0.27), residues: 382 sheet: 0.31 (0.31), residues: 266 loop : -0.91 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 339 TYR 0.021 0.002 TYR E 235 PHE 0.039 0.002 PHE R 91 TRP 0.011 0.002 TRP B 337 HIS 0.016 0.002 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 9180) covalent geometry : angle 0.64185 (12450) SS BOND : bond 0.00300 ( 2) SS BOND : angle 0.80269 ( 4) hydrogen bonds : bond 0.04178 ( 401) hydrogen bonds : angle 4.29749 ( 1140) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 192 time to evaluate : 0.336 Fit side-chains REVERT: A 46 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6680 (mptm) REVERT: A 215 ASP cc_start: 0.7539 (t0) cc_final: 0.7171 (t0) REVERT: A 347 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.8102 (mt) REVERT: B 13 ARG cc_start: 0.6887 (mpp80) cc_final: 0.6431 (mpp80) REVERT: B 24 ARG cc_start: 0.7775 (ttp-110) cc_final: 0.7525 (ttp-110) REVERT: B 135 GLU cc_start: 0.8068 (mp0) cc_final: 0.7591 (mp0) REVERT: B 170 THR cc_start: 0.7543 (t) cc_final: 0.6145 (m) REVERT: B 173 LEU cc_start: 0.8355 (tt) cc_final: 0.8074 (tp) REVERT: B 188 HIS cc_start: 0.8557 (OUTLIER) cc_final: 0.8040 (m-70) REVERT: B 334 THR cc_start: 0.8326 (t) cc_final: 0.8094 (p) REVERT: E 82 MET cc_start: 0.8081 (mmt) cc_final: 0.7663 (mmm) REVERT: E 102 TYR cc_start: 0.8028 (t80) cc_final: 0.7781 (t80) REVERT: E 140 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7389 (mtm) REVERT: E 224 VAL cc_start: 0.8438 (t) cc_final: 0.8197 (p) REVERT: R 108 ASN cc_start: 0.7583 (t0) cc_final: 0.7021 (t0) REVERT: R 137 ASN cc_start: 0.7846 (m-40) cc_final: 0.7590 (m-40) REVERT: R 212 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7872 (tp) REVERT: R 220 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7123 (tm-30) REVERT: R 224 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.6403 (t80) REVERT: R 229 PHE cc_start: 0.7514 (p90) cc_final: 0.7233 (p90) REVERT: R 360 MET cc_start: 0.7695 (tmm) cc_final: 0.7281 (tmm) REVERT: R 364 ILE cc_start: 0.6533 (mt) cc_final: 0.6006 (mt) REVERT: R 367 ILE cc_start: 0.7815 (pt) cc_final: 0.7491 (mt) outliers start: 47 outliers final: 38 residues processed: 222 average time/residue: 0.1024 time to fit residues: 29.7964 Evaluate side-chains 235 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 190 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 321 ARG Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 158 CYS Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 180 SER Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 220 GLU Chi-restraints excluded: chain R residue 224 PHE Chi-restraints excluded: chain R residue 240 MET Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 280 CYS Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 310 CYS Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 350 MET Chi-restraints excluded: chain R residue 361 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.143999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.127520 restraints weight = 12501.207| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.19 r_work: 0.3567 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9182 Z= 0.160 Angle : 0.641 12.439 12454 Z= 0.322 Chirality : 0.044 0.164 1416 Planarity : 0.004 0.054 1580 Dihedral : 4.310 17.779 1244 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.89 % Favored : 95.93 % Rotamer: Outliers : 5.07 % Allowed : 28.02 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.25), residues: 1131 helix: 1.13 (0.27), residues: 382 sheet: 0.28 (0.31), residues: 266 loop : -0.90 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 339 TYR 0.020 0.001 TYR E 235 PHE 0.039 0.002 PHE R 91 TRP 0.012 0.001 TRP B 337 HIS 0.006 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 9180) covalent geometry : angle 0.64101 (12450) SS BOND : bond 0.00234 ( 2) SS BOND : angle 0.72392 ( 4) hydrogen bonds : bond 0.04061 ( 401) hydrogen bonds : angle 4.27873 ( 1140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2488.80 seconds wall clock time: 43 minutes 14.76 seconds (2594.76 seconds total)