Starting phenix.real_space_refine on Sat Jun 7 12:10:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fls_29285/06_2025/8fls_29285.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fls_29285/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fls_29285/06_2025/8fls_29285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fls_29285/06_2025/8fls_29285.map" model { file = "/net/cci-nas-00/data/ceres_data/8fls_29285/06_2025/8fls_29285.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fls_29285/06_2025/8fls_29285.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 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, 'ASN:plan1': 1, 'ASP:plan': 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, 'GLU:plan': 1, 'ASN:plan1': 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: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 115 Time building chain proxies: 5.39, per 1000 atoms: 0.61 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: 2.22 Conformation dependent library (CDL) restraints added in 991.2 milliseconds 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: 0.90 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: 2.49 Time building geometry restraints manager: 2.64 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: 1.630 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.350 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.340 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.021 0.002 TRP B 339 HIS 0.007 0.001 HIS A 357 PHE 0.023 0.002 PHE R 447 TYR 0.011 0.001 TYR R 296 ARG 0.007 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.13608 ( 472) hydrogen bonds : angle 5.89755 ( 1341) SS BOND : bond 0.00860 ( 6) SS BOND : angle 1.32742 ( 12) covalent geometry : bond 0.00433 ( 9041) covalent geometry : angle 0.69972 (12279) *********************** 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 : 0.894 Fit side-chains REVERT: B 59 TYR cc_start: 0.7369 (OUTLIER) cc_final: 0.7052 (t80) REVERT: N 105 ARG cc_start: 0.7528 (ttt90) cc_final: 0.7215 (tmt170) outliers start: 10 outliers final: 4 residues processed: 136 average time/residue: 0.2495 time to fit residues: 44.9437 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 : 0.893 ------------------------------------------------------------------------------- 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 94 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 57 optimal weight: 0.3980 chunk 45 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.192232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.154048 restraints weight = 9547.319| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.70 r_work: 0.3590 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9047 Z= 0.123 Angle : 0.508 6.306 12291 Z= 0.275 Chirality : 0.041 0.193 1379 Planarity : 0.004 0.068 1563 Dihedral : 4.735 53.653 1252 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.11 % Allowed : 7.44 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.25), residues: 1119 helix: 2.61 (0.24), residues: 433 sheet: -0.68 (0.34), residues: 211 loop : -0.02 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 339 HIS 0.005 0.001 HIS A 357 PHE 0.036 0.001 PHE R 335 TYR 0.030 0.001 TYR R 191 ARG 0.005 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 472) hydrogen bonds : angle 4.64884 ( 1341) SS BOND : bond 0.00322 ( 6) SS BOND : angle 0.84900 ( 12) covalent geometry : bond 0.00265 ( 9041) covalent geometry : angle 0.50712 (12279) *********************** 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 130 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.889 Fit side-chains REVERT: A 58 LYS cc_start: 0.7727 (mtpt) cc_final: 0.7382 (tttm) REVERT: A 299 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6024 (mp0) REVERT: B 59 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7388 (t80) REVERT: N 34 MET cc_start: 0.8451 (mmm) cc_final: 0.8242 (mmm) REVERT: N 105 ARG cc_start: 0.8055 (ttt90) cc_final: 0.7025 (tmt170) outliers start: 10 outliers final: 6 residues processed: 124 average time/residue: 0.2655 time to fit residues: 43.6939 Evaluate side-chains 117 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 72 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain R residue 363 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 chunk 93 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.192745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.154554 restraints weight = 9690.306| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.80 r_work: 0.3586 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1152 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= 0.114 Angle : 0.482 6.314 12291 Z= 0.260 Chirality : 0.040 0.161 1379 Planarity : 0.004 0.054 1563 Dihedral : 4.492 49.381 1250 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.33 % Allowed : 8.88 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.26), residues: 1119 helix: 2.80 (0.24), residues: 432 sheet: -0.56 (0.34), residues: 211 loop : 0.03 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.005 0.001 HIS A 357 PHE 0.030 0.001 PHE R 335 TYR 0.030 0.001 TYR R 191 ARG 0.005 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 472) hydrogen bonds : angle 4.43698 ( 1341) SS BOND : bond 0.00271 ( 6) SS BOND : angle 0.78974 ( 12) covalent geometry : bond 0.00247 ( 9041) covalent geometry : angle 0.48120 (12279) *********************** 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 133 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.991 Fit side-chains REVERT: A 58 LYS cc_start: 0.7638 (mtpt) cc_final: 0.7367 (ttpp) REVERT: A 299 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.5950 (mp0) REVERT: B 59 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.7456 (t80) REVERT: B 137 ARG cc_start: 0.6391 (tpt90) cc_final: 0.5951 (ttm-80) REVERT: N 105 ARG cc_start: 0.8040 (ttt90) cc_final: 0.6913 (tmt170) REVERT: R 335 PHE cc_start: 0.6341 (p90) cc_final: 0.5997 (p90) outliers start: 12 outliers final: 8 residues processed: 126 average time/residue: 0.2578 time to fit residues: 43.4060 Evaluate side-chains 123 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 184 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 430 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 8.9990 chunk 83 optimal weight: 30.0000 chunk 26 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 108 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 55 optimal weight: 8.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.189046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.151562 restraints weight = 9609.674| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.63 r_work: 0.3554 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9047 Z= 0.157 Angle : 0.528 7.484 12291 Z= 0.281 Chirality : 0.042 0.236 1379 Planarity : 0.004 0.058 1563 Dihedral : 4.580 49.451 1247 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.44 % Allowed : 10.54 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.26), residues: 1119 helix: 2.64 (0.25), residues: 434 sheet: -0.68 (0.33), residues: 220 loop : -0.07 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.006 0.001 HIS A 357 PHE 0.029 0.002 PHE R 335 TYR 0.030 0.002 TYR R 191 ARG 0.005 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 472) hydrogen bonds : angle 4.54023 ( 1341) SS BOND : bond 0.00414 ( 6) SS BOND : angle 0.90321 ( 12) covalent geometry : bond 0.00360 ( 9041) covalent geometry : angle 0.52714 (12279) *********************** 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 127 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 1.010 Fit side-chains REVERT: A 58 LYS cc_start: 0.7675 (mtpt) cc_final: 0.7379 (ttpp) REVERT: A 299 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6057 (mp0) REVERT: B 59 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.7474 (t80) REVERT: N 105 ARG cc_start: 0.8002 (ttt90) cc_final: 0.6987 (tmt170) REVERT: R 335 PHE cc_start: 0.6491 (p90) cc_final: 0.6133 (p90) outliers start: 13 outliers final: 11 residues processed: 119 average time/residue: 0.2434 time to fit residues: 38.9998 Evaluate side-chains 126 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 39 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 82 optimal weight: 50.0000 chunk 68 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 109 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.185261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.147610 restraints weight = 9629.806| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.63 r_work: 0.3508 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9047 Z= 0.218 Angle : 0.597 9.159 12291 Z= 0.317 Chirality : 0.044 0.194 1379 Planarity : 0.004 0.064 1563 Dihedral : 4.936 48.729 1247 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.89 % Allowed : 12.43 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.25), residues: 1119 helix: 2.18 (0.24), residues: 441 sheet: -0.79 (0.32), residues: 225 loop : -0.18 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.009 0.001 HIS A 357 PHE 0.028 0.002 PHE R 335 TYR 0.030 0.002 TYR R 191 ARG 0.006 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04474 ( 472) hydrogen bonds : angle 4.80497 ( 1341) SS BOND : bond 0.00541 ( 6) SS BOND : angle 1.02933 ( 12) covalent geometry : bond 0.00513 ( 9041) covalent geometry : angle 0.59615 (12279) *********************** 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 121 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.959 Fit side-chains REVERT: A 58 LYS cc_start: 0.7670 (mtpt) cc_final: 0.7326 (ttpp) REVERT: A 278 ASN cc_start: 0.8592 (m110) cc_final: 0.8302 (m110) REVERT: A 299 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.5863 (mp0) REVERT: B 59 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.7486 (t80) REVERT: N 105 ARG cc_start: 0.8106 (ttt90) cc_final: 0.7051 (tmt170) outliers start: 17 outliers final: 14 residues processed: 111 average time/residue: 0.2766 time to fit residues: 41.0944 Evaluate side-chains 118 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 N residue 126 VAL 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 57 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 68 optimal weight: 0.0270 chunk 15 optimal weight: 0.0060 chunk 92 optimal weight: 0.2980 chunk 97 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.3854 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.191917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.154173 restraints weight = 9555.551| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.71 r_work: 0.3595 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9047 Z= 0.097 Angle : 0.468 6.983 12291 Z= 0.252 Chirality : 0.039 0.161 1379 Planarity : 0.004 0.054 1563 Dihedral : 4.292 46.512 1247 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.33 % Allowed : 13.10 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.26), residues: 1119 helix: 2.87 (0.25), residues: 425 sheet: -0.53 (0.32), residues: 218 loop : 0.01 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 298 HIS 0.006 0.001 HIS A 220 PHE 0.028 0.001 PHE R 335 TYR 0.026 0.001 TYR R 191 ARG 0.007 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 472) hydrogen bonds : angle 4.35175 ( 1341) SS BOND : bond 0.00220 ( 6) SS BOND : angle 0.49342 ( 12) covalent geometry : bond 0.00199 ( 9041) covalent geometry : angle 0.46752 (12279) *********************** 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 129 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.901 Fit side-chains REVERT: A 278 ASN cc_start: 0.8419 (m110) cc_final: 0.8168 (m110) REVERT: A 299 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6822 (mp0) REVERT: B 59 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.7376 (t80) REVERT: N 38 ARG cc_start: 0.8284 (ptt180) cc_final: 0.8009 (ptp90) REVERT: N 105 ARG cc_start: 0.8028 (ttt90) cc_final: 0.6989 (tmt170) REVERT: R 335 PHE cc_start: 0.6335 (p90) cc_final: 0.6005 (p90) outliers start: 12 outliers final: 6 residues processed: 125 average time/residue: 0.2371 time to fit residues: 40.0809 Evaluate side-chains 121 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 86 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 107 optimal weight: 0.1980 chunk 108 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 78 optimal weight: 30.0000 chunk 56 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.190630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.154713 restraints weight = 9619.349| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.67 r_work: 0.3577 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9047 Z= 0.120 Angle : 0.486 6.855 12291 Z= 0.259 Chirality : 0.041 0.268 1379 Planarity : 0.004 0.054 1563 Dihedral : 4.242 46.491 1246 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.44 % Allowed : 13.65 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.26), residues: 1119 helix: 2.91 (0.25), residues: 425 sheet: -0.48 (0.32), residues: 218 loop : 0.05 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 298 HIS 0.006 0.001 HIS A 220 PHE 0.028 0.001 PHE R 335 TYR 0.026 0.001 TYR R 191 ARG 0.006 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 472) hydrogen bonds : angle 4.37029 ( 1341) SS BOND : bond 0.00381 ( 6) SS BOND : angle 0.97861 ( 12) covalent geometry : bond 0.00266 ( 9041) covalent geometry : angle 0.48490 (12279) *********************** 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 133 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 1.025 Fit side-chains REVERT: A 278 ASN cc_start: 0.8447 (m110) cc_final: 0.8210 (m110) REVERT: A 299 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6508 (mt-10) REVERT: B 59 TYR cc_start: 0.7819 (OUTLIER) cc_final: 0.7407 (t80) REVERT: N 38 ARG cc_start: 0.8288 (ptt180) cc_final: 0.8022 (ptp90) REVERT: N 105 ARG cc_start: 0.7999 (ttt90) cc_final: 0.6968 (tmt170) REVERT: R 335 PHE cc_start: 0.6334 (p90) cc_final: 0.5978 (p90) REVERT: R 447 PHE cc_start: 0.5545 (OUTLIER) cc_final: 0.4954 (m-10) outliers start: 13 outliers final: 10 residues processed: 129 average time/residue: 0.2701 time to fit residues: 47.2392 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 : 1.149 ------------------------------------------------------------------------------- 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 B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 211 TRP 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: 30.0000 chunk 90 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 85 optimal weight: 30.0000 chunk 28 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.190043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.154275 restraints weight = 9761.536| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.69 r_work: 0.3576 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9047 Z= 0.122 Angle : 0.487 6.579 12291 Z= 0.261 Chirality : 0.041 0.268 1379 Planarity : 0.004 0.054 1563 Dihedral : 4.232 46.422 1246 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.66 % Allowed : 13.76 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.26), residues: 1119 helix: 2.92 (0.25), residues: 425 sheet: -0.55 (0.32), residues: 225 loop : 0.10 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.007 0.001 HIS A 220 PHE 0.028 0.001 PHE R 335 TYR 0.026 0.001 TYR R 191 ARG 0.007 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03699 ( 472) hydrogen bonds : angle 4.34661 ( 1341) SS BOND : bond 0.00365 ( 6) SS BOND : angle 1.04449 ( 12) covalent geometry : bond 0.00273 ( 9041) covalent geometry : angle 0.48626 (12279) *********************** 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 133 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.984 Fit side-chains REVERT: A 58 LYS cc_start: 0.7742 (mtpt) cc_final: 0.7405 (ttpp) REVERT: A 278 ASN cc_start: 0.8456 (m110) cc_final: 0.8203 (m110) REVERT: A 299 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6495 (mt-10) REVERT: B 59 TYR cc_start: 0.7786 (OUTLIER) cc_final: 0.7351 (t80) REVERT: N 38 ARG cc_start: 0.8292 (ptt180) cc_final: 0.8038 (ptp90) REVERT: N 105 ARG cc_start: 0.8025 (ttt90) cc_final: 0.7001 (tmt170) REVERT: R 335 PHE cc_start: 0.6308 (p90) cc_final: 0.5950 (p90) REVERT: R 447 PHE cc_start: 0.5590 (OUTLIER) cc_final: 0.4881 (m-10) outliers start: 15 outliers final: 12 residues processed: 127 average time/residue: 0.2480 time to fit residues: 42.5306 Evaluate side-chains 131 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 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 211 TRP Chi-restraints excluded: chain B residue 232 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 16 optimal weight: 6.9990 chunk 83 optimal weight: 50.0000 chunk 28 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN ** 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 = 0.4058 r_free = 0.4058 target = 0.187360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.149821 restraints weight = 9702.418| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.68 r_work: 0.3535 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9047 Z= 0.176 Angle : 0.547 7.595 12291 Z= 0.290 Chirality : 0.043 0.283 1379 Planarity : 0.004 0.057 1563 Dihedral : 4.516 47.665 1246 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.22 % Allowed : 13.43 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.26), residues: 1119 helix: 2.67 (0.25), residues: 426 sheet: -0.66 (0.31), residues: 228 loop : 0.07 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.007 0.001 HIS A 220 PHE 0.027 0.002 PHE R 335 TYR 0.026 0.002 TYR R 191 ARG 0.006 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 472) hydrogen bonds : angle 4.57807 ( 1341) SS BOND : bond 0.00516 ( 6) SS BOND : angle 1.14785 ( 12) covalent geometry : bond 0.00410 ( 9041) covalent geometry : angle 0.54658 (12279) *********************** 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 131 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.995 Fit side-chains REVERT: A 299 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6084 (mp0) REVERT: B 59 TYR cc_start: 0.7900 (OUTLIER) cc_final: 0.7494 (t80) REVERT: N 105 ARG cc_start: 0.8061 (ttt90) cc_final: 0.6998 (tmt170) REVERT: R 317 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7457 (tm-30) REVERT: R 335 PHE cc_start: 0.6480 (p90) cc_final: 0.6080 (p90) REVERT: R 447 PHE cc_start: 0.5644 (OUTLIER) cc_final: 0.5024 (m-10) outliers start: 20 outliers final: 14 residues processed: 125 average time/residue: 0.2438 time to fit residues: 41.8625 Evaluate side-chains 124 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 211 TRP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 316 SER 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 110 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 81 optimal weight: 0.0050 chunk 109 optimal weight: 0.9980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** 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 = 0.4082 r_free = 0.4082 target = 0.190080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.153537 restraints weight = 9662.192| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.59 r_work: 0.3585 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 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 : 0.003 0.027 9047 Z= 0.120 Angle : 0.489 6.800 12291 Z= 0.262 Chirality : 0.041 0.270 1379 Planarity : 0.004 0.054 1563 Dihedral : 4.295 46.692 1246 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.66 % Allowed : 14.54 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.26), residues: 1119 helix: 2.87 (0.25), residues: 425 sheet: -0.53 (0.32), residues: 221 loop : 0.10 (0.31), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 332 HIS 0.005 0.001 HIS A 220 PHE 0.027 0.001 PHE R 335 TYR 0.025 0.001 TYR R 191 ARG 0.007 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 472) hydrogen bonds : angle 4.38171 ( 1341) SS BOND : bond 0.00343 ( 6) SS BOND : angle 0.90909 ( 12) covalent geometry : bond 0.00264 ( 9041) covalent geometry : angle 0.48809 (12279) ********************** 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 : 0.980 Fit side-chains REVERT: A 58 LYS cc_start: 0.7691 (mtpt) cc_final: 0.7352 (ttpp) REVERT: A 299 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6998 (mt-10) REVERT: B 59 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.7365 (t80) REVERT: N 38 ARG cc_start: 0.8284 (ptt180) cc_final: 0.8035 (ptp90) REVERT: N 105 ARG cc_start: 0.8014 (ttt90) cc_final: 0.7008 (tmt170) REVERT: R 317 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7414 (tm-30) REVERT: R 335 PHE cc_start: 0.6336 (p90) cc_final: 0.5974 (p90) REVERT: R 447 PHE cc_start: 0.5584 (OUTLIER) cc_final: 0.4870 (m-10) outliers start: 15 outliers final: 11 residues processed: 125 average time/residue: 0.2432 time to fit residues: 41.6781 Evaluate side-chains 126 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 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 211 TRP Chi-restraints excluded: chain B residue 232 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 64 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 chunk 23 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.190897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.152208 restraints weight = 9602.666| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.79 r_work: 0.3582 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9047 Z= 0.126 Angle : 0.497 6.976 12291 Z= 0.266 Chirality : 0.041 0.267 1379 Planarity : 0.004 0.055 1563 Dihedral : 4.302 46.831 1246 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.55 % Allowed : 14.54 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.26), residues: 1119 helix: 2.84 (0.25), residues: 425 sheet: -0.53 (0.32), residues: 226 loop : 0.14 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 332 HIS 0.006 0.001 HIS A 220 PHE 0.027 0.001 PHE R 335 TYR 0.025 0.001 TYR R 191 ARG 0.007 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 472) hydrogen bonds : angle 4.37317 ( 1341) SS BOND : bond 0.00353 ( 6) SS BOND : angle 0.92619 ( 12) covalent geometry : bond 0.00282 ( 9041) covalent geometry : angle 0.49675 (12279) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5631.06 seconds wall clock time: 98 minutes 27.51 seconds (5907.51 seconds total)