Starting phenix.real_space_refine on Sat Aug 23 00:15:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fls_29285/08_2025/8fls_29285.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fls_29285/08_2025/8fls_29285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fls_29285/08_2025/8fls_29285.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fls_29285/08_2025/8fls_29285.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fls_29285/08_2025/8fls_29285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fls_29285/08_2025/8fls_29285.map" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5637 2.51 5 N 1543 2.21 5 O 1610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8844 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1900 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2542 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 32 Chain: "G" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 383 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "N" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 953 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 266 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 2800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2800 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain breaks: 3 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 2, 'HIS:plan': 2, 'ARG:plan': 7, 'ASP:plan': 2, 'ASN:plan1': 4, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 115 Time building chain proxies: 2.18, per 1000 atoms: 0.25 Number of scatterers: 8844 At special positions: 0 Unit cell: (73.1, 96.9, 170.85, 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 54 16.00 O 1610 8.00 N 1543 7.00 C 5637 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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=2.01 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " 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: 0.89 Conformation dependent library (CDL) restraints added in 458.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2146 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 43.5% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.720A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 63 Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.997A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.631A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.544A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.867A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.553A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.827A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 25 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 2 through 32 Processing helix chain 'R' and resid 33 through 54 Processing helix chain 'R' and resid 168 through 172 removed outlier: 3.688A pdb=" N LYS R 172 " --> pdb=" O GLU R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 212 removed outlier: 3.958A pdb=" N ARG R 181 " --> pdb=" O GLU R 177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 244 Processing helix chain 'R' and resid 278 through 312 removed outlier: 3.562A pdb=" N ARG R 282 " --> pdb=" O TYR R 278 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 319 Processing helix chain 'R' and resid 320 through 347 Proline residue: R 332 - end of helix Processing helix chain 'R' and resid 357 through 359 No H-bonds generated for 'chain 'R' and resid 357 through 359' Processing helix chain 'R' and resid 360 through 391 Proline residue: R 366 - end of helix removed outlier: 3.716A pdb=" N ILE R 381 " --> pdb=" O LEU R 377 " (cutoff:3.500A) Processing helix chain 'R' and resid 400 through 418 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 420 through 425 removed outlier: 4.001A pdb=" N PHE R 424 " --> pdb=" O HIS R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 434 through 460 removed outlier: 4.548A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 478 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.378A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.445A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.669A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.864A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.788A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.505A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.977A 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: 6.977A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.157A 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: 3.573A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.613A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (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 58 through 60 removed outlier: 6.434A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 111 through 112 Processing sheet with id=AB3, first strand: chain 'R' and resid 125 through 130 removed outlier: 3.560A pdb=" N GLU R 125 " --> pdb=" O CYS R 148 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS R 148 " --> pdb=" O GLU R 125 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1341 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: 1.41 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: 1.20 - 1.32: 1484 1.32 - 1.44: 2523 1.44 - 1.57: 4960 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 9041 Sorted by residual: bond pdb=" CA SER B 331 " pdb=" CB SER B 331 " ideal model delta sigma weight residual 1.532 1.479 0.053 1.68e-02 3.54e+03 9.89e+00 bond pdb=" C PRO N 100 " pdb=" O PRO N 100 " ideal model delta sigma weight residual 1.237 1.199 0.038 1.26e-02 6.30e+03 9.31e+00 bond pdb=" N THR N 111 " pdb=" CA THR N 111 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.10e-02 8.26e+03 9.27e+00 bond pdb=" N VAL B 71 " pdb=" CA VAL B 71 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.14e-02 7.69e+03 9.22e+00 bond pdb=" N VAL B 315 " pdb=" CA VAL B 315 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.10e-02 8.26e+03 8.75e+00 ... (remaining 9036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 11701 1.53 - 3.06: 472 3.06 - 4.59: 83 4.59 - 6.13: 18 6.13 - 7.66: 5 Bond angle restraints: 12279 Sorted by residual: angle pdb=" N HIS R 223 " pdb=" CA HIS R 223 " pdb=" C HIS R 223 " ideal model delta sigma weight residual 110.97 105.65 5.32 1.09e+00 8.42e-01 2.38e+01 angle pdb=" N VAL R 365 " pdb=" CA VAL R 365 " pdb=" CB VAL R 365 " ideal model delta sigma weight residual 110.50 113.45 -2.95 6.30e-01 2.52e+00 2.19e+01 angle pdb=" C PHE R 335 " pdb=" CA PHE R 335 " pdb=" CB PHE R 335 " ideal model delta sigma weight residual 110.85 118.51 -7.66 1.70e+00 3.46e-01 2.03e+01 angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 113.15 108.12 5.03 1.19e+00 7.06e-01 1.78e+01 angle pdb=" N ASP B 333 " pdb=" CA ASP B 333 " pdb=" C ASP B 333 " ideal model delta sigma weight residual 113.15 108.15 5.00 1.19e+00 7.06e-01 1.77e+01 ... (remaining 12274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4805 17.73 - 35.47: 407 35.47 - 53.20: 76 53.20 - 70.94: 17 70.94 - 88.67: 7 Dihedral angle restraints: 5312 sinusoidal: 1989 harmonic: 3323 Sorted by residual: dihedral pdb=" C PHE R 335 " pdb=" N PHE R 335 " pdb=" CA PHE R 335 " pdb=" CB PHE R 335 " ideal model delta harmonic sigma weight residual -122.60 -136.96 14.36 0 2.50e+00 1.60e-01 3.30e+01 dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual 93.00 138.66 -45.66 1 1.00e+01 1.00e-02 2.89e+01 dihedral pdb=" CA LEU A 291 " pdb=" C LEU A 291 " pdb=" N ASN A 292 " pdb=" CA ASN A 292 " ideal model delta harmonic sigma weight residual -180.00 -155.43 -24.57 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 5309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1279 0.095 - 0.190: 86 0.190 - 0.285: 12 0.285 - 0.379: 1 0.379 - 0.474: 1 Chirality restraints: 1379 Sorted by residual: chirality pdb=" CA PHE R 335 " pdb=" N PHE R 335 " pdb=" C PHE R 335 " pdb=" CB PHE R 335 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" CA LYS B 57 " pdb=" N LYS B 57 " pdb=" C LYS B 57 " pdb=" CB LYS B 57 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 1376 not shown) Planarity restraints: 1563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 427 " 0.060 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO R 428 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO R 428 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO R 428 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 360 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.08e+00 pdb=" C LYS R 360 " -0.043 2.00e-02 2.50e+03 pdb=" O LYS R 360 " 0.016 2.00e-02 2.50e+03 pdb=" N TRP R 361 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.040 5.00e-02 4.00e+02 6.16e-02 6.07e+00 pdb=" N PRO G 49 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.034 5.00e-02 4.00e+02 ... (remaining 1560 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1654 2.77 - 3.30: 8570 3.30 - 3.84: 15321 3.84 - 4.37: 18156 4.37 - 4.90: 31472 Nonbonded interactions: 75173 Sorted by model distance: nonbonded pdb=" OE2 GLU P 4 " pdb=" OH TYR R 195 " model vdw 2.239 3.040 nonbonded pdb=" OD1 ASP P 17 " pdb=" NH2 ARG P 20 " model vdw 2.255 3.120 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.265 3.040 nonbonded pdb=" O ALA A 48 " pdb=" OG SER A 51 " model vdw 2.304 3.040 nonbonded pdb=" NH2 ARG B 8 " pdb=" OE1 GLN N 120 " model vdw 2.309 3.120 ... (remaining 75168 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.830 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 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 : 0.004 0.057 9047 Z= 0.279 Angle : 0.701 7.657 12291 Z= 0.454 Chirality : 0.054 0.474 1379 Planarity : 0.005 0.091 1563 Dihedral : 14.012 88.671 3148 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.11 % Allowed : 1.00 % Favored : 97.89 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.25), residues: 1119 helix: 2.25 (0.24), residues: 432 sheet: -0.60 (0.34), residues: 209 loop : -0.02 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 42 TYR 0.011 0.001 TYR R 296 PHE 0.023 0.002 PHE R 447 TRP 0.021 0.002 TRP B 339 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 9041) covalent geometry : angle 0.69972 (12279) SS BOND : bond 0.00860 ( 6) SS BOND : angle 1.32742 ( 12) hydrogen bonds : bond 0.13608 ( 472) hydrogen bonds : angle 5.89755 ( 1341) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.304 Fit side-chains REVERT: B 59 TYR cc_start: 0.7369 (OUTLIER) cc_final: 0.7062 (t80) REVERT: N 105 ARG cc_start: 0.7528 (ttt90) cc_final: 0.7185 (tmt170) outliers start: 10 outliers final: 4 residues processed: 136 average time/residue: 0.1237 time to fit residues: 22.2393 Evaluate side-chains 120 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain R residue 363 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 220 GLN N 31 ASN ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.189828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.151611 restraints weight = 9662.745| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.84 r_work: 0.3552 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9047 Z= 0.150 Angle : 0.536 7.005 12291 Z= 0.289 Chirality : 0.042 0.202 1379 Planarity : 0.004 0.068 1563 Dihedral : 4.859 52.770 1252 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.44 % Allowed : 7.55 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.25), residues: 1119 helix: 2.49 (0.24), residues: 433 sheet: -0.73 (0.34), residues: 211 loop : -0.08 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 42 TYR 0.030 0.002 TYR R 191 PHE 0.037 0.002 PHE R 335 TRP 0.018 0.002 TRP B 339 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9041) covalent geometry : angle 0.53589 (12279) SS BOND : bond 0.00348 ( 6) SS BOND : angle 0.90677 ( 12) hydrogen bonds : bond 0.04325 ( 472) hydrogen bonds : angle 4.74600 ( 1341) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.402 Fit side-chains REVERT: A 58 LYS cc_start: 0.7640 (mtpt) cc_final: 0.7293 (tttm) REVERT: A 299 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6011 (mp0) REVERT: B 59 TYR cc_start: 0.7983 (OUTLIER) cc_final: 0.7337 (t80) REVERT: N 34 MET cc_start: 0.8528 (mmm) cc_final: 0.8304 (mmm) REVERT: N 105 ARG cc_start: 0.8103 (ttt90) cc_final: 0.7060 (tmt170) outliers start: 13 outliers final: 9 residues processed: 120 average time/residue: 0.1245 time to fit residues: 19.8652 Evaluate side-chains 117 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 430 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 94 optimal weight: 0.0980 chunk 96 optimal weight: 3.9990 chunk 46 optimal weight: 0.0070 chunk 93 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 106 optimal weight: 0.4980 chunk 107 optimal weight: 4.9990 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.193882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.156567 restraints weight = 9596.009| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.77 r_work: 0.3621 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9047 Z= 0.099 Angle : 0.467 6.205 12291 Z= 0.253 Chirality : 0.040 0.197 1379 Planarity : 0.004 0.055 1563 Dihedral : 4.445 47.831 1250 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.22 % Allowed : 8.55 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.26), residues: 1119 helix: 2.81 (0.24), residues: 432 sheet: -0.56 (0.33), residues: 211 loop : 0.01 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 42 TYR 0.027 0.001 TYR R 191 PHE 0.031 0.001 PHE R 335 TRP 0.014 0.001 TRP B 339 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 9041) covalent geometry : angle 0.46654 (12279) SS BOND : bond 0.00200 ( 6) SS BOND : angle 0.61747 ( 12) hydrogen bonds : bond 0.03693 ( 472) hydrogen bonds : angle 4.40804 ( 1341) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.352 Fit side-chains REVERT: A 58 LYS cc_start: 0.7733 (mtpt) cc_final: 0.7344 (tttm) REVERT: A 299 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6075 (mp0) REVERT: B 59 TYR cc_start: 0.7775 (OUTLIER) cc_final: 0.7255 (t80) REVERT: N 105 ARG cc_start: 0.8026 (ttt90) cc_final: 0.6933 (tmt170) REVERT: R 335 PHE cc_start: 0.6378 (p90) cc_final: 0.6083 (p90) outliers start: 11 outliers final: 7 residues processed: 131 average time/residue: 0.1237 time to fit residues: 21.5407 Evaluate side-chains 125 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 302 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 82 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 96 optimal weight: 0.0040 chunk 62 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 46 optimal weight: 0.0970 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.187654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.150112 restraints weight = 9815.648| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.72 r_work: 0.3541 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9047 Z= 0.174 Angle : 0.546 7.986 12291 Z= 0.292 Chirality : 0.043 0.224 1379 Planarity : 0.004 0.061 1563 Dihedral : 4.566 48.529 1247 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.44 % Allowed : 11.10 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.26), residues: 1119 helix: 2.53 (0.25), residues: 433 sheet: -0.71 (0.33), residues: 215 loop : -0.10 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 42 TYR 0.027 0.002 TYR R 191 PHE 0.029 0.002 PHE R 335 TRP 0.014 0.002 TRP A 234 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 9041) covalent geometry : angle 0.54526 (12279) SS BOND : bond 0.00450 ( 6) SS BOND : angle 1.04241 ( 12) hydrogen bonds : bond 0.04188 ( 472) hydrogen bonds : angle 4.61150 ( 1341) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.350 Fit side-chains REVERT: A 58 LYS cc_start: 0.7702 (mtpt) cc_final: 0.7406 (ttpp) REVERT: A 299 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6077 (mp0) REVERT: B 59 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.7332 (t80) REVERT: N 105 ARG cc_start: 0.7986 (ttt90) cc_final: 0.6971 (tmt170) REVERT: R 335 PHE cc_start: 0.6526 (p90) cc_final: 0.6156 (p90) REVERT: R 469 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7180 (mm-30) outliers start: 13 outliers final: 11 residues processed: 123 average time/residue: 0.1161 time to fit residues: 19.2661 Evaluate side-chains 125 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 430 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 81 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 0.0270 chunk 63 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 78 optimal weight: 30.0000 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 225 HIS ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.185991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.148347 restraints weight = 9696.715| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.64 r_work: 0.3528 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9047 Z= 0.192 Angle : 0.563 8.380 12291 Z= 0.301 Chirality : 0.043 0.238 1379 Planarity : 0.004 0.063 1563 Dihedral : 4.689 47.663 1246 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.00 % Allowed : 12.65 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.25), residues: 1119 helix: 2.34 (0.25), residues: 432 sheet: -0.75 (0.33), residues: 215 loop : -0.22 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 42 TYR 0.027 0.002 TYR R 191 PHE 0.028 0.002 PHE R 335 TRP 0.016 0.002 TRP A 234 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 9041) covalent geometry : angle 0.56287 (12279) SS BOND : bond 0.00479 ( 6) SS BOND : angle 0.92321 ( 12) hydrogen bonds : bond 0.04298 ( 472) hydrogen bonds : angle 4.71204 ( 1341) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.346 Fit side-chains REVERT: A 299 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.5907 (mp0) REVERT: B 59 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.7377 (t80) REVERT: N 105 ARG cc_start: 0.8076 (ttt90) cc_final: 0.7038 (tmt170) outliers start: 18 outliers final: 14 residues processed: 118 average time/residue: 0.1187 time to fit residues: 18.7904 Evaluate side-chains 123 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 430 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.185442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.147685 restraints weight = 9681.750| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.64 r_work: 0.3513 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9047 Z= 0.199 Angle : 0.571 8.654 12291 Z= 0.305 Chirality : 0.043 0.195 1379 Planarity : 0.004 0.064 1563 Dihedral : 4.771 47.899 1246 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.33 % Allowed : 12.87 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.25), residues: 1119 helix: 2.19 (0.24), residues: 438 sheet: -0.69 (0.32), residues: 217 loop : -0.21 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 42 TYR 0.027 0.002 TYR R 191 PHE 0.028 0.002 PHE R 335 TRP 0.017 0.002 TRP A 234 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 9041) covalent geometry : angle 0.57037 (12279) SS BOND : bond 0.00503 ( 6) SS BOND : angle 0.92542 ( 12) hydrogen bonds : bond 0.04346 ( 472) hydrogen bonds : angle 4.76582 ( 1341) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.348 Fit side-chains REVERT: A 299 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.5849 (mp0) REVERT: B 59 TYR cc_start: 0.7901 (OUTLIER) cc_final: 0.7386 (t80) REVERT: N 105 ARG cc_start: 0.8111 (ttt90) cc_final: 0.7061 (tmt170) REVERT: R 335 PHE cc_start: 0.6608 (p90) cc_final: 0.6181 (p90) REVERT: R 447 PHE cc_start: 0.5611 (OUTLIER) cc_final: 0.5081 (m-10) outliers start: 21 outliers final: 16 residues processed: 121 average time/residue: 0.1197 time to fit residues: 19.4766 Evaluate side-chains 125 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 447 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 82 optimal weight: 40.0000 chunk 67 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 78 optimal weight: 30.0000 chunk 103 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.188885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.151728 restraints weight = 9706.314| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.61 r_work: 0.3573 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9047 Z= 0.126 Angle : 0.498 6.842 12291 Z= 0.268 Chirality : 0.041 0.239 1379 Planarity : 0.004 0.059 1563 Dihedral : 4.465 46.695 1246 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.89 % Allowed : 14.10 % Favored : 84.02 % 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 aren not related in a simple way. whole: 1.30 (0.26), residues: 1119 helix: 2.70 (0.25), residues: 424 sheet: -0.64 (0.32), residues: 219 loop : -0.01 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 42 TYR 0.025 0.001 TYR R 191 PHE 0.027 0.001 PHE R 335 TRP 0.017 0.001 TRP R 298 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9041) covalent geometry : angle 0.49738 (12279) SS BOND : bond 0.00253 ( 6) SS BOND : angle 1.06350 ( 12) hydrogen bonds : bond 0.03848 ( 472) hydrogen bonds : angle 4.54161 ( 1341) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.341 Fit side-chains REVERT: A 299 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6106 (mp0) REVERT: B 59 TYR cc_start: 0.7842 (OUTLIER) cc_final: 0.7373 (t80) REVERT: N 105 ARG cc_start: 0.8063 (ttt90) cc_final: 0.6982 (tmt170) REVERT: R 335 PHE cc_start: 0.6357 (p90) cc_final: 0.5981 (p90) REVERT: R 447 PHE cc_start: 0.5597 (OUTLIER) cc_final: 0.4974 (m-10) outliers start: 17 outliers final: 11 residues processed: 123 average time/residue: 0.1150 time to fit residues: 18.9950 Evaluate side-chains 121 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 447 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 82 optimal weight: 20.0000 chunk 26 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.186096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.148614 restraints weight = 9746.807| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.64 r_work: 0.3522 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9047 Z= 0.184 Angle : 0.555 8.134 12291 Z= 0.295 Chirality : 0.043 0.253 1379 Planarity : 0.004 0.063 1563 Dihedral : 4.653 47.735 1246 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.00 % Allowed : 14.76 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.26), residues: 1119 helix: 2.39 (0.25), residues: 432 sheet: -0.66 (0.32), residues: 219 loop : -0.14 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 42 TYR 0.027 0.002 TYR R 191 PHE 0.027 0.002 PHE R 335 TRP 0.016 0.002 TRP A 234 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 9041) covalent geometry : angle 0.55352 (12279) SS BOND : bond 0.00543 ( 6) SS BOND : angle 1.28478 ( 12) hydrogen bonds : bond 0.04193 ( 472) hydrogen bonds : angle 4.69518 ( 1341) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.319 Fit side-chains REVERT: A 299 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6064 (mp0) REVERT: B 59 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.7382 (t80) REVERT: N 105 ARG cc_start: 0.8099 (ttt90) cc_final: 0.7046 (tmt170) REVERT: R 335 PHE cc_start: 0.6542 (p90) cc_final: 0.6109 (p90) REVERT: R 447 PHE cc_start: 0.5563 (OUTLIER) cc_final: 0.4985 (m-10) outliers start: 18 outliers final: 15 residues processed: 118 average time/residue: 0.1150 time to fit residues: 17.9845 Evaluate side-chains 125 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 447 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 78 optimal weight: 50.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.186802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.149342 restraints weight = 9651.189| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.64 r_work: 0.3529 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9047 Z= 0.168 Angle : 0.538 7.514 12291 Z= 0.288 Chirality : 0.042 0.253 1379 Planarity : 0.004 0.061 1563 Dihedral : 4.621 47.599 1246 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.11 % Allowed : 14.87 % Favored : 83.02 % 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 aren not related in a simple way. whole: 1.17 (0.26), residues: 1119 helix: 2.52 (0.25), residues: 425 sheet: -0.60 (0.33), residues: 217 loop : -0.08 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 42 TYR 0.027 0.002 TYR R 191 PHE 0.027 0.002 PHE R 335 TRP 0.018 0.002 TRP B 332 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9041) covalent geometry : angle 0.53744 (12279) SS BOND : bond 0.00485 ( 6) SS BOND : angle 1.13120 ( 12) hydrogen bonds : bond 0.04099 ( 472) hydrogen bonds : angle 4.66705 ( 1341) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.334 Fit side-chains REVERT: A 299 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6850 (mp0) REVERT: B 59 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.7368 (t80) REVERT: N 105 ARG cc_start: 0.8088 (ttt90) cc_final: 0.7043 (tmt170) REVERT: R 335 PHE cc_start: 0.6497 (p90) cc_final: 0.6064 (p90) REVERT: R 447 PHE cc_start: 0.5607 (OUTLIER) cc_final: 0.5030 (m-10) outliers start: 19 outliers final: 15 residues processed: 116 average time/residue: 0.1179 time to fit residues: 18.1904 Evaluate side-chains 122 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 447 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 0.0050 chunk 65 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.190908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.156096 restraints weight = 9640.824| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.60 r_work: 0.3576 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9047 Z= 0.106 Angle : 0.481 6.786 12291 Z= 0.259 Chirality : 0.040 0.241 1379 Planarity : 0.004 0.056 1563 Dihedral : 4.314 46.403 1246 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.66 % Allowed : 15.21 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.26), residues: 1119 helix: 2.82 (0.25), residues: 424 sheet: -0.52 (0.32), residues: 220 loop : 0.08 (0.31), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 42 TYR 0.025 0.001 TYR R 191 PHE 0.027 0.001 PHE R 335 TRP 0.018 0.001 TRP R 298 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 9041) covalent geometry : angle 0.48059 (12279) SS BOND : bond 0.00317 ( 6) SS BOND : angle 0.99406 ( 12) hydrogen bonds : bond 0.03667 ( 472) hydrogen bonds : angle 4.44125 ( 1341) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.341 Fit side-chains REVERT: A 299 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6846 (mp0) REVERT: B 59 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.7284 (t80) REVERT: N 38 ARG cc_start: 0.8247 (ptt180) cc_final: 0.8019 (ptp90) REVERT: N 105 ARG cc_start: 0.8030 (ttt90) cc_final: 0.6931 (tmt170) REVERT: R 335 PHE cc_start: 0.6342 (p90) cc_final: 0.5978 (p90) REVERT: R 447 PHE cc_start: 0.5521 (OUTLIER) cc_final: 0.4852 (m-10) outliers start: 15 outliers final: 10 residues processed: 124 average time/residue: 0.1199 time to fit residues: 19.8694 Evaluate side-chains 124 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 447 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 7 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 82 optimal weight: 20.0000 chunk 101 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 11 optimal weight: 0.0770 chunk 4 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.188992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.152007 restraints weight = 9564.816| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.64 r_work: 0.3571 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9047 Z= 0.136 Angle : 0.504 6.848 12291 Z= 0.269 Chirality : 0.041 0.252 1379 Planarity : 0.004 0.057 1563 Dihedral : 4.377 46.818 1246 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.55 % Allowed : 14.98 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.26), residues: 1119 helix: 2.76 (0.25), residues: 425 sheet: -0.59 (0.32), residues: 222 loop : 0.13 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 42 TYR 0.026 0.001 TYR R 191 PHE 0.027 0.001 PHE R 335 TRP 0.016 0.002 TRP A 234 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9041) covalent geometry : angle 0.50321 (12279) SS BOND : bond 0.00408 ( 6) SS BOND : angle 1.15863 ( 12) hydrogen bonds : bond 0.03840 ( 472) hydrogen bonds : angle 4.48759 ( 1341) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2555.43 seconds wall clock time: 44 minutes 36.46 seconds (2676.46 seconds total)