Starting phenix.real_space_refine on Sat Jul 4 01:56:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jt6_36634/07_2026/8jt6_36634_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jt6_36634/07_2026/8jt6_36634.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jt6_36634/07_2026/8jt6_36634_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jt6_36634/07_2026/8jt6_36634_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jt6_36634/07_2026/8jt6_36634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jt6_36634/07_2026/8jt6_36634.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 7 Type Number sf(0) Gaussians P 2 5.49 5 S 63 5.16 5 C 5674 2.51 5 N 1465 2.21 5 O 1624 1.98 5 F 1 1.80 5 H 8554 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17383 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3537 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Chain: "B" Number of atoms: 4945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 4945 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 322} Chain: "E" Number of atoms: 3471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3471 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Chain: "G" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 698 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 4, 'TRANS': 40} Chain: "R" Number of atoms: 4497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4497 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 2 Chain: "R" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 235 Unusual residues: {'CLR': 5, 'EZX': 1, 'J40': 1, 'PLM': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'J40:plan-1': 1, 'J40:plan-3': 1, 'J40:plan-4': 1, 'J40:plan-5': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 3.24, per 1000 atoms: 0.19 Number of scatterers: 17383 At special positions: 0 Unit cell: (111.72, 136.08, 110.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 63 16.00 P 2 15.00 F 1 9.00 O 1624 8.00 N 1465 7.00 C 5674 6.00 H 8554 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " 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: 1.55 Conformation dependent library (CDL) restraints added in 499.9 milliseconds 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2054 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 40.4% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 9 through 31 removed outlier: 3.601A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 removed outlier: 4.019A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.438A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.554A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.670A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 352 removed outlier: 4.257A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 26 removed outlier: 3.973A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.977A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.795A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'G' and resid 19 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.830A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'R' and resid 36 through 64 Processing helix chain 'R' and resid 69 through 89 Processing helix chain 'R' and resid 89 through 100 Processing helix chain 'R' and resid 105 through 140 removed outlier: 3.679A pdb=" N LEU R 127 " --> pdb=" O SER R 123 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS R 128 " --> pdb=" O ILE R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 147 Processing helix chain 'R' and resid 149 through 175 removed outlier: 4.025A pdb=" N ALA R 153 " --> pdb=" O THR R 149 " (cutoff:3.500A) Proline residue: R 170 - end of helix removed outlier: 3.843A pdb=" N TRP R 175 " --> pdb=" O PRO R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 204 Processing helix chain 'R' and resid 204 through 228 Processing helix chain 'R' and resid 325 through 372 removed outlier: 3.828A pdb=" N ALA R 329 " --> pdb=" O ASN R 325 " (cutoff:3.500A) Proline residue: R 360 - end of helix Proline residue: R 369 - end of helix Processing helix chain 'R' and resid 378 through 401 removed outlier: 3.634A pdb=" N GLY R 389 " --> pdb=" O ILE R 385 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR R 390 " --> pdb=" O ASN R 386 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN R 392 " --> pdb=" O LEU R 388 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER R 393 " --> pdb=" O GLY R 389 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU R 394 " --> pdb=" O TYR R 390 " (cutoff:3.500A) Proline residue: R 397 - end of helix Processing helix chain 'R' and resid 404 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 7.000A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.524A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.647A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.817A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.501A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.583A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.427A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.224A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.504A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.504A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (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: 3.807A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.807A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN E 231 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1236 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: 3.72 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8520 1.03 - 1.23: 42 1.23 - 1.42: 3738 1.42 - 1.62: 5170 1.62 - 1.81: 107 Bond restraints: 17577 Sorted by residual: bond pdb=" C17 EZX R 509 " pdb=" C7 EZX R 509 " ideal model delta sigma weight residual 1.398 1.117 0.281 2.00e-02 2.50e+03 1.98e+02 bond pdb=" C11 CLR R 502 " pdb=" C9 CLR R 502 " ideal model delta sigma weight residual 1.533 1.754 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C11 CLR R 504 " pdb=" C9 CLR R 504 " ideal model delta sigma weight residual 1.533 1.754 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C11 CLR R 501 " pdb=" C9 CLR R 501 " ideal model delta sigma weight residual 1.533 1.754 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C11 CLR R 506 " pdb=" C9 CLR R 506 " ideal model delta sigma weight residual 1.533 1.754 -0.221 2.00e-02 2.50e+03 1.22e+02 ... (remaining 17572 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 31409 2.70 - 5.41: 129 5.41 - 8.11: 19 8.11 - 10.82: 12 10.82 - 13.52: 1 Bond angle restraints: 31570 Sorted by residual: angle pdb=" CA PRO E 75 " pdb=" N PRO E 75 " pdb=" CD PRO E 75 " ideal model delta sigma weight residual 112.00 98.48 13.52 1.40e+00 5.10e-01 9.33e+01 angle pdb=" CA PRO R 369 " pdb=" N PRO R 369 " pdb=" CD PRO R 369 " ideal model delta sigma weight residual 112.00 104.03 7.97 1.40e+00 5.10e-01 3.24e+01 angle pdb=" N PRO E 75 " pdb=" CD PRO E 75 " pdb=" CG PRO E 75 " ideal model delta sigma weight residual 103.20 95.44 7.76 1.50e+00 4.44e-01 2.68e+01 angle pdb=" N PRO R 369 " pdb=" CD PRO R 369 " pdb=" CG PRO R 369 " ideal model delta sigma weight residual 103.20 96.05 7.15 1.50e+00 4.44e-01 2.27e+01 angle pdb=" C SER R 168 " pdb=" N ILE R 169 " pdb=" CA ILE R 169 " ideal model delta sigma weight residual 120.24 122.89 -2.65 6.30e-01 2.52e+00 1.78e+01 ... (remaining 31565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.44: 8197 26.44 - 52.89: 337 52.89 - 79.33: 55 79.33 - 105.77: 14 105.77 - 132.21: 2 Dihedral angle restraints: 8605 sinusoidal: 4809 harmonic: 3796 Sorted by residual: dihedral pdb=" C18 EZX R 509 " pdb=" C1 EZX R 509 " pdb=" C2 EZX R 509 " pdb=" C3 EZX R 509 " ideal model delta sinusoidal sigma weight residual 185.93 53.72 132.21 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" CA GLY B 272 " pdb=" C GLY B 272 " pdb=" N ILE B 273 " pdb=" CA ILE B 273 " ideal model delta harmonic sigma weight residual -180.00 -159.64 -20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C3 EZX R 509 " pdb=" C4 EZX R 509 " pdb=" N1 EZX R 509 " pdb=" C5 EZX R 509 " ideal model delta sinusoidal sigma weight residual -171.03 -53.99 -117.04 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 8602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1331 0.106 - 0.212: 54 0.212 - 0.318: 7 0.318 - 0.423: 6 0.423 - 0.529: 1 Chirality restraints: 1399 Sorted by residual: chirality pdb=" C1 J40 R 508 " pdb=" C2 J40 R 508 " pdb=" C6 J40 R 508 " pdb=" O1 J40 R 508 " both_signs ideal model delta sigma weight residual False 2.53 2.00 0.53 2.00e-01 2.50e+01 7.00e+00 chirality pdb=" C9 CLR R 502 " pdb=" C10 CLR R 502 " pdb=" C11 CLR R 502 " pdb=" C8 CLR R 502 " both_signs ideal model delta sigma weight residual False -2.45 -2.83 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" C9 CLR R 503 " pdb=" C10 CLR R 503 " pdb=" C11 CLR R 503 " pdb=" C8 CLR R 503 " both_signs ideal model delta sigma weight residual False -2.45 -2.82 0.37 2.00e-01 2.50e+01 3.46e+00 ... (remaining 1396 not shown) Planarity restraints: 2561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 J40 R 508 " 0.084 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C31 J40 R 508 " -0.024 2.00e-02 2.50e+03 pdb=" O18 J40 R 508 " -0.027 2.00e-02 2.50e+03 pdb=" O19 J40 R 508 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 74 " -0.087 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO E 75 " 0.209 5.00e-02 4.00e+02 pdb=" CA PRO E 75 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO E 75 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 368 " 0.070 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO R 369 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO R 369 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO R 369 " 0.055 5.00e-02 4.00e+02 ... (remaining 2558 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 683 2.18 - 2.79: 34010 2.79 - 3.39: 46595 3.39 - 4.00: 60806 4.00 - 4.60: 94979 Nonbonded interactions: 237073 Sorted by model distance: nonbonded pdb=" HG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 1.580 2.450 nonbonded pdb=" OD1 ASP B 195 " pdb=" H ARG B 197 " model vdw 1.583 2.450 nonbonded pdb="HH12 ARG B 22 " pdb=" O ASP B 258 " model vdw 1.590 2.450 nonbonded pdb=" OD1 ASP B 205 " pdb=" HG SER B 207 " model vdw 1.621 2.450 nonbonded pdb=" OD1 ASN A 269 " pdb=" HG1 THR A 324 " model vdw 1.641 2.450 ... (remaining 237068 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: 1.830 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: 0.120 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.380 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.281 9024 Z= 0.594 Angle : 0.723 13.524 12245 Z= 0.355 Chirality : 0.053 0.529 1399 Planarity : 0.005 0.121 1502 Dihedral : 14.244 132.214 3581 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.27), residues: 1080 helix: 3.56 (0.28), residues: 360 sheet: 1.48 (0.32), residues: 271 loop : 0.37 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 227 TYR 0.007 0.001 TYR R 195 PHE 0.008 0.001 PHE R 362 TRP 0.005 0.001 TRP R 387 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.01199 / 0.59 ( 9023) covalent geometry : angle 0.72306 / 0.35 (12243) SS BOND : bond 0.00023 / 0.01 ( 1) SS BOND : angle 0.61903 / 0.28 ( 2) hydrogen bonds : bond 0.19329 / 13.24 ( 436) hydrogen bonds : angle 6.06651 / 4.34 ( 1236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 SER cc_start: 0.7539 (p) cc_final: 0.7169 (m) REVERT: A 243 MET cc_start: 0.8027 (tpp) cc_final: 0.7652 (tpt) REVERT: A 294 ASN cc_start: 0.6987 (m-40) cc_final: 0.6700 (t0) REVERT: A 318 GLU cc_start: 0.7206 (mt-10) cc_final: 0.7000 (mt-10) REVERT: G 21 MET cc_start: 0.7100 (mmm) cc_final: 0.6346 (tpt) REVERT: R 65 ARG cc_start: 0.7521 (ttm170) cc_final: 0.7259 (ttm170) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 1.2326 time to fit residues: 198.9570 Evaluate side-chains 106 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 331 ASN A 346 ASN B 239 ASN E 3 GLN E 186 GLN R 36 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.149029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.116384 restraints weight = 31612.139| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.89 r_work: 0.3224 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9024 Z= 0.151 Angle : 0.557 6.272 12245 Z= 0.295 Chirality : 0.041 0.187 1399 Planarity : 0.005 0.060 1502 Dihedral : 9.329 133.318 1622 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.07 % Allowed : 9.51 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.26), residues: 1080 helix: 3.24 (0.28), residues: 368 sheet: 1.27 (0.32), residues: 263 loop : -0.20 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 129 TYR 0.011 0.001 TYR B 59 PHE 0.020 0.002 PHE B 292 TRP 0.008 0.001 TRP B 339 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 9023) covalent geometry : angle 0.55650 / 0.29 (12243) SS BOND : bond 0.00190 / 0.10 ( 1) SS BOND : angle 0.98039 / 0.46 ( 2) hydrogen bonds : bond 0.05291 / 3.47 ( 436) hydrogen bonds : angle 4.64527 / 3.24 ( 1236) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 44 SER cc_start: 0.7341 (p) cc_final: 0.7084 (m) REVERT: A 242 ARG cc_start: 0.6695 (mtm-85) cc_final: 0.6465 (mtm-85) REVERT: A 248 LYS cc_start: 0.7802 (tttm) cc_final: 0.7434 (mtmm) REVERT: A 294 ASN cc_start: 0.7324 (m-40) cc_final: 0.6792 (t0) REVERT: B 19 ARG cc_start: 0.6277 (OUTLIER) cc_final: 0.5626 (ttm110) REVERT: B 152 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8382 (mp) REVERT: G 21 MET cc_start: 0.6699 (mmm) cc_final: 0.6192 (tpt) REVERT: R 65 ARG cc_start: 0.8195 (ttm170) cc_final: 0.7918 (ttm170) REVERT: R 185 ASP cc_start: 0.6950 (t0) cc_final: 0.6722 (t0) REVERT: R 351 MET cc_start: 0.8209 (mmm) cc_final: 0.8000 (tpt) outliers start: 10 outliers final: 5 residues processed: 128 average time/residue: 1.3954 time to fit residues: 189.9601 Evaluate side-chains 116 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 69 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 237 ASN B 239 ASN E 186 GLN R 36 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.142243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.108743 restraints weight = 31610.217| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.88 r_work: 0.3051 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9024 Z= 0.194 Angle : 0.592 7.939 12245 Z= 0.316 Chirality : 0.042 0.199 1399 Planarity : 0.006 0.072 1502 Dihedral : 10.212 151.628 1622 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.14 % Allowed : 11.54 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.25), residues: 1080 helix: 2.65 (0.27), residues: 375 sheet: 0.93 (0.32), residues: 248 loop : -0.56 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 333 TYR 0.017 0.002 TYR B 105 PHE 0.023 0.002 PHE B 292 TRP 0.010 0.001 TRP B 339 HIS 0.005 0.002 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 ( 9023) covalent geometry : angle 0.59179 / 0.32 (12243) SS BOND : bond 0.00375 / 0.20 ( 1) SS BOND : angle 1.41123 / 0.68 ( 2) hydrogen bonds : bond 0.06060 / 3.90 ( 436) hydrogen bonds : angle 4.68538 / 3.27 ( 1236) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 43 LYS cc_start: 0.8137 (mtmm) cc_final: 0.7828 (mppt) REVERT: G 21 MET cc_start: 0.6725 (mmm) cc_final: 0.6400 (tpt) outliers start: 20 outliers final: 10 residues processed: 128 average time/residue: 1.3797 time to fit residues: 187.4705 Evaluate side-chains 117 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 40 SER Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 1 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 GLN B 340 ASN E 186 GLN R 36 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.141372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.109448 restraints weight = 31813.749| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.80 r_work: 0.3157 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9024 Z= 0.102 Angle : 0.495 7.020 12245 Z= 0.263 Chirality : 0.039 0.203 1399 Planarity : 0.004 0.051 1502 Dihedral : 8.848 135.055 1622 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.92 % Allowed : 11.97 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.26), residues: 1080 helix: 3.02 (0.27), residues: 374 sheet: 0.76 (0.32), residues: 257 loop : -0.56 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 333 TYR 0.011 0.001 TYR R 198 PHE 0.019 0.001 PHE B 292 TRP 0.007 0.001 TRP B 63 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 ( 9023) covalent geometry : angle 0.49502 / 0.26 (12243) SS BOND : bond 0.00001 / 0.00 ( 1) SS BOND : angle 0.63902 / 0.33 ( 2) hydrogen bonds : bond 0.04547 / 2.92 ( 436) hydrogen bonds : angle 4.32466 / 3.01 ( 1236) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8335 (ttm-80) cc_final: 0.8072 (ttm110) REVERT: A 248 LYS cc_start: 0.7890 (tttm) cc_final: 0.7509 (mtmm) REVERT: B 15 LYS cc_start: 0.6216 (ttpp) cc_final: 0.5599 (tptp) REVERT: B 44 GLN cc_start: 0.7340 (mt0) cc_final: 0.6781 (pm20) REVERT: G 21 MET cc_start: 0.6799 (mmm) cc_final: 0.6458 (tpt) outliers start: 18 outliers final: 6 residues processed: 127 average time/residue: 1.3740 time to fit residues: 185.5761 Evaluate side-chains 114 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain R residue 40 SER Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 76 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 104 optimal weight: 0.1980 chunk 79 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN B 239 ASN B 340 ASN E 3 GLN R 36 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.144912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.111810 restraints weight = 31258.460| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.88 r_work: 0.3127 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9024 Z= 0.096 Angle : 0.480 6.181 12245 Z= 0.253 Chirality : 0.039 0.226 1399 Planarity : 0.004 0.048 1502 Dihedral : 8.285 130.545 1622 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.96 % Allowed : 13.78 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.26), residues: 1080 helix: 3.18 (0.27), residues: 374 sheet: 0.71 (0.31), residues: 257 loop : -0.51 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 333 TYR 0.012 0.001 TYR R 198 PHE 0.019 0.001 PHE B 292 TRP 0.007 0.001 TRP B 63 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 ( 9023) covalent geometry : angle 0.47957 / 0.25 (12243) SS BOND : bond 0.00014 / 0.01 ( 1) SS BOND : angle 0.55265 / 0.26 ( 2) hydrogen bonds : bond 0.04220 / 2.72 ( 436) hydrogen bonds : angle 4.15934 / 2.89 ( 1236) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8353 (ttm-80) cc_final: 0.8028 (ttm110) REVERT: A 248 LYS cc_start: 0.7872 (tttm) cc_final: 0.7464 (mtmm) REVERT: A 318 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7392 (mt-10) REVERT: B 15 LYS cc_start: 0.6312 (ttpp) cc_final: 0.5751 (tptp) REVERT: B 44 GLN cc_start: 0.7371 (mt0) cc_final: 0.6801 (pm20) REVERT: E 186 GLN cc_start: 0.8411 (pt0) cc_final: 0.8158 (pt0) REVERT: G 21 MET cc_start: 0.6792 (mmm) cc_final: 0.6432 (tpt) outliers start: 9 outliers final: 4 residues processed: 119 average time/residue: 1.3431 time to fit residues: 170.0442 Evaluate side-chains 112 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 25 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN B 237 ASN B 239 ASN R 36 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.144174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.111092 restraints weight = 31081.379| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.87 r_work: 0.3099 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9024 Z= 0.123 Angle : 0.508 7.207 12245 Z= 0.267 Chirality : 0.040 0.223 1399 Planarity : 0.004 0.050 1502 Dihedral : 8.773 135.350 1622 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.60 % Allowed : 13.89 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.26), residues: 1080 helix: 3.06 (0.27), residues: 374 sheet: 0.65 (0.32), residues: 257 loop : -0.57 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 333 TYR 0.014 0.001 TYR R 198 PHE 0.018 0.001 PHE B 292 TRP 0.008 0.001 TRP B 63 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 9023) covalent geometry : angle 0.50754 / 0.27 (12243) SS BOND : bond 0.00127 / 0.07 ( 1) SS BOND : angle 0.78869 / 0.38 ( 2) hydrogen bonds : bond 0.04661 / 2.99 ( 436) hydrogen bonds : angle 4.22117 / 2.93 ( 1236) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 LYS cc_start: 0.7930 (tttm) cc_final: 0.7472 (mtmm) REVERT: B 44 GLN cc_start: 0.7464 (mt0) cc_final: 0.6790 (pm20) REVERT: G 19 LEU cc_start: 0.5959 (OUTLIER) cc_final: 0.5578 (mt) REVERT: G 21 MET cc_start: 0.6742 (mmm) cc_final: 0.6437 (tpt) outliers start: 15 outliers final: 7 residues processed: 117 average time/residue: 1.3664 time to fit residues: 170.0042 Evaluate side-chains 116 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 40 SER Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 64 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 46 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN R 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.144212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112843 restraints weight = 31414.592| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.85 r_work: 0.3183 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9024 Z= 0.099 Angle : 0.483 5.967 12245 Z= 0.255 Chirality : 0.039 0.224 1399 Planarity : 0.004 0.070 1502 Dihedral : 8.344 128.872 1622 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.85 % Allowed : 14.96 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.26), residues: 1080 helix: 3.20 (0.27), residues: 374 sheet: 0.62 (0.32), residues: 257 loop : -0.54 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 333 TYR 0.012 0.001 TYR R 198 PHE 0.019 0.001 PHE B 292 TRP 0.007 0.001 TRP B 63 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 9023) covalent geometry : angle 0.48269 / 0.26 (12243) SS BOND : bond 0.00032 / 0.02 ( 1) SS BOND : angle 0.56835 / 0.27 ( 2) hydrogen bonds : bond 0.04237 / 2.72 ( 436) hydrogen bonds : angle 4.09631 / 2.85 ( 1236) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8345 (ttm-80) cc_final: 0.7997 (ttm110) REVERT: A 248 LYS cc_start: 0.7887 (tttm) cc_final: 0.7518 (mtmm) REVERT: B 15 LYS cc_start: 0.6322 (ttpp) cc_final: 0.5762 (tptp) REVERT: B 44 GLN cc_start: 0.7460 (mt0) cc_final: 0.6838 (pm20) REVERT: E 160 ARG cc_start: 0.7221 (ttp-110) cc_final: 0.6714 (ttm110) REVERT: G 21 MET cc_start: 0.6801 (mmm) cc_final: 0.6459 (tpt) outliers start: 8 outliers final: 6 residues processed: 115 average time/residue: 1.3102 time to fit residues: 160.6652 Evaluate side-chains 115 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 40 SER Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 85 optimal weight: 0.1980 chunk 38 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN R 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.141350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.109090 restraints weight = 31687.838| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.82 r_work: 0.3122 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9024 Z= 0.132 Angle : 0.519 7.324 12245 Z= 0.274 Chirality : 0.040 0.217 1399 Planarity : 0.005 0.056 1502 Dihedral : 9.022 134.402 1622 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.18 % Allowed : 15.28 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.26), residues: 1080 helix: 2.98 (0.27), residues: 377 sheet: 0.76 (0.32), residues: 248 loop : -0.64 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 333 TYR 0.014 0.001 TYR R 198 PHE 0.019 0.001 PHE B 292 TRP 0.008 0.001 TRP B 63 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 9023) covalent geometry : angle 0.51875 / 0.27 (12243) SS BOND : bond 0.00171 / 0.09 ( 1) SS BOND : angle 0.84451 / 0.41 ( 2) hydrogen bonds : bond 0.04792 / 3.07 ( 436) hydrogen bonds : angle 4.20313 / 2.92 ( 1236) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8424 (ttm-80) cc_final: 0.8120 (ttm110) REVERT: A 248 LYS cc_start: 0.7950 (tttm) cc_final: 0.7496 (mtmm) REVERT: B 44 GLN cc_start: 0.7450 (mt0) cc_final: 0.6770 (pm20) REVERT: B 45 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.6874 (mpp) REVERT: B 237 ASN cc_start: 0.7944 (t0) cc_final: 0.7734 (t0) REVERT: E 160 ARG cc_start: 0.7253 (ttp-110) cc_final: 0.6676 (ttm110) REVERT: G 21 MET cc_start: 0.6757 (mmm) cc_final: 0.6391 (tpt) outliers start: 11 outliers final: 4 residues processed: 116 average time/residue: 1.3525 time to fit residues: 167.1205 Evaluate side-chains 111 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 79 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.141104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.109861 restraints weight = 31507.790| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.82 r_work: 0.3088 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9024 Z= 0.129 Angle : 0.514 7.202 12245 Z= 0.273 Chirality : 0.040 0.215 1399 Planarity : 0.005 0.059 1502 Dihedral : 9.130 135.787 1622 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.18 % Allowed : 15.49 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.26), residues: 1080 helix: 2.92 (0.27), residues: 382 sheet: 0.72 (0.32), residues: 248 loop : -0.64 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 333 TYR 0.012 0.001 TYR R 198 PHE 0.021 0.001 PHE B 292 TRP 0.008 0.001 TRP B 63 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 9023) covalent geometry : angle 0.51354 / 0.27 (12243) SS BOND : bond 0.00145 / 0.08 ( 1) SS BOND : angle 0.85327 / 0.42 ( 2) hydrogen bonds : bond 0.04800 / 3.07 ( 436) hydrogen bonds : angle 4.21551 / 2.93 ( 1236) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8339 (ttm-80) cc_final: 0.8053 (ttm110) REVERT: A 248 LYS cc_start: 0.7909 (tttm) cc_final: 0.7455 (mtmm) REVERT: B 44 GLN cc_start: 0.7474 (mt0) cc_final: 0.6800 (pm20) REVERT: B 45 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.6866 (mpp) REVERT: E 160 ARG cc_start: 0.7267 (ttp-110) cc_final: 0.6764 (ttm110) REVERT: G 21 MET cc_start: 0.6831 (mmm) cc_final: 0.6490 (tpt) outliers start: 11 outliers final: 6 residues processed: 112 average time/residue: 1.3283 time to fit residues: 158.5588 Evaluate side-chains 112 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 367 VAL Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 84 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 65 optimal weight: 0.0980 chunk 14 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN B 237 ASN R 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.143064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.112339 restraints weight = 31124.406| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.81 r_work: 0.3135 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9024 Z= 0.095 Angle : 0.482 5.561 12245 Z= 0.256 Chirality : 0.039 0.216 1399 Planarity : 0.004 0.058 1502 Dihedral : 8.447 126.196 1622 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.53 % Allowed : 16.56 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.26), residues: 1080 helix: 3.15 (0.27), residues: 380 sheet: 0.61 (0.31), residues: 254 loop : -0.58 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 333 TYR 0.012 0.001 TYR R 198 PHE 0.022 0.001 PHE B 292 TRP 0.007 0.001 TRP B 63 HIS 0.001 0.000 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 ( 9023) covalent geometry : angle 0.48168 / 0.26 (12243) SS BOND : bond 0.00026 / 0.01 ( 1) SS BOND : angle 0.57848 / 0.30 ( 2) hydrogen bonds : bond 0.04142 / 2.65 ( 436) hydrogen bonds : angle 4.07331 / 2.83 ( 1236) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8304 (ttm-80) cc_final: 0.8003 (ttm110) REVERT: A 248 LYS cc_start: 0.7904 (tttm) cc_final: 0.7541 (pttp) REVERT: B 44 GLN cc_start: 0.7498 (mt0) cc_final: 0.6824 (pm20) REVERT: B 45 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.6816 (mpp) REVERT: G 21 MET cc_start: 0.6827 (mmm) cc_final: 0.6485 (tpt) outliers start: 5 outliers final: 5 residues processed: 111 average time/residue: 1.3329 time to fit residues: 157.5752 Evaluate side-chains 110 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 394 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 106 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 7 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.142344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.111486 restraints weight = 31666.642| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.82 r_work: 0.3126 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9024 Z= 0.094 Angle : 0.470 5.067 12245 Z= 0.251 Chirality : 0.039 0.197 1399 Planarity : 0.004 0.060 1502 Dihedral : 8.239 121.165 1622 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.18 % Allowed : 16.03 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.26), residues: 1080 helix: 3.22 (0.27), residues: 380 sheet: 0.58 (0.31), residues: 257 loop : -0.56 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 333 TYR 0.013 0.001 TYR R 198 PHE 0.021 0.001 PHE B 292 TRP 0.008 0.001 TRP B 63 HIS 0.002 0.000 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 ( 9023) covalent geometry : angle 0.46988 / 0.25 (12243) SS BOND : bond 0.00023 / 0.01 ( 1) SS BOND : angle 0.61910 / 0.32 ( 2) hydrogen bonds : bond 0.03993 / 2.56 ( 436) hydrogen bonds : angle 4.00906 / 2.79 ( 1236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6436.01 seconds wall clock time: 109 minutes 51.74 seconds (6591.74 seconds total)