Starting phenix.real_space_refine on Sat Sep 12 05:27:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ckx_30393/09_2026/7ckx_30393.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ckx_30393/09_2026/7ckx_30393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ckx_30393/09_2026/7ckx_30393.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ckx_30393/09_2026/7ckx_30393.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ckx_30393/09_2026/7ckx_30393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ckx_30393/09_2026/7ckx_30393.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ckx_30393/09_2026/7ckx_30393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ckx_30393/09_2026/7ckx_30393.map" } resolution = 3.54 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 ------------------------------------------------------------------------------- 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7230 atoms to isotropic. 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 5165 2.51 5 N 1406 2.21 5 O 1488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8112 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1906 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2587 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2159 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 263} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'CLR': 1, 'G3O': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.65, per 1000 atoms: 0.20 Number of scatterers: 8112 At special positions: 0 Unit cell: (118, 102, 85, 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 1488 8.00 N 1406 7.00 C 5165 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 298 " - pdb=" SG CYS R 307 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 255.9 milliseconds 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 41.4% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 15 through 39 removed outlier: 4.125A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.549A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.522A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 removed outlier: 4.320A pdb=" N THR A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.959A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.542A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.983A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 392 removed outlier: 3.740A pdb=" N ASP A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.526A pdb=" N ILE B 33 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.929A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 51 removed outlier: 4.072A pdb=" N THR R 26 " --> pdb=" O VAL R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 57 through 59 No H-bonds generated for 'chain 'R' and resid 57 through 59' Processing helix chain 'R' and resid 60 through 73 Processing helix chain 'R' and resid 77 through 88 removed outlier: 4.216A pdb=" N ALA R 87 " --> pdb=" O VAL R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 127 Processing helix chain 'R' and resid 127 through 135 Processing helix chain 'R' and resid 136 through 162 removed outlier: 4.321A pdb=" N ILE R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Proline residue: R 158 - end of helix Processing helix chain 'R' and resid 193 through 203 removed outlier: 3.942A pdb=" N SER R 197 " --> pdb=" O THR R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 236 removed outlier: 3.857A pdb=" N LYS R 223 " --> pdb=" O ARG R 219 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU R 231 " --> pdb=" O ARG R 227 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA R 234 " --> pdb=" O ALA R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 283 removed outlier: 3.936A pdb=" N VAL R 270 " --> pdb=" O ARG R 266 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU R 271 " --> pdb=" O GLU R 267 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N PHE R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 285 through 293 removed outlier: 4.090A pdb=" N LEU R 291 " --> pdb=" O PRO R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 309 through 331 removed outlier: 3.510A pdb=" N PHE R 313 " --> pdb=" O ASP R 309 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP R 314 " --> pdb=" O SER R 310 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL R 315 " --> pdb=" O ASN R 311 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP R 318 " --> pdb=" O ASP R 314 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER R 325 " --> pdb=" O TRP R 321 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 334 through 344 removed outlier: 3.544A pdb=" N LEU R 344 " --> pdb=" O ALA R 340 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 3.796A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 50 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.887A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 6.798A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.824A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.865A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 5.946A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.444A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.584A pdb=" N CYS N 99 " --> pdb=" O LYS N 33 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LYS N 33 " --> pdb=" O CYS N 99 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 396 hydrogen bonds defined for protein. 1116 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: 1.20 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2633 1.35 - 1.46: 2039 1.46 - 1.58: 3540 1.58 - 1.70: 1 1.70 - 1.82: 72 Bond restraints: 8285 Sorted by residual: bond pdb=" C05 G3O R 501 " pdb=" C06 G3O R 501 " ideal model delta sigma weight residual 1.398 1.294 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" C08 G3O R 501 " pdb=" C13 G3O R 501 " ideal model delta sigma weight residual 1.534 1.613 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C10 G3O R 501 " pdb=" O09 G3O R 501 " ideal model delta sigma weight residual 1.403 1.479 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C17 G3O R 501 " pdb=" C18 G3O R 501 " ideal model delta sigma weight residual 1.531 1.473 0.058 2.00e-02 2.50e+03 8.42e+00 bond pdb=" C02 G3O R 501 " pdb=" O23 G3O R 501 " ideal model delta sigma weight residual 1.351 1.405 -0.054 2.00e-02 2.50e+03 7.36e+00 ... (remaining 8280 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 11116 1.75 - 3.49: 104 3.49 - 5.24: 22 5.24 - 6.99: 3 6.99 - 8.73: 1 Bond angle restraints: 11246 Sorted by residual: angle pdb=" N VAL R 22 " pdb=" CA VAL R 22 " pdb=" C VAL R 22 " ideal model delta sigma weight residual 112.96 109.06 3.90 1.00e+00 1.00e+00 1.52e+01 angle pdb=" C07 G3O R 501 " pdb=" C08 G3O R 501 " pdb=" C13 G3O R 501 " ideal model delta sigma weight residual 115.56 108.88 6.68 3.00e+00 1.11e-01 4.95e+00 angle pdb=" N VAL R 75 " pdb=" CA VAL R 75 " pdb=" C VAL R 75 " ideal model delta sigma weight residual 112.96 110.78 2.18 1.00e+00 1.00e+00 4.74e+00 angle pdb=" CB LYS B 301 " pdb=" CG LYS B 301 " pdb=" CD LYS B 301 " ideal model delta sigma weight residual 111.30 115.67 -4.37 2.30e+00 1.89e-01 3.62e+00 angle pdb=" CA VAL R 22 " pdb=" C VAL R 22 " pdb=" O VAL R 22 " ideal model delta sigma weight residual 119.29 120.85 -1.56 8.40e-01 1.42e+00 3.44e+00 ... (remaining 11241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4445 17.96 - 35.92: 381 35.92 - 53.88: 62 53.88 - 71.84: 7 71.84 - 89.80: 7 Dihedral angle restraints: 4902 sinusoidal: 1886 harmonic: 3016 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -32.80 -53.20 1 1.00e+01 1.00e-02 3.85e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -163.62 -16.38 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA ASP R 120 " pdb=" CB ASP R 120 " pdb=" CG ASP R 120 " pdb=" OD1 ASP R 120 " ideal model delta sinusoidal sigma weight residual -30.00 -86.23 56.23 1 2.00e+01 2.50e-03 1.07e+01 ... (remaining 4899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 969 0.042 - 0.085: 245 0.085 - 0.127: 65 0.127 - 0.169: 2 0.169 - 0.212: 2 Chirality restraints: 1283 Sorted by residual: chirality pdb=" C08 G3O R 501 " pdb=" C07 G3O R 501 " pdb=" C13 G3O R 501 " pdb=" O09 G3O R 501 " both_signs ideal model delta sigma weight residual False -2.38 -2.59 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" C20 G3O R 501 " pdb=" C19 G3O R 501 " pdb=" C21 G3O R 501 " pdb=" C22 G3O R 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.95 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" C10 G3O R 501 " pdb=" C05 G3O R 501 " pdb=" C11 G3O R 501 " pdb=" O09 G3O R 501 " both_signs ideal model delta sigma weight residual False 2.41 2.54 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 1280 not shown) Planarity restraints: 1418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 205 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO R 206 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO R 206 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 206 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET R 78 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO R 79 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO R 79 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 79 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP R 103 " 0.006 2.00e-02 2.50e+03 1.19e-02 1.42e+00 pdb=" CG ASP R 103 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASP R 103 " 0.007 2.00e-02 2.50e+03 pdb=" OD2 ASP R 103 " 0.007 2.00e-02 2.50e+03 ... (remaining 1415 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 277 2.71 - 3.26: 8391 3.26 - 3.80: 13777 3.80 - 4.35: 17726 4.35 - 4.90: 29017 Nonbonded interactions: 69188 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.160 3.040 nonbonded pdb=" OD1 ASP B 228 " pdb=" OH TYR N 117 " model vdw 2.178 3.040 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.208 3.040 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.222 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" OD1 ASP B 290 " model vdw 2.234 3.040 ... (remaining 69183 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 group one per residue 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.980 Find NCS groups from input model: 0.040 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 8289 Z= 0.159 Angle : 0.499 8.733 11254 Z= 0.281 Chirality : 0.039 0.212 1283 Planarity : 0.003 0.036 1418 Dihedral : 13.483 89.798 2930 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.09 % Allowed : 11.03 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.24), residues: 1015 helix: -1.25 (0.23), residues: 384 sheet: -2.74 (0.30), residues: 218 loop : -2.23 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 98 TYR 0.006 0.001 TYR N 95 PHE 0.007 0.001 PHE N 103 TRP 0.011 0.001 TRP B 82 HIS 0.001 0.000 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 ( 8285) covalent geometry : angle 0.49839 / 0.28 (11246) SS BOND : bond 0.00205 / 0.10 ( 4) SS BOND : angle 0.79732 / 0.45 ( 8) hydrogen bonds : bond 0.15274 / 10.75 ( 396) hydrogen bonds : angle 6.43231 / 4.49 ( 1116) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 345 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7331 (mtm180) cc_final: 0.7069 (ttp-170) REVERT: A 310 ASP cc_start: 0.6882 (m-30) cc_final: 0.6438 (t0) REVERT: A 311 TYR cc_start: 0.7831 (m-80) cc_final: 0.7301 (m-80) REVERT: A 323 ASP cc_start: 0.7432 (p0) cc_final: 0.7061 (p0) REVERT: A 339 TYR cc_start: 0.8328 (m-80) cc_final: 0.7345 (m-80) REVERT: A 343 ASP cc_start: 0.7630 (m-30) cc_final: 0.7128 (m-30) REVERT: A 381 ASP cc_start: 0.7330 (m-30) cc_final: 0.6855 (m-30) REVERT: B 14 LEU cc_start: 0.9036 (mp) cc_final: 0.8546 (mt) REVERT: B 88 ASN cc_start: 0.8084 (m-40) cc_final: 0.7710 (t0) REVERT: B 153 ASP cc_start: 0.7378 (p0) cc_final: 0.7074 (p0) REVERT: B 175 GLN cc_start: 0.7445 (tm-30) cc_final: 0.7241 (tm-30) REVERT: B 205 ASP cc_start: 0.7102 (p0) cc_final: 0.6841 (p0) REVERT: B 210 LEU cc_start: 0.8898 (tp) cc_final: 0.8492 (tp) REVERT: B 261 LEU cc_start: 0.9014 (mt) cc_final: 0.8423 (mp) REVERT: G 21 MET cc_start: 0.7798 (ttm) cc_final: 0.7391 (tpt) REVERT: G 22 GLU cc_start: 0.7458 (tp30) cc_final: 0.7132 (tp30) REVERT: G 25 ILE cc_start: 0.5625 (pt) cc_final: 0.5407 (pt) REVERT: G 44 HIS cc_start: 0.7806 (m90) cc_final: 0.7465 (m-70) REVERT: N 12 VAL cc_start: 0.6563 (OUTLIER) cc_final: 0.6216 (m) REVERT: N 43 LYS cc_start: 0.5479 (mttm) cc_final: 0.5022 (mtpt) REVERT: N 51 ILE cc_start: 0.8790 (tt) cc_final: 0.8476 (pt) REVERT: N 107 CYS cc_start: 0.5266 (m) cc_final: 0.4782 (m) REVERT: R 138 LYS cc_start: 0.8360 (tmtt) cc_final: 0.7909 (tppt) REVERT: R 142 ILE cc_start: 0.7670 (mt) cc_final: 0.7400 (mt) REVERT: R 331 TYR cc_start: 0.8506 (m-80) cc_final: 0.8302 (m-80) REVERT: R 333 PHE cc_start: 0.5423 (t80) cc_final: 0.5163 (t80) outliers start: 18 outliers final: 11 residues processed: 354 average time/residue: 0.1083 time to fit residues: 49.9208 Evaluate side-chains 279 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 267 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 117 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A 271 ASN A 278 ASN A 371 ASN B 62 HIS B 230 ASN B 237 ASN B 340 ASN G 24 ASN G 44 HIS N 5 GLN N 31 ASN R 164 HIS R 222 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.168718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.137673 restraints weight = 11766.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.142702 restraints weight = 6331.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.146046 restraints weight = 4277.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.148239 restraints weight = 3319.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.149486 restraints weight = 2796.292| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8289 Z= 0.156 Angle : 0.598 10.595 11254 Z= 0.308 Chirality : 0.043 0.139 1283 Planarity : 0.005 0.060 1418 Dihedral : 5.320 54.621 1151 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.41 % Allowed : 17.89 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.25), residues: 1015 helix: -0.44 (0.25), residues: 398 sheet: -2.14 (0.35), residues: 182 loop : -1.92 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 49 TYR 0.017 0.002 TYR N 60 PHE 0.014 0.001 PHE N 103 TRP 0.021 0.002 TRP B 297 HIS 0.006 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 8285) covalent geometry : angle 0.59816 / 0.31 (11246) SS BOND : bond 0.00164 / 0.08 ( 4) SS BOND : angle 0.74030 / 0.41 ( 8) hydrogen bonds : bond 0.03743 / 2.61 ( 396) hydrogen bonds : angle 5.37022 / 3.69 ( 1116) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 307 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7489 (mtm180) cc_final: 0.7133 (ttp-170) REVERT: A 265 ARG cc_start: 0.7128 (mtp85) cc_final: 0.6694 (mtp85) REVERT: A 267 GLN cc_start: 0.8592 (tp40) cc_final: 0.8239 (tp40) REVERT: A 310 ASP cc_start: 0.7084 (m-30) cc_final: 0.6840 (t0) REVERT: A 311 TYR cc_start: 0.8034 (m-80) cc_final: 0.7211 (m-80) REVERT: A 318 TYR cc_start: 0.7417 (t80) cc_final: 0.6828 (t80) REVERT: A 323 ASP cc_start: 0.7502 (p0) cc_final: 0.7240 (p0) REVERT: A 343 ASP cc_start: 0.7867 (m-30) cc_final: 0.7404 (m-30) REVERT: A 381 ASP cc_start: 0.7588 (m-30) cc_final: 0.7185 (m-30) REVERT: B 14 LEU cc_start: 0.9021 (mp) cc_final: 0.8801 (mp) REVERT: B 135 VAL cc_start: 0.7027 (p) cc_final: 0.6699 (p) REVERT: B 150 ARG cc_start: 0.8435 (mmt-90) cc_final: 0.8126 (mmt180) REVERT: B 205 ASP cc_start: 0.7392 (p0) cc_final: 0.6959 (p0) REVERT: B 217 MET cc_start: 0.7396 (ppp) cc_final: 0.7154 (ppp) REVERT: B 220 GLN cc_start: 0.7630 (mm-40) cc_final: 0.7119 (mm-40) REVERT: B 298 ASP cc_start: 0.8127 (t0) cc_final: 0.7732 (p0) REVERT: N 43 LYS cc_start: 0.5563 (mttm) cc_final: 0.5092 (mtpt) REVERT: N 74 ASN cc_start: 0.8077 (m-40) cc_final: 0.7733 (m-40) REVERT: N 107 CYS cc_start: 0.5635 (m) cc_final: 0.5334 (m) REVERT: R 41 ASN cc_start: 0.5439 (m110) cc_final: 0.4981 (m110) REVERT: R 65 SER cc_start: 0.9111 (t) cc_final: 0.8885 (p) REVERT: R 70 ASP cc_start: 0.7701 (t0) cc_final: 0.6873 (t70) REVERT: R 71 LEU cc_start: 0.8663 (tp) cc_final: 0.8383 (tp) REVERT: R 138 LYS cc_start: 0.8356 (tmtt) cc_final: 0.7894 (tppt) REVERT: R 142 ILE cc_start: 0.7571 (mt) cc_final: 0.7319 (mt) REVERT: R 321 TRP cc_start: 0.7812 (m-10) cc_final: 0.7607 (m-90) REVERT: R 333 PHE cc_start: 0.5458 (t80) cc_final: 0.5028 (t80) outliers start: 38 outliers final: 22 residues processed: 322 average time/residue: 0.0970 time to fit residues: 41.8809 Evaluate side-chains 299 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 277 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 336 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 86 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN N 31 ASN R 237 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.165731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.134343 restraints weight = 11621.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.139369 restraints weight = 6344.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.142742 restraints weight = 4298.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.144914 restraints weight = 3330.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.146223 restraints weight = 2812.329| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8289 Z= 0.156 Angle : 0.599 11.476 11254 Z= 0.306 Chirality : 0.043 0.153 1283 Planarity : 0.004 0.055 1418 Dihedral : 5.141 53.131 1143 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.11 % Allowed : 19.16 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.26), residues: 1015 helix: -0.11 (0.26), residues: 396 sheet: -2.22 (0.34), residues: 201 loop : -1.64 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 27 TYR 0.018 0.002 TYR N 60 PHE 0.018 0.001 PHE B 151 TRP 0.022 0.002 TRP B 297 HIS 0.008 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 8285) covalent geometry : angle 0.59907 / 0.31 (11246) SS BOND : bond 0.00158 / 0.08 ( 4) SS BOND : angle 0.80988 / 0.44 ( 8) hydrogen bonds : bond 0.03445 / 2.40 ( 396) hydrogen bonds : angle 5.27683 / 3.59 ( 1116) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 284 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8627 (tp40) cc_final: 0.8344 (tp40) REVERT: A 268 GLU cc_start: 0.7974 (tt0) cc_final: 0.7489 (tt0) REVERT: A 311 TYR cc_start: 0.8071 (m-80) cc_final: 0.7330 (m-80) REVERT: A 318 TYR cc_start: 0.7362 (t80) cc_final: 0.6985 (t80) REVERT: A 323 ASP cc_start: 0.7560 (p0) cc_final: 0.7335 (p0) REVERT: A 339 TYR cc_start: 0.8798 (m-80) cc_final: 0.7987 (m-80) REVERT: A 343 ASP cc_start: 0.7959 (m-30) cc_final: 0.7605 (m-30) REVERT: A 381 ASP cc_start: 0.7645 (m-30) cc_final: 0.7337 (m-30) REVERT: B 15 LYS cc_start: 0.9090 (mmmt) cc_final: 0.8773 (mtpt) REVERT: B 119 ASN cc_start: 0.6483 (m110) cc_final: 0.6078 (m-40) REVERT: B 150 ARG cc_start: 0.8441 (mmt-90) cc_final: 0.8136 (mmt180) REVERT: B 205 ASP cc_start: 0.7444 (p0) cc_final: 0.7049 (p0) REVERT: B 217 MET cc_start: 0.7350 (ppp) cc_final: 0.7079 (ppp) REVERT: B 289 TYR cc_start: 0.8963 (m-10) cc_final: 0.8157 (m-80) REVERT: B 298 ASP cc_start: 0.8151 (t0) cc_final: 0.7636 (p0) REVERT: G 20 LYS cc_start: 0.8618 (mtmm) cc_final: 0.8069 (mtmm) REVERT: N 38 ARG cc_start: 0.8499 (ptm-80) cc_final: 0.8241 (ptm-80) REVERT: N 43 LYS cc_start: 0.5829 (mttm) cc_final: 0.5296 (mtpt) REVERT: N 74 ASN cc_start: 0.8113 (m-40) cc_final: 0.7493 (m-40) REVERT: N 107 CYS cc_start: 0.5779 (m) cc_final: 0.5412 (m) REVERT: R 138 LYS cc_start: 0.8334 (tmtt) cc_final: 0.8105 (tppt) REVERT: R 321 TRP cc_start: 0.7906 (m-10) cc_final: 0.7596 (m-90) REVERT: R 327 ASN cc_start: 0.7871 (OUTLIER) cc_final: 0.7649 (t0) REVERT: R 333 PHE cc_start: 0.5646 (t80) cc_final: 0.5139 (t80) outliers start: 44 outliers final: 24 residues processed: 305 average time/residue: 0.0932 time to fit residues: 38.6757 Evaluate side-chains 294 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 269 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 324 SER Chi-restraints excluded: chain R residue 327 ASN Chi-restraints excluded: chain R residue 336 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 59 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN N 31 ASN ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.162814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.131176 restraints weight = 11930.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.136172 restraints weight = 6415.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.139518 restraints weight = 4341.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.141693 restraints weight = 3359.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.143119 restraints weight = 2837.184| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8289 Z= 0.174 Angle : 0.608 11.970 11254 Z= 0.312 Chirality : 0.043 0.206 1283 Planarity : 0.004 0.040 1418 Dihedral : 5.160 51.626 1143 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.34 % Allowed : 22.76 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.26), residues: 1015 helix: 0.00 (0.26), residues: 399 sheet: -2.19 (0.35), residues: 195 loop : -1.39 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 49 TYR 0.021 0.002 TYR N 95 PHE 0.014 0.001 PHE B 253 TRP 0.030 0.002 TRP B 169 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 ( 8285) covalent geometry : angle 0.60787 / 0.31 (11246) SS BOND : bond 0.00154 / 0.07 ( 4) SS BOND : angle 0.82788 / 0.44 ( 8) hydrogen bonds : bond 0.03388 / 2.34 ( 396) hydrogen bonds : angle 5.27176 / 3.57 ( 1116) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 279 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7634 (mtm180) cc_final: 0.7243 (ttp-170) REVERT: A 267 GLN cc_start: 0.8663 (tp40) cc_final: 0.7913 (tp-100) REVERT: A 268 GLU cc_start: 0.7984 (tt0) cc_final: 0.7502 (tt0) REVERT: A 318 TYR cc_start: 0.7361 (t80) cc_final: 0.7036 (t80) REVERT: A 323 ASP cc_start: 0.7594 (p0) cc_final: 0.7375 (p0) REVERT: A 339 TYR cc_start: 0.8858 (m-80) cc_final: 0.8044 (m-80) REVERT: A 343 ASP cc_start: 0.7965 (m-30) cc_final: 0.7638 (m-30) REVERT: A 381 ASP cc_start: 0.7763 (m-30) cc_final: 0.7541 (m-30) REVERT: B 150 ARG cc_start: 0.8523 (mmt-90) cc_final: 0.8161 (mmt180) REVERT: B 205 ASP cc_start: 0.7598 (p0) cc_final: 0.7188 (p0) REVERT: B 210 LEU cc_start: 0.8931 (tp) cc_final: 0.8390 (tp) REVERT: B 217 MET cc_start: 0.7462 (ppp) cc_final: 0.7220 (ppp) REVERT: B 220 GLN cc_start: 0.7472 (mm-40) cc_final: 0.7082 (mm-40) REVERT: B 253 PHE cc_start: 0.9122 (m-80) cc_final: 0.8912 (m-80) REVERT: B 298 ASP cc_start: 0.7899 (t0) cc_final: 0.7671 (p0) REVERT: G 20 LYS cc_start: 0.8654 (mtmm) cc_final: 0.8123 (mtmm) REVERT: N 31 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8166 (t0) REVERT: N 38 ARG cc_start: 0.8550 (ptm-80) cc_final: 0.8276 (ptm-80) REVERT: N 43 LYS cc_start: 0.5979 (mttm) cc_final: 0.5440 (mtpt) REVERT: N 74 ASN cc_start: 0.8339 (m-40) cc_final: 0.7697 (m-40) REVERT: R 138 LYS cc_start: 0.8352 (tmtt) cc_final: 0.8107 (tppt) REVERT: R 321 TRP cc_start: 0.8013 (m-10) cc_final: 0.7526 (m-90) REVERT: R 333 PHE cc_start: 0.5640 (t80) cc_final: 0.5048 (t80) outliers start: 46 outliers final: 31 residues processed: 303 average time/residue: 0.0865 time to fit residues: 36.2190 Evaluate side-chains 304 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 272 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 92 PHE Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 324 SER Chi-restraints excluded: chain R residue 327 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 74 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.163636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.132011 restraints weight = 11885.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.136979 restraints weight = 6442.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.140268 restraints weight = 4366.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.142414 restraints weight = 3386.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.143806 restraints weight = 2867.675| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8289 Z= 0.149 Angle : 0.602 11.024 11254 Z= 0.305 Chirality : 0.043 0.170 1283 Planarity : 0.004 0.046 1418 Dihedral : 4.963 50.151 1141 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 5.69 % Allowed : 23.46 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.27), residues: 1015 helix: 0.13 (0.26), residues: 396 sheet: -2.13 (0.35), residues: 195 loop : -1.28 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 265 TYR 0.020 0.002 TYR N 60 PHE 0.020 0.001 PHE A 315 TRP 0.035 0.002 TRP B 169 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 8285) covalent geometry : angle 0.60181 / 0.31 (11246) SS BOND : bond 0.00054 / 0.03 ( 4) SS BOND : angle 0.74024 / 0.41 ( 8) hydrogen bonds : bond 0.03234 / 2.22 ( 396) hydrogen bonds : angle 5.27029 / 3.55 ( 1116) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 274 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7621 (mtm180) cc_final: 0.7282 (ttp-170) REVERT: A 265 ARG cc_start: 0.7074 (mmm160) cc_final: 0.6656 (mmm160) REVERT: A 267 GLN cc_start: 0.8660 (tp40) cc_final: 0.7932 (tp-100) REVERT: A 268 GLU cc_start: 0.7977 (tt0) cc_final: 0.7403 (tt0) REVERT: A 318 TYR cc_start: 0.7293 (t80) cc_final: 0.7013 (t80) REVERT: A 323 ASP cc_start: 0.7601 (p0) cc_final: 0.7389 (p0) REVERT: A 336 ARG cc_start: 0.8569 (tmm-80) cc_final: 0.8263 (tmm-80) REVERT: A 339 TYR cc_start: 0.8840 (m-80) cc_final: 0.8029 (m-80) REVERT: A 343 ASP cc_start: 0.7942 (m-30) cc_final: 0.7594 (m-30) REVERT: A 381 ASP cc_start: 0.7749 (m-30) cc_final: 0.7466 (m-30) REVERT: B 13 GLN cc_start: 0.8445 (tm-30) cc_final: 0.8198 (tm-30) REVERT: B 99 TRP cc_start: 0.7013 (m-90) cc_final: 0.6513 (m-90) REVERT: B 123 ILE cc_start: 0.8987 (mm) cc_final: 0.8724 (mm) REVERT: B 150 ARG cc_start: 0.8432 (mmt-90) cc_final: 0.8097 (mmt180) REVERT: B 169 TRP cc_start: 0.8062 (m100) cc_final: 0.7844 (m100) REVERT: B 205 ASP cc_start: 0.7626 (p0) cc_final: 0.7211 (p0) REVERT: B 210 LEU cc_start: 0.8908 (tp) cc_final: 0.8436 (tp) REVERT: B 217 MET cc_start: 0.7520 (ppp) cc_final: 0.7242 (ppp) REVERT: B 298 ASP cc_start: 0.7894 (t0) cc_final: 0.7675 (p0) REVERT: G 20 LYS cc_start: 0.8652 (mtmm) cc_final: 0.8336 (mtmm) REVERT: G 27 ARG cc_start: 0.7136 (ttm170) cc_final: 0.6866 (ttm-80) REVERT: N 31 ASN cc_start: 0.8482 (t0) cc_final: 0.8132 (t0) REVERT: N 38 ARG cc_start: 0.8570 (ptm-80) cc_final: 0.8330 (ptm-80) REVERT: N 43 LYS cc_start: 0.6060 (mttm) cc_final: 0.5416 (mtpt) REVERT: N 74 ASN cc_start: 0.8167 (m-40) cc_final: 0.7643 (m-40) REVERT: R 57 LYS cc_start: 0.7175 (tppt) cc_final: 0.6910 (tppt) REVERT: R 138 LYS cc_start: 0.8344 (tmtt) cc_final: 0.8122 (tppt) REVERT: R 327 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.7769 (t0) REVERT: R 333 PHE cc_start: 0.5585 (t80) cc_final: 0.5037 (t80) outliers start: 49 outliers final: 31 residues processed: 299 average time/residue: 0.0946 time to fit residues: 38.3029 Evaluate side-chains 294 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 262 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 92 PHE Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 327 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 66 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.164536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.133659 restraints weight = 11745.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.138566 restraints weight = 6332.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.141822 restraints weight = 4284.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.143955 restraints weight = 3316.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.145164 restraints weight = 2794.701| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8289 Z= 0.138 Angle : 0.602 10.743 11254 Z= 0.304 Chirality : 0.043 0.218 1283 Planarity : 0.004 0.039 1418 Dihedral : 4.943 50.188 1141 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 5.46 % Allowed : 24.39 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.26), residues: 1015 helix: 0.16 (0.26), residues: 396 sheet: -1.98 (0.35), residues: 189 loop : -1.32 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 374 TYR 0.021 0.002 TYR N 60 PHE 0.022 0.001 PHE A 222 TRP 0.034 0.002 TRP B 99 HIS 0.006 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 8285) covalent geometry : angle 0.60242 / 0.30 (11246) SS BOND : bond 0.00041 / 0.02 ( 4) SS BOND : angle 0.67459 / 0.38 ( 8) hydrogen bonds : bond 0.03152 / 2.15 ( 396) hydrogen bonds : angle 5.18471 / 3.49 ( 1116) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 277 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 ARG cc_start: 0.6975 (mmm160) cc_final: 0.6657 (mmm160) REVERT: A 267 GLN cc_start: 0.8629 (tp40) cc_final: 0.7922 (tp-100) REVERT: A 268 GLU cc_start: 0.8009 (tt0) cc_final: 0.7552 (tt0) REVERT: A 318 TYR cc_start: 0.7240 (t80) cc_final: 0.6883 (t80) REVERT: A 323 ASP cc_start: 0.7576 (p0) cc_final: 0.7369 (p0) REVERT: A 336 ARG cc_start: 0.8507 (tmm-80) cc_final: 0.8170 (ptm160) REVERT: A 339 TYR cc_start: 0.8823 (m-80) cc_final: 0.7995 (m-80) REVERT: A 343 ASP cc_start: 0.7962 (m-30) cc_final: 0.7360 (m-30) REVERT: A 381 ASP cc_start: 0.7730 (m-30) cc_final: 0.7450 (m-30) REVERT: B 169 TRP cc_start: 0.8054 (m100) cc_final: 0.7836 (m100) REVERT: B 205 ASP cc_start: 0.7636 (p0) cc_final: 0.7236 (p0) REVERT: B 210 LEU cc_start: 0.8891 (tp) cc_final: 0.8453 (tp) REVERT: B 217 MET cc_start: 0.7501 (ppp) cc_final: 0.7201 (ppp) REVERT: B 264 TYR cc_start: 0.8992 (m-10) cc_final: 0.8713 (m-10) REVERT: B 296 VAL cc_start: 0.8994 (t) cc_final: 0.8615 (m) REVERT: B 297 TRP cc_start: 0.7875 (m100) cc_final: 0.7594 (m-10) REVERT: B 298 ASP cc_start: 0.7855 (t0) cc_final: 0.7624 (p0) REVERT: G 20 LYS cc_start: 0.8861 (mtmm) cc_final: 0.8375 (mtmm) REVERT: N 29 PHE cc_start: 0.8844 (t80) cc_final: 0.7936 (t80) REVERT: N 31 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.8229 (t0) REVERT: N 33 LYS cc_start: 0.9116 (ttmm) cc_final: 0.8885 (ttpp) REVERT: N 38 ARG cc_start: 0.8547 (ptm-80) cc_final: 0.8343 (ptm-80) REVERT: N 43 LYS cc_start: 0.6149 (mttm) cc_final: 0.5399 (mtpt) REVERT: N 74 ASN cc_start: 0.8123 (m-40) cc_final: 0.7656 (m-40) REVERT: R 138 LYS cc_start: 0.8374 (tmtt) cc_final: 0.8149 (tppt) REVERT: R 277 ILE cc_start: 0.8094 (pt) cc_final: 0.7834 (mt) REVERT: R 327 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7753 (t0) REVERT: R 333 PHE cc_start: 0.5598 (t80) cc_final: 0.4992 (t80) outliers start: 47 outliers final: 32 residues processed: 299 average time/residue: 0.0916 time to fit residues: 37.2369 Evaluate side-chains 299 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 265 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 92 PHE Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 327 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 58 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 16 optimal weight: 0.3980 chunk 62 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.160379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.128656 restraints weight = 11845.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.133452 restraints weight = 6497.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.136630 restraints weight = 4450.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.138757 restraints weight = 3482.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.139937 restraints weight = 2953.056| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8289 Z= 0.197 Angle : 0.656 12.108 11254 Z= 0.331 Chirality : 0.044 0.170 1283 Planarity : 0.004 0.056 1418 Dihedral : 5.044 50.706 1141 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 5.34 % Allowed : 25.44 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.27), residues: 1015 helix: 0.22 (0.26), residues: 398 sheet: -2.06 (0.35), residues: 197 loop : -1.19 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 96 TYR 0.023 0.002 TYR N 60 PHE 0.048 0.002 PHE A 222 TRP 0.062 0.003 TRP B 99 HIS 0.008 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 ( 8285) covalent geometry : angle 0.65616 / 0.33 (11246) SS BOND : bond 0.00135 / 0.07 ( 4) SS BOND : angle 0.89928 / 0.48 ( 8) hydrogen bonds : bond 0.03392 / 2.32 ( 396) hydrogen bonds : angle 5.27346 / 3.55 ( 1116) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 275 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 265 ARG cc_start: 0.6937 (mmm160) cc_final: 0.6652 (mmm160) REVERT: A 267 GLN cc_start: 0.8699 (tp40) cc_final: 0.8156 (tp40) REVERT: A 268 GLU cc_start: 0.8030 (tt0) cc_final: 0.7563 (tt0) REVERT: A 318 TYR cc_start: 0.7250 (t80) cc_final: 0.6867 (t80) REVERT: A 323 ASP cc_start: 0.7643 (p0) cc_final: 0.7424 (p0) REVERT: A 339 TYR cc_start: 0.8865 (m-80) cc_final: 0.8013 (m-80) REVERT: A 343 ASP cc_start: 0.7973 (m-30) cc_final: 0.7642 (m-30) REVERT: A 381 ASP cc_start: 0.7889 (m-30) cc_final: 0.7639 (m-30) REVERT: B 118 ASP cc_start: 0.7294 (t0) cc_final: 0.6990 (t0) REVERT: B 205 ASP cc_start: 0.7791 (p0) cc_final: 0.7355 (p0) REVERT: B 210 LEU cc_start: 0.8934 (tp) cc_final: 0.8476 (tp) REVERT: B 217 MET cc_start: 0.7535 (ppp) cc_final: 0.7239 (ppp) REVERT: B 225 HIS cc_start: 0.7865 (OUTLIER) cc_final: 0.7578 (t-90) REVERT: B 296 VAL cc_start: 0.9177 (t) cc_final: 0.8692 (p) REVERT: G 20 LYS cc_start: 0.8876 (mtmm) cc_final: 0.8427 (mtmm) REVERT: N 31 ASN cc_start: 0.8523 (m-40) cc_final: 0.8282 (t0) REVERT: N 43 LYS cc_start: 0.6267 (mttm) cc_final: 0.5553 (mtpt) REVERT: N 74 ASN cc_start: 0.8175 (m-40) cc_final: 0.7764 (m-40) REVERT: R 138 LYS cc_start: 0.8361 (tmtt) cc_final: 0.8129 (tppt) REVERT: R 327 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7761 (t0) REVERT: R 333 PHE cc_start: 0.5618 (t80) cc_final: 0.4974 (t80) outliers start: 46 outliers final: 33 residues processed: 297 average time/residue: 0.0881 time to fit residues: 36.2422 Evaluate side-chains 297 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 262 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 92 PHE Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 327 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 100 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 0.0050 chunk 63 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 0.0670 chunk 19 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.0136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.162114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.130472 restraints weight = 11693.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.135332 restraints weight = 6420.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.138578 restraints weight = 4390.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.140705 restraints weight = 3427.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.142087 restraints weight = 2903.897| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8289 Z= 0.176 Angle : 0.684 14.925 11254 Z= 0.340 Chirality : 0.045 0.220 1283 Planarity : 0.004 0.042 1418 Dihedral : 5.151 50.695 1141 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.99 % Allowed : 26.95 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.27), residues: 1015 helix: 0.21 (0.26), residues: 398 sheet: -2.07 (0.34), residues: 197 loop : -1.18 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 96 TYR 0.022 0.002 TYR N 60 PHE 0.033 0.002 PHE A 222 TRP 0.080 0.003 TRP B 99 HIS 0.008 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 8285) covalent geometry : angle 0.68326 / 0.34 (11246) SS BOND : bond 0.00060 / 0.03 ( 4) SS BOND : angle 1.05175 / 0.61 ( 8) hydrogen bonds : bond 0.03352 / 2.29 ( 396) hydrogen bonds : angle 5.30725 / 3.59 ( 1116) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 273 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7015 (mmm160) cc_final: 0.6638 (mtp85) REVERT: A 267 GLN cc_start: 0.8685 (tp40) cc_final: 0.8170 (tp40) REVERT: A 268 GLU cc_start: 0.8008 (tt0) cc_final: 0.7381 (tt0) REVERT: A 318 TYR cc_start: 0.7243 (t80) cc_final: 0.6915 (t80) REVERT: A 336 ARG cc_start: 0.8442 (tmm-80) cc_final: 0.8239 (ptm160) REVERT: A 339 TYR cc_start: 0.8864 (m-80) cc_final: 0.8001 (m-80) REVERT: A 343 ASP cc_start: 0.7931 (m-30) cc_final: 0.7574 (m-30) REVERT: A 381 ASP cc_start: 0.7804 (m-30) cc_final: 0.7560 (m-30) REVERT: B 88 ASN cc_start: 0.8568 (m-40) cc_final: 0.8270 (t0) REVERT: B 118 ASP cc_start: 0.7441 (t0) cc_final: 0.7107 (t0) REVERT: B 119 ASN cc_start: 0.6598 (m-40) cc_final: 0.6224 (m-40) REVERT: B 161 SER cc_start: 0.9198 (t) cc_final: 0.8991 (t) REVERT: B 205 ASP cc_start: 0.7774 (p0) cc_final: 0.7388 (p0) REVERT: B 210 LEU cc_start: 0.8932 (tp) cc_final: 0.8488 (tp) REVERT: B 217 MET cc_start: 0.7548 (ppp) cc_final: 0.7236 (ppp) REVERT: B 258 ASP cc_start: 0.7217 (t0) cc_final: 0.6856 (t0) REVERT: B 296 VAL cc_start: 0.9151 (t) cc_final: 0.8738 (p) REVERT: G 20 LYS cc_start: 0.8863 (mtmm) cc_final: 0.8416 (mtmm) REVERT: N 29 PHE cc_start: 0.8654 (t80) cc_final: 0.8405 (t80) REVERT: N 31 ASN cc_start: 0.8569 (m-40) cc_final: 0.8292 (t0) REVERT: N 33 LYS cc_start: 0.8994 (ttmm) cc_final: 0.8599 (ptmm) REVERT: N 43 LYS cc_start: 0.6312 (mttm) cc_final: 0.5598 (mtpt) REVERT: R 138 LYS cc_start: 0.8369 (tmtt) cc_final: 0.8143 (tppt) REVERT: R 327 ASN cc_start: 0.8070 (OUTLIER) cc_final: 0.7442 (t0) REVERT: R 333 PHE cc_start: 0.5659 (t80) cc_final: 0.4987 (t80) outliers start: 43 outliers final: 35 residues processed: 293 average time/residue: 0.0840 time to fit residues: 34.3946 Evaluate side-chains 303 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 267 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 92 PHE Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 327 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.163308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.131828 restraints weight = 11757.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.136723 restraints weight = 6420.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.140012 restraints weight = 4361.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.142105 restraints weight = 3396.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.143608 restraints weight = 2874.132| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8289 Z= 0.166 Angle : 0.696 15.374 11254 Z= 0.344 Chirality : 0.045 0.226 1283 Planarity : 0.004 0.042 1418 Dihedral : 5.190 50.960 1141 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 5.11 % Allowed : 27.87 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.27), residues: 1015 helix: 0.22 (0.26), residues: 398 sheet: -2.04 (0.35), residues: 194 loop : -1.20 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 96 TYR 0.024 0.002 TYR N 95 PHE 0.027 0.001 PHE A 222 TRP 0.060 0.003 TRP B 99 HIS 0.007 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 8285) covalent geometry : angle 0.69511 / 0.34 (11246) SS BOND : bond 0.00326 / 0.16 ( 4) SS BOND : angle 1.13202 / 0.66 ( 8) hydrogen bonds : bond 0.03329 / 2.28 ( 396) hydrogen bonds : angle 5.26263 / 3.57 ( 1116) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 266 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7041 (mmm160) cc_final: 0.6603 (mtp85) REVERT: A 267 GLN cc_start: 0.8652 (tp40) cc_final: 0.8179 (tp40) REVERT: A 268 GLU cc_start: 0.8023 (tt0) cc_final: 0.7358 (tt0) REVERT: A 343 ASP cc_start: 0.7921 (m-30) cc_final: 0.7547 (m-30) REVERT: B 57 LYS cc_start: 0.8853 (pttm) cc_final: 0.8640 (pttp) REVERT: B 88 ASN cc_start: 0.8591 (m-40) cc_final: 0.8326 (t0) REVERT: B 98 SER cc_start: 0.8130 (m) cc_final: 0.7432 (t) REVERT: B 118 ASP cc_start: 0.7436 (t0) cc_final: 0.7098 (t0) REVERT: B 205 ASP cc_start: 0.7745 (p0) cc_final: 0.7371 (p0) REVERT: B 210 LEU cc_start: 0.8919 (tp) cc_final: 0.8495 (tp) REVERT: B 217 MET cc_start: 0.7470 (ppp) cc_final: 0.7203 (ppp) REVERT: B 225 HIS cc_start: 0.7906 (OUTLIER) cc_final: 0.7470 (t-90) REVERT: B 258 ASP cc_start: 0.7216 (t0) cc_final: 0.6854 (t0) REVERT: B 296 VAL cc_start: 0.9114 (t) cc_final: 0.8721 (p) REVERT: G 20 LYS cc_start: 0.8861 (mtmm) cc_final: 0.8422 (mtmm) REVERT: N 31 ASN cc_start: 0.8538 (m-40) cc_final: 0.8298 (t0) REVERT: N 33 LYS cc_start: 0.8934 (ttmm) cc_final: 0.8706 (ptmm) REVERT: N 43 LYS cc_start: 0.6202 (mttm) cc_final: 0.5559 (mtpt) REVERT: R 138 LYS cc_start: 0.8384 (tmtt) cc_final: 0.8129 (tppt) REVERT: R 327 ASN cc_start: 0.8273 (t0) cc_final: 0.8007 (t0) REVERT: R 333 PHE cc_start: 0.5558 (t80) cc_final: 0.4923 (t80) outliers start: 44 outliers final: 36 residues processed: 288 average time/residue: 0.0859 time to fit residues: 34.5751 Evaluate side-chains 293 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 256 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 61 PHE Chi-restraints excluded: chain R residue 92 PHE Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 51 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 97 optimal weight: 0.0370 chunk 86 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 12 optimal weight: 0.0870 chunk 57 optimal weight: 0.5980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.166905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.136712 restraints weight = 11685.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.141607 restraints weight = 6283.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.144872 restraints weight = 4248.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.147110 restraints weight = 3273.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.148515 restraints weight = 2737.650| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8289 Z= 0.144 Angle : 0.706 11.232 11254 Z= 0.351 Chirality : 0.045 0.244 1283 Planarity : 0.004 0.042 1418 Dihedral : 5.221 51.501 1141 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.95 % Allowed : 29.97 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.26), residues: 1015 helix: 0.15 (0.26), residues: 400 sheet: -2.00 (0.36), residues: 180 loop : -1.22 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 251 TYR 0.023 0.001 TYR N 95 PHE 0.028 0.002 PHE A 222 TRP 0.065 0.003 TRP B 99 HIS 0.007 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 8285) covalent geometry : angle 0.70584 / 0.35 (11246) SS BOND : bond 0.00205 / 0.10 ( 4) SS BOND : angle 1.18421 / 0.67 ( 8) hydrogen bonds : bond 0.03261 / 2.24 ( 396) hydrogen bonds : angle 5.23576 / 3.56 ( 1116) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 260 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8129 (ttp-110) cc_final: 0.7844 (ttm110) REVERT: A 265 ARG cc_start: 0.6993 (mmm160) cc_final: 0.6608 (mtp85) REVERT: A 267 GLN cc_start: 0.8598 (tp40) cc_final: 0.8095 (tp-100) REVERT: A 268 GLU cc_start: 0.7947 (tt0) cc_final: 0.7246 (tt0) REVERT: A 336 ARG cc_start: 0.8279 (ttt90) cc_final: 0.6684 (tpt-90) REVERT: A 343 ASP cc_start: 0.7897 (m-30) cc_final: 0.7272 (m-30) REVERT: B 98 SER cc_start: 0.7635 (m) cc_final: 0.7064 (t) REVERT: B 118 ASP cc_start: 0.7252 (t0) cc_final: 0.6995 (t0) REVERT: B 205 ASP cc_start: 0.7714 (p0) cc_final: 0.7339 (p0) REVERT: B 217 MET cc_start: 0.7528 (ppp) cc_final: 0.7225 (ppp) REVERT: B 225 HIS cc_start: 0.7835 (OUTLIER) cc_final: 0.7391 (t-90) REVERT: B 296 VAL cc_start: 0.9061 (t) cc_final: 0.8653 (p) REVERT: G 20 LYS cc_start: 0.8823 (mtmm) cc_final: 0.8388 (mtmm) REVERT: N 31 ASN cc_start: 0.8541 (m-40) cc_final: 0.8335 (t0) REVERT: N 33 LYS cc_start: 0.8850 (ttmm) cc_final: 0.8521 (ptmm) REVERT: N 43 LYS cc_start: 0.6102 (mttm) cc_final: 0.5465 (mtpt) REVERT: R 132 GLU cc_start: 0.8183 (tp30) cc_final: 0.7966 (tp30) REVERT: R 138 LYS cc_start: 0.8376 (tmtt) cc_final: 0.8133 (tppt) REVERT: R 327 ASN cc_start: 0.8228 (t0) cc_final: 0.7941 (t0) REVERT: R 333 PHE cc_start: 0.5526 (t80) cc_final: 0.4463 (t80) outliers start: 34 outliers final: 29 residues processed: 279 average time/residue: 0.0905 time to fit residues: 34.7224 Evaluate side-chains 281 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 251 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 61 PHE Chi-restraints excluded: chain R residue 92 PHE Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 78 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 55 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.165551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.134091 restraints weight = 11792.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.139043 restraints weight = 6470.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.142306 restraints weight = 4430.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.144480 restraints weight = 3438.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.145967 restraints weight = 2902.089| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8289 Z= 0.159 Angle : 0.709 12.165 11254 Z= 0.354 Chirality : 0.045 0.225 1283 Planarity : 0.004 0.042 1418 Dihedral : 5.137 51.335 1139 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.95 % Allowed : 31.01 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.27), residues: 1015 helix: 0.25 (0.26), residues: 392 sheet: -1.95 (0.36), residues: 181 loop : -1.05 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 336 TYR 0.023 0.001 TYR N 95 PHE 0.027 0.002 PHE A 222 TRP 0.063 0.003 TRP B 99 HIS 0.007 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 8285) covalent geometry : angle 0.70487 / 0.35 (11246) SS BOND : bond 0.00161 / 0.08 ( 4) SS BOND : angle 2.78755 / 1.48 ( 8) hydrogen bonds : bond 0.03279 / 2.24 ( 396) hydrogen bonds : angle 5.24818 / 3.56 ( 1116) =============================================================================== Job complete usr+sys time: 1741.34 seconds wall clock time: 30 minutes 53.88 seconds (1853.88 seconds total)