Starting phenix.real_space_refine on Tue Mar 3 23:49:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v0x_64674/03_2026/9v0x_64674.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v0x_64674/03_2026/9v0x_64674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v0x_64674/03_2026/9v0x_64674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v0x_64674/03_2026/9v0x_64674.map" model { file = "/net/cci-nas-00/data/ceres_data/9v0x_64674/03_2026/9v0x_64674.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v0x_64674/03_2026/9v0x_64674.cif" } resolution = 2.66 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= 0.013 sd= 0.057 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 53 5.16 5 C 5810 2.51 5 N 1593 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9126 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1885 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "E" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1782 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "G" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 400 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 82 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2346 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'KUT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'KUT:plan-6': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 2.13, per 1000 atoms: 0.23 Number of scatterers: 9126 At special positions: 0 Unit cell: (86.14, 121.18, 129.21, 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 53 16.00 O 1670 8.00 N 1593 7.00 C 5810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 134 " - pdb=" SG CYS R 211 " distance=1.21 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 354.1 milliseconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 38.6% alpha, 22.9% 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 33 Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.539A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.466A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 298 through 319 removed outlier: 3.631A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 removed outlier: 3.575A pdb=" N ARG A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 30 removed outlier: 3.542A pdb=" N CYS B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 40 removed outlier: 3.523A pdb=" N ILE B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 55 removed outlier: 3.884A 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 61 through 64 Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.979A pdb=" N THR E 90 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.602A pdb=" N ILE G 24 " --> pdb=" O MET G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 43 removed outlier: 3.555A pdb=" N ALA G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 47 Processing helix chain 'R' and resid 59 through 86 removed outlier: 4.050A pdb=" N VAL R 76 " --> pdb=" O VAL R 72 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY R 77 " --> pdb=" O VAL R 73 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN R 78 " --> pdb=" O GLY R 74 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU R 81 " --> pdb=" O GLY R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 92 Processing helix chain 'R' and resid 93 through 122 removed outlier: 3.865A pdb=" N LEU R 98 " --> pdb=" O VAL R 94 " (cutoff:3.500A) Proline residue: R 115 - end of helix Processing helix chain 'R' and resid 132 through 164 removed outlier: 3.918A pdb=" N LEU R 136 " --> pdb=" O GLY R 132 " (cutoff:3.500A) Proline residue: R 142 - end of helix Processing helix chain 'R' and resid 172 through 191 removed outlier: 3.664A pdb=" N SER R 176 " --> pdb=" O SER R 172 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TRP R 184 " --> pdb=" O VAL R 180 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA R 185 " --> pdb=" O LEU R 181 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 196 Processing helix chain 'R' and resid 203 through 207 Processing helix chain 'R' and resid 219 through 231 Processing helix chain 'R' and resid 234 through 255 removed outlier: 3.638A pdb=" N ILE R 241 " --> pdb=" O PRO R 237 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU R 243 " --> pdb=" O LEU R 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 304 removed outlier: 3.527A pdb=" N THR R 276 " --> pdb=" O ARG R 272 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL R 284 " --> pdb=" O LEU R 280 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP R 291 " --> pdb=" O PHE R 287 " (cutoff:3.500A) Proline residue: R 293 - end of helix Processing helix chain 'R' and resid 309 through 336 removed outlier: 4.166A pdb=" N GLY R 314 " --> pdb=" O PRO R 310 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LEU R 315 " --> pdb=" O TYR R 311 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER R 327 " --> pdb=" O LEU R 323 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA R 328 " --> pdb=" O ALA R 324 " (cutoff:3.500A) Proline residue: R 332 - end of helix Processing helix chain 'R' and resid 339 through 351 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.462A pdb=" N LEU A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N PHE A 199 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N VAL A 201 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LEU A 38 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56 removed outlier: 6.907A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.877A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS B 96 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.251A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.694A pdb=" N SER B 166 " --> pdb=" O THR B 170 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.162A 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 removed outlier: 6.740A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 3.860A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 3.719A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.850A 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 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.890A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.531A 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: 4.232A 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 removed outlier: 3.541A pdb=" N THR E 141 " --> pdb=" O ARG E 160 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.426A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1233 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.34 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1467 1.31 - 1.44: 2589 1.44 - 1.56: 5189 1.56 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 9319 Sorted by residual: bond pdb=" N KUT L 401 " pdb=" C17 KUT L 401 " ideal model delta sigma weight residual 1.341 1.452 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C27 KUT L 401 " pdb=" N2 KUT L 401 " ideal model delta sigma weight residual 1.342 1.451 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C21 KUT L 401 " pdb=" N1 KUT L 401 " ideal model delta sigma weight residual 1.346 1.451 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" N ARG L 5 " pdb=" CA ARG L 5 " ideal model delta sigma weight residual 1.457 1.502 -0.045 1.41e-02 5.03e+03 1.02e+01 bond pdb=" N HIS R 306 " pdb=" CA HIS R 306 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.16e-02 7.43e+03 9.33e+00 ... (remaining 9314 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 12384 1.80 - 3.60: 198 3.60 - 5.39: 42 5.39 - 7.19: 5 7.19 - 8.99: 2 Bond angle restraints: 12631 Sorted by residual: angle pdb=" N ILE B 275 " pdb=" CA ILE B 275 " pdb=" C ILE B 275 " ideal model delta sigma weight residual 113.53 108.93 4.60 9.80e-01 1.04e+00 2.20e+01 angle pdb=" N VAL R 164 " pdb=" CA VAL R 164 " pdb=" C VAL R 164 " ideal model delta sigma weight residual 113.53 109.00 4.53 9.80e-01 1.04e+00 2.14e+01 angle pdb=" N VAL R 240 " pdb=" CA VAL R 240 " pdb=" C VAL R 240 " ideal model delta sigma weight residual 111.81 108.32 3.49 8.60e-01 1.35e+00 1.65e+01 angle pdb=" N VAL R 162 " pdb=" CA VAL R 162 " pdb=" C VAL R 162 " ideal model delta sigma weight residual 113.47 109.55 3.92 1.01e+00 9.80e-01 1.51e+01 angle pdb=" CA ARG R 169 " pdb=" C ARG R 169 " pdb=" O ARG R 169 " ideal model delta sigma weight residual 120.82 117.17 3.65 1.05e+00 9.07e-01 1.21e+01 ... (remaining 12626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.56: 5375 27.56 - 55.12: 134 55.12 - 82.68: 17 82.68 - 110.24: 8 110.24 - 137.80: 2 Dihedral angle restraints: 5536 sinusoidal: 2193 harmonic: 3343 Sorted by residual: dihedral pdb=" C17 KUT L 401 " pdb=" N KUT L 401 " pdb=" C18 KUT L 401 " pdb=" C19 KUT L 401 " ideal model delta sinusoidal sigma weight residual -67.99 69.81 -137.80 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" C KUT L 401 " pdb=" C10 KUT L 401 " pdb=" C11 KUT L 401 " pdb=" C12 KUT L 401 " ideal model delta sinusoidal sigma weight residual 179.13 -59.14 -121.73 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C5 KUT L 401 " pdb=" C6 KUT L 401 " pdb=" C7 KUT L 401 " pdb=" C8 KUT L 401 " ideal model delta sinusoidal sigma weight residual 179.11 76.14 102.97 1 3.00e+01 1.11e-03 1.31e+01 ... (remaining 5533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1300 0.071 - 0.141: 125 0.141 - 0.212: 2 0.212 - 0.283: 0 0.283 - 0.354: 1 Chirality restraints: 1428 Sorted by residual: chirality pdb=" C18 KUT L 401 " pdb=" N KUT L 401 " pdb=" C19 KUT L 401 " pdb=" C34 KUT L 401 " both_signs ideal model delta sigma weight residual False -2.25 -2.60 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA GLU R 123 " pdb=" N GLU R 123 " pdb=" C GLU R 123 " pdb=" CB GLU R 123 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CA LEU R 186 " pdb=" N LEU R 186 " pdb=" C LEU R 186 " pdb=" CB LEU R 186 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.94e-01 ... (remaining 1425 not shown) Planarity restraints: 1603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY L 3 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C GLY L 3 " -0.030 2.00e-02 2.50e+03 pdb=" O GLY L 3 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS L 4 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 236 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO R 237 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO R 237 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO R 237 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 5 " -0.023 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO L 6 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO L 6 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO L 6 " -0.019 5.00e-02 4.00e+02 ... (remaining 1600 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 51 2.50 - 3.10: 6746 3.10 - 3.70: 13594 3.70 - 4.30: 20177 4.30 - 4.90: 33943 Nonbonded interactions: 74511 Sorted by model distance: nonbonded pdb=" O LEU R 229 " pdb=" OG1 THR R 233 " model vdw 1.901 3.040 nonbonded pdb=" OG1 THR B 170 " pdb=" O PHE B 185 " model vdw 2.038 3.040 nonbonded pdb=" O ARG A 35 " pdb=" OG1 THR A 219 " model vdw 2.050 3.040 nonbonded pdb=" ND2 ASN B 160 " pdb=" OD1 ASP B 175 " model vdw 2.051 3.120 nonbonded pdb=" OG SER B 286 " pdb=" OD2 ASP G 47 " model vdw 2.080 3.040 ... (remaining 74506 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: 3.820 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.540 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 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 : 0.013 0.821 9322 Z= 1.058 Angle : 0.678 38.624 12633 Z= 0.385 Chirality : 0.041 0.354 1428 Planarity : 0.003 0.040 1603 Dihedral : 12.547 137.801 3375 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.35 % Allowed : 1.85 % Favored : 97.80 % Rotamer: Outliers : 1.02 % Allowed : 6.40 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.30 (0.26), residues: 1134 helix: 1.51 (0.29), residues: 388 sheet: 1.39 (0.33), residues: 279 loop : 0.06 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 347 TYR 0.005 0.001 TYR E 190 PHE 0.006 0.001 PHE B 156 TRP 0.012 0.001 TRP R 127 HIS 0.002 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9319) covalent geometry : angle 0.58025 (12631) SS BOND : bond 0.82060 ( 1) SS BOND : angle 27.84054 ( 2) hydrogen bonds : bond 0.19588 ( 439) hydrogen bonds : angle 6.78572 ( 1233) Misc. bond : bond 0.64824 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 240 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ILE cc_start: 0.7914 (mt) cc_final: 0.7223 (mt) REVERT: R 306 HIS cc_start: 0.6246 (OUTLIER) cc_final: 0.5485 (m-70) REVERT: R 334 ILE cc_start: 0.8175 (tp) cc_final: 0.7935 (pt) outliers start: 10 outliers final: 1 residues processed: 246 average time/residue: 0.5736 time to fit residues: 149.8043 Evaluate side-chains 168 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 166 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 GLN Chi-restraints excluded: chain R residue 306 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 352 GLN B 273 ASN E 171 ASN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 331 ASN R 339 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.114148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.092229 restraints weight = 16503.587| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.04 r_work: 0.3352 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9322 Z= 0.216 Angle : 0.661 7.661 12633 Z= 0.348 Chirality : 0.046 0.210 1428 Planarity : 0.005 0.041 1603 Dihedral : 11.211 159.084 1307 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.65 % Favored : 97.18 % Rotamer: Outliers : 4.97 % Allowed : 14.31 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.25), residues: 1134 helix: 1.09 (0.27), residues: 395 sheet: 1.29 (0.32), residues: 259 loop : -0.12 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 5 TYR 0.032 0.002 TYR B 269 PHE 0.022 0.002 PHE B 283 TRP 0.016 0.002 TRP B 174 HIS 0.007 0.001 HIS R 197 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 9319) covalent geometry : angle 0.66066 (12631) SS BOND : bond 0.01986 ( 1) SS BOND : angle 2.68130 ( 2) hydrogen bonds : bond 0.04804 ( 439) hydrogen bonds : angle 4.70080 ( 1233) Misc. bond : bond 0.00136 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 174 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8424 (mtmm) cc_final: 0.7894 (mmtt) REVERT: A 188 LYS cc_start: 0.8090 (ttmt) cc_final: 0.7457 (pmtt) REVERT: A 207 GLU cc_start: 0.6857 (tp30) cc_final: 0.6149 (tt0) REVERT: A 217 ASP cc_start: 0.7850 (p0) cc_final: 0.7576 (p0) REVERT: A 337 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7642 (mm-30) REVERT: B 98 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7747 (mp) REVERT: B 176 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7837 (mt) REVERT: B 224 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7334 (ptp-170) REVERT: B 272 ASP cc_start: 0.8412 (m-30) cc_final: 0.8153 (m-30) REVERT: E 17 ARG cc_start: 0.8887 (tpp-160) cc_final: 0.8642 (tpt170) REVERT: E 72 ASP cc_start: 0.8031 (t70) cc_final: 0.7827 (t0) REVERT: E 223 ASP cc_start: 0.7961 (m-30) cc_final: 0.7670 (m-30) REVERT: G 18 LEU cc_start: 0.7159 (mt) cc_final: 0.6951 (mt) REVERT: R 57 HIS cc_start: 0.7108 (m-70) cc_final: 0.6857 (m90) REVERT: R 125 ARG cc_start: 0.8055 (mpt90) cc_final: 0.7786 (mmm160) REVERT: R 306 HIS cc_start: 0.6390 (OUTLIER) cc_final: 0.5597 (m-70) REVERT: R 334 ILE cc_start: 0.8501 (tp) cc_final: 0.8301 (pt) REVERT: R 345 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6446 (mp0) outliers start: 49 outliers final: 18 residues processed: 208 average time/residue: 0.6096 time to fit residues: 134.3197 Evaluate side-chains 178 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain L residue 4 LYS Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 206 HIS Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain R residue 345 GLU Chi-restraints excluded: chain R residue 349 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 90 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN B 181 GLN E 171 ASN E 186 GLN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.113471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.091421 restraints weight = 16304.540| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.05 r_work: 0.3333 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9322 Z= 0.150 Angle : 0.554 6.115 12633 Z= 0.294 Chirality : 0.042 0.158 1428 Planarity : 0.004 0.037 1603 Dihedral : 10.963 168.597 1304 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.29 % Favored : 97.62 % Rotamer: Outliers : 5.79 % Allowed : 16.04 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.25), residues: 1134 helix: 1.36 (0.26), residues: 393 sheet: 1.19 (0.31), residues: 255 loop : -0.21 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 301 TYR 0.021 0.002 TYR R 199 PHE 0.018 0.001 PHE B 156 TRP 0.012 0.001 TRP B 174 HIS 0.004 0.001 HIS R 197 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9319) covalent geometry : angle 0.55357 (12631) SS BOND : bond 0.00479 ( 1) SS BOND : angle 2.11381 ( 2) hydrogen bonds : bond 0.04140 ( 439) hydrogen bonds : angle 4.37218 ( 1233) Misc. bond : bond 0.00272 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 161 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 GLU cc_start: 0.6943 (tp30) cc_final: 0.6150 (tt0) REVERT: A 217 ASP cc_start: 0.7942 (p0) cc_final: 0.7578 (p0) REVERT: A 247 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7576 (ptp90) REVERT: A 337 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7534 (mm-30) REVERT: B 98 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7600 (mp) REVERT: B 176 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7774 (mt) REVERT: B 202 ARG cc_start: 0.8603 (mtt180) cc_final: 0.8392 (mtt-85) REVERT: B 272 ASP cc_start: 0.8407 (m-30) cc_final: 0.8108 (m-30) REVERT: E 17 ARG cc_start: 0.8856 (tpp-160) cc_final: 0.8515 (tpt-90) REVERT: E 223 ASP cc_start: 0.8024 (m-30) cc_final: 0.7709 (m-30) REVERT: G 18 LEU cc_start: 0.7275 (mt) cc_final: 0.7032 (mt) REVERT: R 125 ARG cc_start: 0.7953 (mpt90) cc_final: 0.7730 (mmm160) REVERT: R 306 HIS cc_start: 0.6224 (OUTLIER) cc_final: 0.5416 (m-70) REVERT: R 334 ILE cc_start: 0.8553 (tp) cc_final: 0.8280 (pt) REVERT: R 345 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6400 (mp0) outliers start: 57 outliers final: 27 residues processed: 195 average time/residue: 0.6165 time to fit residues: 127.2987 Evaluate side-chains 182 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain L residue 4 LYS Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 206 HIS Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 345 GLU Chi-restraints excluded: chain R residue 349 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 42 optimal weight: 0.3980 chunk 25 optimal weight: 0.0570 chunk 57 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 81 optimal weight: 6.9990 chunk 61 optimal weight: 0.1980 chunk 85 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.2298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 ASN E 171 ASN E 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.116344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.094526 restraints weight = 16569.318| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.08 r_work: 0.3391 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9322 Z= 0.101 Angle : 0.506 7.090 12633 Z= 0.266 Chirality : 0.040 0.150 1428 Planarity : 0.004 0.038 1603 Dihedral : 10.638 176.884 1304 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.03 % Favored : 97.88 % Rotamer: Outliers : 3.65 % Allowed : 19.49 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.14 (0.25), residues: 1134 helix: 1.77 (0.26), residues: 392 sheet: 0.85 (0.31), residues: 271 loop : -0.09 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 139 TYR 0.015 0.001 TYR R 199 PHE 0.014 0.001 PHE B 156 TRP 0.014 0.001 TRP B 302 HIS 0.006 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 9319) covalent geometry : angle 0.50556 (12631) SS BOND : bond 0.00135 ( 1) SS BOND : angle 1.42588 ( 2) hydrogen bonds : bond 0.03296 ( 439) hydrogen bonds : angle 4.04047 ( 1233) Misc. bond : bond 0.00187 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8187 (mtmm) cc_final: 0.7646 (mmtt) REVERT: A 207 GLU cc_start: 0.7135 (tp30) cc_final: 0.6462 (tt0) REVERT: A 216 ASN cc_start: 0.7467 (t0) cc_final: 0.6987 (t160) REVERT: A 217 ASP cc_start: 0.7769 (p0) cc_final: 0.7380 (p0) REVERT: A 247 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7514 (ptp90) REVERT: A 337 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7615 (mm-30) REVERT: B 272 ASP cc_start: 0.8434 (m-30) cc_final: 0.8075 (m-30) REVERT: B 319 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8138 (ttt-90) REVERT: E 17 ARG cc_start: 0.8836 (tpp-160) cc_final: 0.8613 (tpt170) REVERT: E 79 PHE cc_start: 0.8241 (m-80) cc_final: 0.8006 (m-80) REVERT: G 16 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7795 (mt-10) REVERT: G 18 LEU cc_start: 0.7204 (mt) cc_final: 0.6997 (mp) REVERT: R 306 HIS cc_start: 0.5986 (OUTLIER) cc_final: 0.5247 (m-70) REVERT: R 334 ILE cc_start: 0.8408 (tp) cc_final: 0.8193 (tp) REVERT: R 345 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6340 (mp0) outliers start: 36 outliers final: 14 residues processed: 182 average time/residue: 0.6156 time to fit residues: 118.8011 Evaluate side-chains 169 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain L residue 4 LYS Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 87 ARG Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 255 ARG Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 315 LEU Chi-restraints excluded: chain R residue 345 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 57 optimal weight: 0.2980 chunk 3 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 93 ASN B 181 GLN B 225 GLN E 76 ASN E 171 ASN R 96 ASN R 298 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.113989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.091446 restraints weight = 16178.651| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.09 r_work: 0.3330 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9322 Z= 0.139 Angle : 0.540 6.059 12633 Z= 0.285 Chirality : 0.041 0.155 1428 Planarity : 0.004 0.039 1603 Dihedral : 10.547 176.964 1304 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.73 % Favored : 97.18 % Rotamer: Outliers : 4.47 % Allowed : 18.68 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.19 (0.25), residues: 1134 helix: 1.84 (0.26), residues: 393 sheet: 1.03 (0.30), residues: 255 loop : -0.17 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 139 TYR 0.013 0.001 TYR R 199 PHE 0.013 0.001 PHE G 60 TRP 0.011 0.001 TRP B 174 HIS 0.005 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9319) covalent geometry : angle 0.53944 (12631) SS BOND : bond 0.00201 ( 1) SS BOND : angle 1.71449 ( 2) hydrogen bonds : bond 0.03713 ( 439) hydrogen bonds : angle 4.13391 ( 1233) Misc. bond : bond 0.00172 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 0.352 Fit side-chains REVERT: A 24 GLN cc_start: 0.7815 (mm110) cc_final: 0.7530 (tp40) REVERT: A 207 GLU cc_start: 0.7063 (tp30) cc_final: 0.6288 (tt0) REVERT: A 216 ASN cc_start: 0.7551 (t0) cc_final: 0.7276 (t160) REVERT: A 247 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7607 (ptp90) REVERT: A 337 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7658 (mm-30) REVERT: B 98 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7454 (mp) REVERT: B 192 VAL cc_start: 0.8174 (OUTLIER) cc_final: 0.7890 (t) REVERT: B 219 ARG cc_start: 0.7861 (mtm110) cc_final: 0.7627 (mpp-170) REVERT: B 267 MET cc_start: 0.8859 (mmt) cc_final: 0.8596 (tpp) REVERT: B 272 ASP cc_start: 0.8405 (m-30) cc_final: 0.8101 (m-30) REVERT: E 17 ARG cc_start: 0.8841 (tpp-160) cc_final: 0.8624 (tpt170) REVERT: E 202 ARG cc_start: 0.7166 (mtm-85) cc_final: 0.6828 (ptt180) REVERT: G 16 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7774 (mt-10) REVERT: G 18 LEU cc_start: 0.7163 (mt) cc_final: 0.6950 (mp) REVERT: R 125 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7153 (mtm110) REVERT: R 306 HIS cc_start: 0.6078 (OUTLIER) cc_final: 0.5409 (m-70) REVERT: R 334 ILE cc_start: 0.8480 (tp) cc_final: 0.8264 (tp) REVERT: R 345 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6418 (mp0) outliers start: 44 outliers final: 22 residues processed: 180 average time/residue: 0.5605 time to fit residues: 107.4696 Evaluate side-chains 167 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain R residue 125 ARG Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 206 HIS Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 315 LEU Chi-restraints excluded: chain R residue 345 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 24 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 82 optimal weight: 0.0980 chunk 30 optimal weight: 2.9990 chunk 84 optimal weight: 0.0970 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN E 171 ASN E 183 GLN E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.113307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.090513 restraints weight = 16113.617| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.12 r_work: 0.3307 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9322 Z= 0.142 Angle : 0.539 6.073 12633 Z= 0.284 Chirality : 0.042 0.151 1428 Planarity : 0.004 0.040 1603 Dihedral : 10.124 166.687 1304 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.38 % Favored : 97.53 % Rotamer: Outliers : 5.38 % Allowed : 17.77 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.18 (0.25), residues: 1134 helix: 1.93 (0.26), residues: 393 sheet: 0.93 (0.31), residues: 255 loop : -0.21 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 31 TYR 0.013 0.001 TYR R 199 PHE 0.015 0.001 PHE G 60 TRP 0.012 0.001 TRP B 104 HIS 0.006 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9319) covalent geometry : angle 0.53818 (12631) SS BOND : bond 0.00315 ( 1) SS BOND : angle 1.76470 ( 2) hydrogen bonds : bond 0.03739 ( 439) hydrogen bonds : angle 4.16887 ( 1233) Misc. bond : bond 0.00126 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 151 time to evaluate : 0.347 Fit side-chains REVERT: A 24 GLN cc_start: 0.7836 (mm110) cc_final: 0.7534 (tp40) REVERT: A 207 GLU cc_start: 0.7064 (tp30) cc_final: 0.6196 (tt0) REVERT: A 216 ASN cc_start: 0.7629 (t0) cc_final: 0.7348 (t0) REVERT: A 247 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7606 (ptp90) REVERT: A 330 PHE cc_start: 0.7627 (m-10) cc_final: 0.7414 (m-10) REVERT: A 337 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7662 (mm-30) REVERT: B 98 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7493 (mp) REVERT: B 176 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7713 (mt) REVERT: B 192 VAL cc_start: 0.8145 (OUTLIER) cc_final: 0.7864 (t) REVERT: B 272 ASP cc_start: 0.8399 (m-30) cc_final: 0.8101 (m-30) REVERT: E 17 ARG cc_start: 0.8823 (tpp-160) cc_final: 0.8531 (tpt-90) REVERT: G 18 LEU cc_start: 0.7177 (mt) cc_final: 0.6960 (mp) REVERT: R 125 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7196 (mtm110) REVERT: R 306 HIS cc_start: 0.6199 (OUTLIER) cc_final: 0.5459 (m-70) REVERT: R 334 ILE cc_start: 0.8525 (tp) cc_final: 0.8302 (tp) REVERT: R 345 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6301 (mp0) outliers start: 53 outliers final: 26 residues processed: 192 average time/residue: 0.5420 time to fit residues: 111.3085 Evaluate side-chains 176 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 87 ARG Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain R residue 125 ARG Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 206 HIS Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 315 LEU Chi-restraints excluded: chain R residue 345 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 66 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 73 optimal weight: 0.0070 chunk 108 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 213 GLN E 183 GLN E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.112876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.090565 restraints weight = 16260.599| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.09 r_work: 0.3322 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9322 Z= 0.122 Angle : 0.514 6.999 12633 Z= 0.272 Chirality : 0.041 0.148 1428 Planarity : 0.004 0.040 1603 Dihedral : 9.919 159.683 1304 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.38 % Favored : 97.53 % Rotamer: Outliers : 4.37 % Allowed : 19.70 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.19 (0.25), residues: 1134 helix: 2.04 (0.26), residues: 385 sheet: 0.89 (0.31), residues: 250 loop : -0.21 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 31 TYR 0.014 0.001 TYR A 230 PHE 0.012 0.001 PHE B 156 TRP 0.016 0.001 TRP R 268 HIS 0.004 0.001 HIS R 197 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9319) covalent geometry : angle 0.51306 (12631) SS BOND : bond 0.00048 ( 1) SS BOND : angle 1.80786 ( 2) hydrogen bonds : bond 0.03547 ( 439) hydrogen bonds : angle 4.11307 ( 1233) Misc. bond : bond 0.00115 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 146 time to evaluate : 0.296 Fit side-chains REVERT: A 24 GLN cc_start: 0.7813 (mm110) cc_final: 0.7538 (tp40) REVERT: A 207 GLU cc_start: 0.7068 (tp30) cc_final: 0.6215 (tt0) REVERT: A 216 ASN cc_start: 0.7594 (t0) cc_final: 0.7310 (t0) REVERT: A 247 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7632 (ptp90) REVERT: A 281 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7132 (tm-30) REVERT: A 337 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7665 (mm-30) REVERT: B 98 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7412 (mp) REVERT: B 192 VAL cc_start: 0.8119 (OUTLIER) cc_final: 0.7815 (t) REVERT: B 272 ASP cc_start: 0.8411 (m-30) cc_final: 0.8112 (m-30) REVERT: E 17 ARG cc_start: 0.8816 (tpp-160) cc_final: 0.8532 (tpt-90) REVERT: G 18 LEU cc_start: 0.7193 (mt) cc_final: 0.6972 (mp) REVERT: R 125 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7152 (mtm110) REVERT: R 218 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7291 (pm20) REVERT: R 223 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7591 (mt0) REVERT: R 306 HIS cc_start: 0.6249 (OUTLIER) cc_final: 0.5463 (m-70) REVERT: R 334 ILE cc_start: 0.8491 (tp) cc_final: 0.8272 (tp) REVERT: R 345 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6357 (mp0) outliers start: 43 outliers final: 25 residues processed: 177 average time/residue: 0.5904 time to fit residues: 111.2283 Evaluate side-chains 172 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 87 ARG Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain R residue 125 ARG Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 206 HIS Chi-restraints excluded: chain R residue 218 GLN Chi-restraints excluded: chain R residue 223 GLN Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 315 LEU Chi-restraints excluded: chain R residue 345 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 112 optimal weight: 0.4980 chunk 56 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN E 183 GLN E 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.111930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.089324 restraints weight = 16173.374| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.10 r_work: 0.3287 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9322 Z= 0.154 Angle : 0.561 8.192 12633 Z= 0.294 Chirality : 0.042 0.149 1428 Planarity : 0.004 0.040 1603 Dihedral : 9.781 150.543 1304 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.56 % Favored : 97.35 % Rotamer: Outliers : 4.57 % Allowed : 19.70 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.18 (0.25), residues: 1134 helix: 1.92 (0.26), residues: 390 sheet: 0.85 (0.31), residues: 248 loop : -0.12 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 191 TYR 0.012 0.002 TYR A 327 PHE 0.014 0.001 PHE G 60 TRP 0.011 0.002 TRP B 104 HIS 0.006 0.001 HIS R 197 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9319) covalent geometry : angle 0.56072 (12631) SS BOND : bond 0.00327 ( 1) SS BOND : angle 1.97696 ( 2) hydrogen bonds : bond 0.03811 ( 439) hydrogen bonds : angle 4.23687 ( 1233) Misc. bond : bond 0.00123 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 0.352 Fit side-chains REVERT: A 24 GLN cc_start: 0.7827 (mm110) cc_final: 0.7549 (tp40) REVERT: A 207 GLU cc_start: 0.7144 (tp30) cc_final: 0.6294 (tt0) REVERT: A 216 ASN cc_start: 0.7655 (t0) cc_final: 0.7391 (t0) REVERT: A 247 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7617 (ptp90) REVERT: A 281 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7153 (tm-30) REVERT: A 337 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7630 (mm-30) REVERT: B 98 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7547 (mp) REVERT: B 134 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8088 (ptm160) REVERT: B 176 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7763 (mt) REVERT: B 192 VAL cc_start: 0.8174 (OUTLIER) cc_final: 0.7927 (t) REVERT: B 202 ARG cc_start: 0.8762 (ttm-80) cc_final: 0.8540 (ttm-80) REVERT: B 272 ASP cc_start: 0.8413 (m-30) cc_final: 0.8101 (m-30) REVERT: E 17 ARG cc_start: 0.8793 (tpp-160) cc_final: 0.8508 (tpt-90) REVERT: G 18 LEU cc_start: 0.7252 (mt) cc_final: 0.6975 (mp) REVERT: R 125 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7193 (mtm110) REVERT: R 218 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7323 (pm20) REVERT: R 223 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7684 (mt0) REVERT: R 334 ILE cc_start: 0.8540 (tp) cc_final: 0.8322 (tp) REVERT: R 345 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6343 (mp0) outliers start: 45 outliers final: 28 residues processed: 179 average time/residue: 0.5606 time to fit residues: 106.9185 Evaluate side-chains 173 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain R residue 125 ARG Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 206 HIS Chi-restraints excluded: chain R residue 218 GLN Chi-restraints excluded: chain R residue 223 GLN Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 315 LEU Chi-restraints excluded: chain R residue 345 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.0020 chunk 5 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 102 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 213 GLN A 245 ASN E 183 GLN E 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.113361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.091124 restraints weight = 16143.645| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.09 r_work: 0.3328 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9322 Z= 0.112 Angle : 0.512 9.589 12633 Z= 0.269 Chirality : 0.040 0.146 1428 Planarity : 0.004 0.040 1603 Dihedral : 9.493 155.065 1304 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.65 % Favored : 97.27 % Rotamer: Outliers : 3.55 % Allowed : 20.41 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.30 (0.25), residues: 1134 helix: 2.08 (0.26), residues: 388 sheet: 0.93 (0.31), residues: 252 loop : -0.11 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 31 TYR 0.012 0.001 TYR R 199 PHE 0.013 0.001 PHE B 156 TRP 0.011 0.001 TRP B 174 HIS 0.003 0.001 HIS R 197 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 9319) covalent geometry : angle 0.51176 (12631) SS BOND : bond 0.00258 ( 1) SS BOND : angle 1.66117 ( 2) hydrogen bonds : bond 0.03432 ( 439) hydrogen bonds : angle 4.04202 ( 1233) Misc. bond : bond 0.00104 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.337 Fit side-chains REVERT: A 24 GLN cc_start: 0.7781 (mm110) cc_final: 0.7528 (tp40) REVERT: A 31 ARG cc_start: 0.7383 (mmt90) cc_final: 0.7166 (mmt90) REVERT: A 207 GLU cc_start: 0.7171 (tp30) cc_final: 0.6350 (tt0) REVERT: A 216 ASN cc_start: 0.7610 (t0) cc_final: 0.7339 (t0) REVERT: A 247 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7649 (ptp90) REVERT: A 281 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7090 (tm-30) REVERT: A 337 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7611 (mm-30) REVERT: B 98 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7327 (mp) REVERT: B 134 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8220 (ptm160) REVERT: B 176 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7616 (mt) REVERT: B 272 ASP cc_start: 0.8411 (m-30) cc_final: 0.8056 (m-30) REVERT: E 17 ARG cc_start: 0.8775 (tpp-160) cc_final: 0.8542 (tpt170) REVERT: G 18 LEU cc_start: 0.7277 (mt) cc_final: 0.6992 (mp) REVERT: R 125 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7129 (mtm110) REVERT: R 218 GLN cc_start: 0.7523 (mp10) cc_final: 0.7310 (pm20) REVERT: R 334 ILE cc_start: 0.8450 (tp) cc_final: 0.8242 (tp) REVERT: R 345 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6337 (mp0) outliers start: 35 outliers final: 22 residues processed: 161 average time/residue: 0.6123 time to fit residues: 104.7201 Evaluate side-chains 160 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 87 ARG Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain R residue 125 ARG Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 206 HIS Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 306 HIS Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 315 LEU Chi-restraints excluded: chain R residue 345 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.09 > 50: distance: 0 - 1: 6.310 distance: 1 - 2: 7.118 distance: 1 - 4: 41.495 distance: 2 - 3: 41.091 distance: 2 - 6: 57.173 distance: 4 - 5: 40.692 distance: 6 - 7: 50.076 distance: 7 - 8: 8.101 distance: 7 - 10: 30.561 distance: 8 - 17: 56.888 distance: 10 - 11: 39.715 distance: 13 - 14: 36.073 distance: 14 - 15: 3.735 distance: 14 - 16: 3.490 distance: 17 - 18: 41.103 distance: 18 - 19: 37.424 distance: 19 - 20: 20.384 distance: 19 - 21: 19.670 distance: 20 - 182: 35.105 distance: 21 - 22: 57.741 distance: 22 - 23: 39.840 distance: 22 - 25: 68.969 distance: 23 - 24: 56.727 distance: 25 - 26: 21.427 distance: 26 - 27: 30.538 distance: 27 - 28: 18.116 distance: 28 - 29: 40.024 distance: 29 - 217: 34.161 distance: 31 - 32: 25.252 distance: 31 - 34: 50.960 distance: 32 - 33: 42.724 distance: 32 - 41: 23.638 distance: 34 - 35: 37.936 distance: 35 - 36: 23.545 distance: 37 - 38: 18.300 distance: 38 - 39: 38.889 distance: 38 - 40: 40.372 distance: 41 - 42: 40.102 distance: 41 - 47: 40.856 distance: 42 - 43: 39.117 distance: 42 - 45: 40.331 distance: 43 - 44: 13.242 distance: 43 - 48: 41.214 distance: 45 - 46: 33.912 distance: 48 - 49: 68.209 distance: 49 - 50: 40.938 distance: 49 - 52: 56.925 distance: 50 - 55: 5.985 distance: 52 - 53: 21.018 distance: 55 - 56: 48.332 distance: 56 - 57: 10.339 distance: 57 - 58: 31.706 distance: 57 - 59: 3.958 distance: 59 - 60: 30.602 distance: 60 - 61: 40.329 distance: 61 - 70: 34.068 distance: 63 - 64: 55.643 distance: 66 - 67: 13.948 distance: 67 - 68: 25.393 distance: 67 - 69: 31.240