Starting phenix.real_space_refine on Thu Jul 2 16:01:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7d77_30603/07_2026/7d77_30603.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d77_30603/07_2026/7d77_30603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7d77_30603/07_2026/7d77_30603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d77_30603/07_2026/7d77_30603.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d77_30603/07_2026/7d77_30603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d77_30603/07_2026/7d77_30603.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7d77_30603/07_2026/7d77_30603.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7d77_30603/07_2026/7d77_30603.cif" } resolution = 2.9 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5645 2.51 5 N 1466 2.21 5 O 1618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 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: 8785 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1711 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "R" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2097 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 4, 'TRANS': 260} Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 154 Unusual residues: {'CLR': 2, 'HCY': 1, 'PLM': 2, 'Y01': 1} Classifications: {'undetermined': 6, 'water': 1} Link IDs: {None: 6} Time building chain proxies: 1.42, per 1000 atoms: 0.16 Number of scatterers: 8785 At special positions: 0 Unit cell: (105.456, 126.75, 112.554, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1618 8.00 N 1466 7.00 C 5645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 338 " - pdb=" SG CYS R 420 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 224.5 milliseconds 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 15 sheets defined 33.6% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 208 through 213 removed outlier: 3.950A pdb=" N TRP A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 217 Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 271 through 279 removed outlier: 3.622A pdb=" N PHE A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.908A pdb=" N ILE A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.765A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 43 Processing helix chain 'R' and resid 264 through 297 removed outlier: 4.068A pdb=" N PHE R 282 " --> pdb=" O VAL R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 303 removed outlier: 3.850A pdb=" N GLU R 303 " --> pdb=" O PHE R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 329 Processing helix chain 'R' and resid 334 through 368 removed outlier: 3.816A pdb=" N CYS R 338 " --> pdb=" O SER R 334 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA R 340 " --> pdb=" O ALA R 336 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA R 360 " --> pdb=" O MET R 356 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 400 Proline residue: R 390 - end of helix removed outlier: 3.723A pdb=" N ALA R 400 " --> pdb=" O GLY R 396 " (cutoff:3.500A) Processing helix chain 'R' and resid 428 through 435 removed outlier: 4.323A pdb=" N TYR R 432 " --> pdb=" O MET R 428 " (cutoff:3.500A) Processing helix chain 'R' and resid 435 through 461 Processing helix chain 'R' and resid 471 through 495 removed outlier: 3.673A pdb=" N LYS R 475 " --> pdb=" O LYS R 471 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU R 477 " --> pdb=" O ARG R 473 " (cutoff:3.500A) Processing helix chain 'R' and resid 502 through 525 removed outlier: 3.549A pdb=" N PHE R 506 " --> pdb=" O THR R 502 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE R 517 " --> pdb=" O GLN R 513 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 188 removed outlier: 3.503A pdb=" N VAL A 186 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 188 removed outlier: 3.503A pdb=" N VAL A 186 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL A 34 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE A 200 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU A 36 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS A 225 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE A 265 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N HIS A 322 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A 267 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.449A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.521A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.884A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.835A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.709A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.801A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.451A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 403 through 409 removed outlier: 3.577A pdb=" N LEU R 417 " --> pdb=" O ILE R 408 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.627A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.147A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR S 94 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.147A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR S 94 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.440A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 143 through 147 405 hydrogen bonds defined for protein. 1152 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: 0.97 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1407 1.32 - 1.45: 2518 1.45 - 1.58: 4964 1.58 - 1.70: 8 1.70 - 1.83: 80 Bond restraints: 8977 Sorted by residual: bond pdb=" CAS Y01 R 601 " pdb=" CAU Y01 R 601 " ideal model delta sigma weight residual 1.530 1.304 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" CBE Y01 R 601 " pdb=" CBI Y01 R 601 " ideal model delta sigma weight residual 1.550 1.375 0.175 2.00e-02 2.50e+03 7.65e+01 bond pdb=" CAS Y01 R 601 " pdb=" CBF Y01 R 601 " ideal model delta sigma weight residual 1.533 1.363 0.170 2.00e-02 2.50e+03 7.21e+01 bond pdb=" CBF Y01 R 601 " pdb=" CBH Y01 R 601 " ideal model delta sigma weight residual 1.550 1.689 -0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" CAP Y01 R 601 " pdb=" CAQ Y01 R 601 " ideal model delta sigma weight residual 1.541 1.654 -0.113 2.00e-02 2.50e+03 3.17e+01 ... (remaining 8972 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 11902 2.20 - 4.39: 213 4.39 - 6.59: 34 6.59 - 8.78: 10 8.78 - 10.98: 4 Bond angle restraints: 12163 Sorted by residual: angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 121.54 132.52 -10.98 1.91e+00 2.74e-01 3.30e+01 angle pdb=" N ARG R 411 " pdb=" CA ARG R 411 " pdb=" C ARG R 411 " ideal model delta sigma weight residual 112.54 105.87 6.67 1.22e+00 6.72e-01 2.99e+01 angle pdb=" CBD Y01 R 601 " pdb=" CBG Y01 R 601 " pdb=" CBI Y01 R 601 " ideal model delta sigma weight residual 115.11 105.59 9.52 3.00e+00 1.11e-01 1.01e+01 angle pdb=" N ASN A 295 " pdb=" CA ASN A 295 " pdb=" C ASN A 295 " ideal model delta sigma weight residual 108.52 113.97 -5.45 1.74e+00 3.30e-01 9.82e+00 angle pdb=" CBB Y01 R 601 " pdb=" CBE Y01 R 601 " pdb=" CBI Y01 R 601 " ideal model delta sigma weight residual 119.27 110.15 9.12 3.00e+00 1.11e-01 9.24e+00 ... (remaining 12158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.33: 4908 21.33 - 42.66: 306 42.66 - 63.99: 28 63.99 - 85.32: 7 85.32 - 106.65: 2 Dihedral angle restraints: 5251 sinusoidal: 2072 harmonic: 3179 Sorted by residual: dihedral pdb=" CB CYS R 338 " pdb=" SG CYS R 338 " pdb=" SG CYS R 420 " pdb=" CB CYS R 420 " ideal model delta sinusoidal sigma weight residual -86.00 -33.18 -52.82 1 1.00e+01 1.00e-02 3.80e+01 dihedral pdb=" CA GLN A 52 " pdb=" C GLN A 52 " pdb=" N MET A 53 " pdb=" CA MET A 53 " ideal model delta harmonic sigma weight residual -180.00 -157.51 -22.49 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA THR A 188 " pdb=" C THR A 188 " pdb=" N HIS A 189 " pdb=" CA HIS A 189 " ideal model delta harmonic sigma weight residual -180.00 -158.84 -21.16 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 5248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1314 0.109 - 0.217: 53 0.217 - 0.326: 7 0.326 - 0.434: 2 0.434 - 0.543: 1 Chirality restraints: 1377 Sorted by residual: chirality pdb=" CBG Y01 R 601 " pdb=" CAQ Y01 R 601 " pdb=" CBD Y01 R 601 " pdb=" CBI Y01 R 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.87 0.54 2.00e-01 2.50e+01 7.37e+00 chirality pdb=" C14 CLR R 606 " pdb=" C13 CLR R 606 " pdb=" C15 CLR R 606 " pdb=" C8 CLR R 606 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C14 CLR R 605 " pdb=" C13 CLR R 605 " pdb=" C15 CLR R 605 " pdb=" C8 CLR R 605 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 1374 not shown) Planarity restraints: 1511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 HCY R 604 " -0.022 2.00e-02 2.50e+03 7.73e-02 7.46e+01 pdb=" C3 HCY R 604 " 0.095 2.00e-02 2.50e+03 pdb=" C4 HCY R 604 " -0.121 2.00e-02 2.50e+03 pdb=" C5 HCY R 604 " -0.023 2.00e-02 2.50e+03 pdb=" C6 HCY R 604 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 235 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.73e+00 pdb=" C PHE B 235 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE B 235 " -0.016 2.00e-02 2.50e+03 pdb=" N PRO B 236 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 410 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" C ASP R 410 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP R 410 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG R 411 " 0.012 2.00e-02 2.50e+03 ... (remaining 1508 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 154 2.67 - 3.22: 8050 3.22 - 3.78: 12843 3.78 - 4.34: 18190 4.34 - 4.90: 31345 Nonbonded interactions: 70582 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.107 3.040 nonbonded pdb=" NZ LYS A 210 " pdb=" OD2 ASP B 228 " model vdw 2.132 3.120 nonbonded pdb=" O THR R 397 " pdb=" OG SER R 402 " model vdw 2.135 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.136 3.040 nonbonded pdb=" OG SER S 149 " pdb=" O LYS S 151 " model vdw 2.157 3.040 ... (remaining 70577 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 6.990 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 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 : 0.008 0.226 8980 Z= 0.382 Angle : 0.779 10.977 12167 Z= 0.404 Chirality : 0.056 0.543 1377 Planarity : 0.004 0.077 1511 Dihedral : 13.513 106.650 3205 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.21 % Allowed : 4.83 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.58 (0.22), residues: 1091 helix: -0.32 (0.25), residues: 352 sheet: -1.90 (0.28), residues: 274 loop : -2.64 (0.24), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 49 TYR 0.015 0.002 TYR S 178 PHE 0.016 0.002 PHE A 190 TRP 0.014 0.002 TRP R 339 HIS 0.008 0.001 HIS R 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00830 / 0.38 ( 8977) covalent geometry : angle 0.77824 / 0.40 (12163) SS BOND : bond 0.00865 / 0.44 ( 2) SS BOND : angle 2.35053 / 1.34 ( 4) hydrogen bonds : bond 0.16814 / 11.07 ( 401) hydrogen bonds : angle 6.29731 / 4.37 ( 1152) Misc. bond : bond 0.00050 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7982 (ttp-110) cc_final: 0.7774 (ttp80) REVERT: B 124 TYR cc_start: 0.8913 (m-80) cc_final: 0.8592 (m-80) REVERT: B 130 GLU cc_start: 0.7681 (mp0) cc_final: 0.7465 (mp0) REVERT: B 138 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8475 (mt-10) REVERT: B 153 ASP cc_start: 0.7626 (m-30) cc_final: 0.7394 (m-30) REVERT: R 447 MET cc_start: 0.6609 (mmt) cc_final: 0.6388 (mpt) REVERT: S 168 ARG cc_start: 0.7769 (mtt90) cc_final: 0.7522 (mtt90) REVERT: S 174 GLN cc_start: 0.8810 (pt0) cc_final: 0.8591 (pt0) REVERT: S 194 SER cc_start: 0.8264 (t) cc_final: 0.8025 (p) outliers start: 2 outliers final: 1 residues processed: 140 average time/residue: 0.4918 time to fit residues: 72.7212 Evaluate side-chains 97 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.3980 chunk 106 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN R 362 HIS S 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.161457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.123131 restraints weight = 9993.030| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.33 r_work: 0.3117 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8980 Z= 0.111 Angle : 0.530 7.944 12167 Z= 0.276 Chirality : 0.041 0.147 1377 Planarity : 0.003 0.038 1511 Dihedral : 7.149 94.797 1278 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.72 % Allowed : 11.06 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.07 (0.24), residues: 1091 helix: 1.49 (0.28), residues: 355 sheet: -1.38 (0.28), residues: 269 loop : -2.04 (0.25), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 197 TYR 0.017 0.001 TYR S 178 PHE 0.023 0.001 PHE R 285 TRP 0.022 0.001 TRP B 169 HIS 0.005 0.001 HIS R 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 8977) covalent geometry : angle 0.52988 / 0.28 (12163) SS BOND : bond 0.00394 / 0.20 ( 2) SS BOND : angle 1.41474 / 0.77 ( 4) hydrogen bonds : bond 0.03698 / 2.42 ( 401) hydrogen bonds : angle 4.29457 / 2.96 ( 1152) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.213 Fit side-chains REVERT: A 43 ASN cc_start: 0.7559 (t0) cc_final: 0.7141 (t0) REVERT: A 248 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6862 (tt) REVERT: A 341 ASP cc_start: 0.8174 (t70) cc_final: 0.7923 (t0) REVERT: B 138 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8583 (mt-10) REVERT: B 153 ASP cc_start: 0.7528 (m-30) cc_final: 0.7315 (m-30) REVERT: B 155 ASN cc_start: 0.7879 (t0) cc_final: 0.7555 (t0) REVERT: B 175 GLN cc_start: 0.8154 (mm110) cc_final: 0.7677 (mm110) REVERT: R 459 THR cc_start: 0.8025 (t) cc_final: 0.7726 (p) REVERT: S 194 SER cc_start: 0.7919 (t) cc_final: 0.7704 (p) REVERT: S 211 ASP cc_start: 0.8438 (m-30) cc_final: 0.8174 (m-30) outliers start: 16 outliers final: 7 residues processed: 134 average time/residue: 0.4701 time to fit residues: 67.2045 Evaluate side-chains 113 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain S residue 82 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 22 optimal weight: 5.9990 chunk 5 optimal weight: 0.3980 chunk 40 optimal weight: 0.0870 chunk 77 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 59 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN B 340 ASN S 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.160535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.121117 restraints weight = 9985.067| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.35 r_work: 0.3127 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8980 Z= 0.098 Angle : 0.499 6.788 12167 Z= 0.258 Chirality : 0.040 0.138 1377 Planarity : 0.003 0.036 1511 Dihedral : 6.455 80.535 1278 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.40 % Allowed : 14.82 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.41 (0.25), residues: 1091 helix: 2.18 (0.28), residues: 353 sheet: -1.05 (0.28), residues: 275 loop : -1.76 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 197 TYR 0.014 0.001 TYR B 105 PHE 0.009 0.001 PHE B 241 TRP 0.016 0.001 TRP B 169 HIS 0.004 0.001 HIS R 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 8977) covalent geometry : angle 0.49894 / 0.26 (12163) SS BOND : bond 0.00266 / 0.13 ( 2) SS BOND : angle 1.26519 / 0.65 ( 4) hydrogen bonds : bond 0.03334 / 2.21 ( 401) hydrogen bonds : angle 3.91458 / 2.70 ( 1152) Misc. bond : bond 0.00023 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.197 Fit side-chains REVERT: A 43 ASN cc_start: 0.7476 (t0) cc_final: 0.7124 (t0) REVERT: A 341 ASP cc_start: 0.8188 (t70) cc_final: 0.7960 (t0) REVERT: B 138 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8466 (mt-10) REVERT: B 155 ASN cc_start: 0.7803 (t0) cc_final: 0.7400 (t0) REVERT: B 175 GLN cc_start: 0.8132 (mm110) cc_final: 0.7639 (mm110) REVERT: B 197 ARG cc_start: 0.8038 (ttm110) cc_final: 0.7832 (ttm110) REVERT: B 214 ARG cc_start: 0.7425 (mpt90) cc_final: 0.7203 (mpt90) REVERT: R 447 MET cc_start: 0.6853 (mmt) cc_final: 0.6594 (mpt) REVERT: R 459 THR cc_start: 0.7959 (t) cc_final: 0.7582 (p) REVERT: S 190 ARG cc_start: 0.7674 (mtm110) cc_final: 0.7424 (mtp180) REVERT: S 211 ASP cc_start: 0.8467 (m-30) cc_final: 0.8204 (m-30) outliers start: 13 outliers final: 6 residues processed: 126 average time/residue: 0.4915 time to fit residues: 65.8734 Evaluate side-chains 114 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 264 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.156708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.117860 restraints weight = 10095.024| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.35 r_work: 0.3093 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8980 Z= 0.185 Angle : 0.567 8.254 12167 Z= 0.291 Chirality : 0.043 0.162 1377 Planarity : 0.003 0.038 1511 Dihedral : 6.353 59.356 1278 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.26 % Allowed : 15.15 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.30 (0.25), residues: 1091 helix: 2.05 (0.28), residues: 360 sheet: -0.85 (0.29), residues: 272 loop : -1.64 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.015 0.001 TYR S 178 PHE 0.024 0.002 PHE R 285 TRP 0.013 0.002 TRP B 169 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.18 ( 8977) covalent geometry : angle 0.56607 / 0.29 (12163) SS BOND : bond 0.00628 / 0.32 ( 2) SS BOND : angle 1.51711 / 0.77 ( 4) hydrogen bonds : bond 0.03972 / 2.63 ( 401) hydrogen bonds : angle 3.99943 / 2.76 ( 1152) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.224 Fit side-chains REVERT: A 43 ASN cc_start: 0.7606 (t0) cc_final: 0.7245 (t0) REVERT: A 341 ASP cc_start: 0.8239 (t70) cc_final: 0.7985 (t0) REVERT: B 138 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8515 (mt-10) REVERT: B 155 ASN cc_start: 0.7908 (t0) cc_final: 0.7530 (t0) REVERT: B 175 GLN cc_start: 0.8211 (mm110) cc_final: 0.7757 (mm110) outliers start: 21 outliers final: 14 residues processed: 123 average time/residue: 0.4969 time to fit residues: 65.1740 Evaluate side-chains 114 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 356 MET Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain R residue 407 THR Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 67 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 2 optimal weight: 0.3980 chunk 54 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.159004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.119643 restraints weight = 10080.386| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.42 r_work: 0.3128 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8980 Z= 0.105 Angle : 0.508 8.540 12167 Z= 0.263 Chirality : 0.040 0.201 1377 Planarity : 0.003 0.041 1511 Dihedral : 5.877 59.382 1278 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.61 % Allowed : 16.86 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.05 (0.25), residues: 1091 helix: 2.34 (0.28), residues: 358 sheet: -0.60 (0.29), residues: 265 loop : -1.63 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 197 TYR 0.014 0.001 TYR S 178 PHE 0.025 0.001 PHE R 292 TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS R 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 8977) covalent geometry : angle 0.50783 / 0.26 (12163) SS BOND : bond 0.00329 / 0.17 ( 2) SS BOND : angle 1.27189 / 0.62 ( 4) hydrogen bonds : bond 0.03315 / 2.20 ( 401) hydrogen bonds : angle 3.81321 / 2.63 ( 1152) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.315 Fit side-chains REVERT: A 43 ASN cc_start: 0.7639 (t0) cc_final: 0.7329 (t0) REVERT: A 341 ASP cc_start: 0.8235 (t70) cc_final: 0.7977 (t0) REVERT: B 138 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8484 (mt-10) REVERT: B 155 ASN cc_start: 0.7744 (t0) cc_final: 0.7338 (t0) REVERT: B 175 GLN cc_start: 0.8218 (mm110) cc_final: 0.7862 (mm110) REVERT: R 447 MET cc_start: 0.6894 (mmt) cc_final: 0.6665 (mpt) REVERT: R 459 THR cc_start: 0.7944 (t) cc_final: 0.7549 (p) REVERT: S 84 THR cc_start: 0.8673 (m) cc_final: 0.8320 (p) outliers start: 15 outliers final: 13 residues processed: 122 average time/residue: 0.4223 time to fit residues: 55.4368 Evaluate side-chains 126 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 356 MET Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain R residue 407 THR Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 75 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 54 optimal weight: 0.3980 chunk 90 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.0770 chunk 105 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 overall best weight: 1.0944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.159594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.121313 restraints weight = 9999.709| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.30 r_work: 0.3128 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8980 Z= 0.122 Angle : 0.516 8.758 12167 Z= 0.267 Chirality : 0.041 0.203 1377 Planarity : 0.003 0.045 1511 Dihedral : 5.797 59.192 1278 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.15 % Allowed : 17.72 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.05 (0.25), residues: 1091 helix: 2.41 (0.28), residues: 358 sheet: -0.65 (0.29), residues: 271 loop : -1.49 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 197 TYR 0.014 0.001 TYR S 178 PHE 0.026 0.001 PHE R 285 TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 8977) covalent geometry : angle 0.51538 / 0.27 (12163) SS BOND : bond 0.00458 / 0.23 ( 2) SS BOND : angle 1.28521 / 0.63 ( 4) hydrogen bonds : bond 0.03365 / 2.23 ( 401) hydrogen bonds : angle 3.78534 / 2.61 ( 1152) Misc. bond : bond 0.00008 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.186 Fit side-chains REVERT: A 43 ASN cc_start: 0.7729 (t0) cc_final: 0.7371 (t0) REVERT: A 341 ASP cc_start: 0.8226 (t70) cc_final: 0.7963 (t0) REVERT: B 138 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8431 (mt-10) REVERT: B 155 ASN cc_start: 0.7714 (t0) cc_final: 0.7269 (t0) REVERT: B 175 GLN cc_start: 0.8233 (mm110) cc_final: 0.7916 (mm110) REVERT: B 219 ARG cc_start: 0.8006 (mtm180) cc_final: 0.7367 (mtt-85) REVERT: R 447 MET cc_start: 0.6903 (mmt) cc_final: 0.6619 (mpt) REVERT: S 34 MET cc_start: 0.9140 (mmt) cc_final: 0.8848 (mmt) REVERT: S 84 THR cc_start: 0.8685 (m) cc_final: 0.8284 (p) outliers start: 20 outliers final: 14 residues processed: 131 average time/residue: 0.4907 time to fit residues: 68.4305 Evaluate side-chains 122 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 356 MET Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain R residue 407 THR Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 93 optimal weight: 7.9990 chunk 96 optimal weight: 0.0970 chunk 43 optimal weight: 0.0970 chunk 46 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 chunk 48 optimal weight: 0.6980 chunk 70 optimal weight: 0.2980 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.163503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.125251 restraints weight = 9940.517| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.28 r_work: 0.3210 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8980 Z= 0.087 Angle : 0.481 8.941 12167 Z= 0.248 Chirality : 0.040 0.190 1377 Planarity : 0.003 0.047 1511 Dihedral : 5.230 58.052 1278 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.07 % Allowed : 19.01 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.38 (0.26), residues: 1091 helix: 2.63 (0.28), residues: 358 sheet: -0.33 (0.30), residues: 265 loop : -1.34 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 197 TYR 0.012 0.001 TYR S 178 PHE 0.031 0.001 PHE R 292 TRP 0.017 0.001 TRP B 169 HIS 0.002 0.000 HIS R 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00180 / 0.09 ( 8977) covalent geometry : angle 0.48077 / 0.25 (12163) SS BOND : bond 0.00346 / 0.18 ( 2) SS BOND : angle 1.25336 / 0.62 ( 4) hydrogen bonds : bond 0.02740 / 1.81 ( 401) hydrogen bonds : angle 3.55731 / 2.46 ( 1152) Misc. bond : bond 0.00004 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.291 Fit side-chains REVERT: A 43 ASN cc_start: 0.7661 (t0) cc_final: 0.7306 (t0) REVERT: A 303 TYR cc_start: 0.8371 (t80) cc_final: 0.8090 (t80) REVERT: A 341 ASP cc_start: 0.8173 (t70) cc_final: 0.7912 (t0) REVERT: B 138 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8393 (mt-10) REVERT: B 155 ASN cc_start: 0.7578 (t0) cc_final: 0.7060 (t0) REVERT: B 175 GLN cc_start: 0.8055 (mm110) cc_final: 0.7765 (mm110) REVERT: B 197 ARG cc_start: 0.8059 (ttm110) cc_final: 0.7736 (ttm-80) REVERT: R 459 THR cc_start: 0.7924 (t) cc_final: 0.7537 (p) REVERT: S 34 MET cc_start: 0.9039 (mmt) cc_final: 0.8791 (mmt) REVERT: S 174 GLN cc_start: 0.8673 (pt0) cc_final: 0.8448 (pt0) outliers start: 10 outliers final: 5 residues processed: 126 average time/residue: 0.4486 time to fit residues: 60.7847 Evaluate side-chains 122 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 117 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 87 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 45 optimal weight: 0.0470 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.161484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.122225 restraints weight = 9991.790| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.37 r_work: 0.3162 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 8980 Z= 0.105 Angle : 0.523 9.749 12167 Z= 0.269 Chirality : 0.042 0.246 1377 Planarity : 0.003 0.055 1511 Dihedral : 5.363 59.449 1278 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.72 % Allowed : 18.69 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.50 (0.26), residues: 1091 helix: 2.65 (0.28), residues: 358 sheet: -0.10 (0.30), residues: 254 loop : -1.28 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 197 TYR 0.012 0.001 TYR S 178 PHE 0.028 0.001 PHE R 516 TRP 0.014 0.001 TRP B 169 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 8977) covalent geometry : angle 0.51858 / 0.27 (12163) SS BOND : bond 0.00585 / 0.30 ( 2) SS BOND : angle 3.95933 / 1.83 ( 4) hydrogen bonds : bond 0.03039 / 2.01 ( 401) hydrogen bonds : angle 3.73964 / 2.58 ( 1152) Misc. bond : bond 0.00004 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.199 Fit side-chains REVERT: A 43 ASN cc_start: 0.7696 (t0) cc_final: 0.7332 (t0) REVERT: A 341 ASP cc_start: 0.8176 (t70) cc_final: 0.7905 (t0) REVERT: B 138 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8374 (mt-10) REVERT: B 155 ASN cc_start: 0.7606 (t0) cc_final: 0.7045 (t0) REVERT: B 175 GLN cc_start: 0.8040 (mm110) cc_final: 0.7756 (mm110) REVERT: B 214 ARG cc_start: 0.7347 (mpt90) cc_final: 0.7064 (mpt90) REVERT: R 423 ARG cc_start: 0.7480 (ptt90) cc_final: 0.7048 (ptm-80) REVERT: S 34 MET cc_start: 0.9064 (mmt) cc_final: 0.8791 (mmt) REVERT: S 174 GLN cc_start: 0.8723 (pt0) cc_final: 0.8519 (pt0) outliers start: 16 outliers final: 10 residues processed: 130 average time/residue: 0.4437 time to fit residues: 61.7281 Evaluate side-chains 118 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 356 MET Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain R residue 407 THR Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 81 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.156289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.117271 restraints weight = 9995.215| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.36 r_work: 0.3099 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8980 Z= 0.179 Angle : 0.595 10.362 12167 Z= 0.304 Chirality : 0.044 0.286 1377 Planarity : 0.004 0.068 1511 Dihedral : 5.909 58.810 1278 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.93 % Allowed : 18.69 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.35 (0.25), residues: 1091 helix: 2.45 (0.28), residues: 360 sheet: -0.29 (0.30), residues: 259 loop : -1.25 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 197 TYR 0.014 0.001 TYR S 178 PHE 0.033 0.002 PHE R 292 TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 ( 8977) covalent geometry : angle 0.59096 / 0.30 (12163) SS BOND : bond 0.00335 / 0.16 ( 2) SS BOND : angle 3.83371 / 1.77 ( 4) hydrogen bonds : bond 0.03847 / 2.56 ( 401) hydrogen bonds : angle 3.94874 / 2.73 ( 1152) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.337 Fit side-chains REVERT: A 43 ASN cc_start: 0.7767 (t0) cc_final: 0.7463 (t0) REVERT: A 341 ASP cc_start: 0.8275 (t70) cc_final: 0.7998 (t0) REVERT: B 138 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8461 (mt-10) REVERT: B 155 ASN cc_start: 0.7778 (t0) cc_final: 0.7289 (t0) REVERT: B 175 GLN cc_start: 0.8138 (mm110) cc_final: 0.7846 (mm110) REVERT: R 423 ARG cc_start: 0.7583 (ptt90) cc_final: 0.7079 (ptm-80) REVERT: S 174 GLN cc_start: 0.8795 (pt0) cc_final: 0.8585 (pt0) outliers start: 18 outliers final: 14 residues processed: 115 average time/residue: 0.4242 time to fit residues: 52.4563 Evaluate side-chains 114 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 356 MET Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain R residue 407 THR Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 3 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 50 optimal weight: 0.0670 chunk 21 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.160167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.121589 restraints weight = 9997.969| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.32 r_work: 0.3167 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8980 Z= 0.097 Angle : 0.527 9.926 12167 Z= 0.268 Chirality : 0.041 0.283 1377 Planarity : 0.003 0.051 1511 Dihedral : 5.458 58.754 1278 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.18 % Allowed : 20.09 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.51 (0.26), residues: 1091 helix: 2.60 (0.28), residues: 360 sheet: -0.12 (0.30), residues: 256 loop : -1.22 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 197 TYR 0.014 0.001 TYR B 124 PHE 0.028 0.001 PHE R 516 TRP 0.017 0.001 TRP B 169 HIS 0.002 0.000 HIS R 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 8977) covalent geometry : angle 0.52447 / 0.27 (12163) SS BOND : bond 0.00270 / 0.13 ( 2) SS BOND : angle 2.87633 / 1.33 ( 4) hydrogen bonds : bond 0.03051 / 2.02 ( 401) hydrogen bonds : angle 3.76581 / 2.59 ( 1152) Misc. bond : bond 0.00007 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.322 Fit side-chains REVERT: A 43 ASN cc_start: 0.7745 (t0) cc_final: 0.7450 (t0) REVERT: A 341 ASP cc_start: 0.8232 (t70) cc_final: 0.7962 (t0) REVERT: B 42 ARG cc_start: 0.7441 (ttp80) cc_final: 0.7181 (tmt170) REVERT: B 138 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8403 (mt-10) REVERT: B 155 ASN cc_start: 0.7670 (t0) cc_final: 0.7156 (t0) REVERT: B 175 GLN cc_start: 0.8111 (mm110) cc_final: 0.7844 (mm110) REVERT: R 423 ARG cc_start: 0.7554 (ptt90) cc_final: 0.7058 (ptm-80) REVERT: R 459 THR cc_start: 0.7911 (t) cc_final: 0.7517 (p) REVERT: R 525 TYR cc_start: 0.8094 (m-80) cc_final: 0.7771 (m-80) REVERT: S 43 LYS cc_start: 0.8291 (mtpp) cc_final: 0.7674 (mttm) REVERT: S 174 GLN cc_start: 0.8767 (pt0) cc_final: 0.8562 (pt0) outliers start: 11 outliers final: 10 residues processed: 119 average time/residue: 0.4569 time to fit residues: 58.5064 Evaluate side-chains 124 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 356 MET Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain R residue 407 THR Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 107 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.160730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.121761 restraints weight = 9798.463| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.34 r_work: 0.3113 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8980 Z= 0.118 Angle : 0.542 9.904 12167 Z= 0.275 Chirality : 0.042 0.291 1377 Planarity : 0.003 0.046 1511 Dihedral : 5.442 58.514 1278 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.61 % Allowed : 19.66 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.53 (0.26), residues: 1091 helix: 2.57 (0.28), residues: 361 sheet: -0.07 (0.31), residues: 256 loop : -1.20 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 197 TYR 0.014 0.001 TYR S 178 PHE 0.035 0.001 PHE R 292 TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 8977) covalent geometry : angle 0.53895 / 0.27 (12163) SS BOND : bond 0.00304 / 0.14 ( 2) SS BOND : angle 2.95644 / 1.37 ( 4) hydrogen bonds : bond 0.03236 / 2.15 ( 401) hydrogen bonds : angle 3.79216 / 2.61 ( 1152) Misc. bond : bond 0.00003 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2841.10 seconds wall clock time: 49 minutes 5.70 seconds (2945.70 seconds total)