Starting phenix.real_space_refine on Thu Mar 13 07:44:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fls_29285/03_2025/8fls_29285.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fls_29285/03_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_29285/03_2025/8fls_29285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fls_29285/03_2025/8fls_29285.map" model { file = "/net/cci-nas-00/data/ceres_data/8fls_29285/03_2025/8fls_29285.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fls_29285/03_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-5624/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: 5.70, per 1000 atoms: 0.64 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: 2.40 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.99 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: 2.54 Time building geometry restraints manager: 2.81 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.390 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.290 ------------------------------------------------------------------------------- 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 9041 Z= 0.285 Angle : 0.700 7.657 12279 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 *********************** 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 : 0.968 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: 0.2839 time to fit residues: 51.4399 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 : 1.024 ------------------------------------------------------------------------------- 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 9041 Z= 0.172 Angle : 0.507 6.306 12279 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 *********************** 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 : 1.185 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: 0.2968 time to fit residues: 48.9750 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 : 1.103 ------------------------------------------------------------------------------- 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: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.192125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.154321 restraints weight = 9722.165| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.80 r_work: 0.3582 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9041 Z= 0.162 Angle : 0.483 6.321 12279 Z= 0.261 Chirality : 0.040 0.162 1379 Planarity : 0.004 0.055 1563 Dihedral : 4.510 49.624 1250 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.33 % Allowed : 8.77 % Favored : 89.90 % 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: -0.57 (0.34), residues: 211 loop : 0.02 (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 *********************** 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 132 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 1.028 Fit side-chains REVERT: A 58 LYS cc_start: 0.7774 (mtpt) cc_final: 0.7474 (ttpp) REVERT: A 299 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6124 (mp0) REVERT: B 59 TYR cc_start: 0.7911 (OUTLIER) cc_final: 0.7437 (t80) REVERT: B 137 ARG cc_start: 0.6526 (tpt90) cc_final: 0.6132 (ttm-80) REVERT: N 105 ARG cc_start: 0.8015 (ttt90) cc_final: 0.6999 (tmt170) REVERT: R 335 PHE cc_start: 0.6447 (p90) cc_final: 0.6140 (p90) outliers start: 12 outliers final: 8 residues processed: 125 average time/residue: 0.2471 time to fit residues: 41.1828 Evaluate side-chains 121 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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: 6.9990 chunk 83 optimal weight: 30.0000 chunk 26 optimal weight: 0.0470 chunk 23 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 105 optimal weight: 0.0870 chunk 108 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 chunk 55 optimal weight: 8.9990 overall best weight: 1.1058 ------------------------------------------------------------------------------- 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 = 0.4075 r_free = 0.4075 target = 0.189332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.152018 restraints weight = 9618.716| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.63 r_work: 0.3574 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9041 Z= 0.223 Angle : 0.519 7.152 12279 Z= 0.277 Chirality : 0.042 0.235 1379 Planarity : 0.004 0.057 1563 Dihedral : 4.543 49.491 1247 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.44 % Allowed : 10.77 % Favored : 87.79 % 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: 1.29 (0.26), residues: 1119 helix: 2.66 (0.25), residues: 434 sheet: -0.65 (0.33), residues: 215 loop : -0.07 (0.29), residues: 470 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 0.001 TYR R 191 ARG 0.005 0.000 ARG B 42 *********************** 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 126 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.922 Fit side-chains REVERT: A 58 LYS cc_start: 0.7619 (mtpt) cc_final: 0.7328 (ttpp) REVERT: A 299 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.5982 (mp0) REVERT: B 59 TYR cc_start: 0.7946 (OUTLIER) cc_final: 0.7488 (t80) REVERT: N 105 ARG cc_start: 0.8019 (ttt90) cc_final: 0.6959 (tmt170) REVERT: R 335 PHE cc_start: 0.6443 (p90) cc_final: 0.6085 (p90) outliers start: 13 outliers final: 11 residues processed: 118 average time/residue: 0.2588 time to fit residues: 40.8906 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 : 0.916 ------------------------------------------------------------------------------- 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: 0.4980 chunk 82 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 chunk 95 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.190113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.154091 restraints weight = 9577.002| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.69 r_work: 0.3563 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9041 Z= 0.190 Angle : 0.495 6.402 12279 Z= 0.265 Chirality : 0.041 0.241 1379 Planarity : 0.004 0.055 1563 Dihedral : 4.408 47.763 1247 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.55 % Allowed : 11.65 % Favored : 86.79 % 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: 1.35 (0.26), residues: 1119 helix: 2.73 (0.25), residues: 432 sheet: -0.60 (0.33), residues: 215 loop : -0.04 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.005 0.001 HIS A 220 PHE 0.028 0.001 PHE R 335 TYR 0.028 0.001 TYR R 191 ARG 0.006 0.000 ARG B 42 *********************** 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 133 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 1.005 Fit side-chains REVERT: A 58 LYS cc_start: 0.7650 (mtpt) cc_final: 0.7351 (ttpp) REVERT: A 278 ASN cc_start: 0.8553 (m110) cc_final: 0.8288 (m110) REVERT: A 299 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6031 (mp0) REVERT: B 59 TYR cc_start: 0.7808 (OUTLIER) cc_final: 0.7396 (t80) REVERT: N 105 ARG cc_start: 0.8051 (ttt90) cc_final: 0.6991 (tmt170) REVERT: R 335 PHE cc_start: 0.6395 (p90) cc_final: 0.6031 (p90) outliers start: 14 outliers final: 11 residues processed: 125 average time/residue: 0.2440 time to fit residues: 41.2970 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 : 1.307 ------------------------------------------------------------------------------- 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 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 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 57 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 72 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.191428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.153655 restraints weight = 9507.326| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.67 r_work: 0.3597 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9041 Z= 0.197 Angle : 0.500 6.426 12279 Z= 0.267 Chirality : 0.041 0.259 1379 Planarity : 0.004 0.054 1563 Dihedral : 4.339 47.397 1246 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.89 % Allowed : 12.54 % 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: 2.84 (0.25), residues: 425 sheet: -0.57 (0.33), residues: 220 loop : 0.06 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.006 0.001 HIS A 220 PHE 0.028 0.001 PHE R 335 TYR 0.027 0.001 TYR R 191 ARG 0.006 0.000 ARG B 42 *********************** 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 133 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.924 Fit side-chains REVERT: A 58 LYS cc_start: 0.7719 (mtpt) cc_final: 0.7398 (ttpp) REVERT: A 278 ASN cc_start: 0.8492 (m110) cc_final: 0.8266 (m110) REVERT: A 299 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6165 (mp0) REVERT: B 59 TYR cc_start: 0.7795 (OUTLIER) cc_final: 0.7325 (t80) REVERT: N 105 ARG cc_start: 0.8011 (ttt90) cc_final: 0.6995 (tmt170) REVERT: R 335 PHE cc_start: 0.6403 (p90) cc_final: 0.6043 (p90) outliers start: 17 outliers final: 14 residues processed: 125 average time/residue: 0.2360 time to fit residues: 39.9087 Evaluate side-chains 129 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 86 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 46 optimal weight: 0.0670 chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 50.0000 chunk 56 optimal weight: 10.0000 overall best weight: 0.9120 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.189609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.154171 restraints weight = 9635.822| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.69 r_work: 0.3570 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9041 Z= 0.194 Angle : 0.496 6.419 12279 Z= 0.265 Chirality : 0.041 0.260 1379 Planarity : 0.004 0.054 1563 Dihedral : 4.318 47.277 1246 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.89 % Allowed : 12.76 % 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 (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: 1.50 (0.26), residues: 1119 helix: 2.86 (0.25), residues: 425 sheet: -0.53 (0.33), residues: 220 loop : 0.10 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 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 *********************** 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 134 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 1.243 Fit side-chains REVERT: A 58 LYS cc_start: 0.7664 (mtpt) cc_final: 0.7331 (ttpp) REVERT: A 278 ASN cc_start: 0.8470 (m110) cc_final: 0.8198 (m110) REVERT: A 299 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6136 (mp0) REVERT: B 59 TYR cc_start: 0.7808 (OUTLIER) cc_final: 0.7392 (t80) REVERT: N 105 ARG cc_start: 0.8023 (ttt90) cc_final: 0.6971 (tmt170) REVERT: R 335 PHE cc_start: 0.6370 (p90) cc_final: 0.5995 (p90) outliers start: 17 outliers final: 15 residues processed: 125 average time/residue: 0.2704 time to fit residues: 46.0623 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 : 0.896 ------------------------------------------------------------------------------- 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 274 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 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: 3.9990 chunk 20 optimal weight: 0.0670 chunk 102 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 28 optimal weight: 0.2980 chunk 57 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.193124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.154202 restraints weight = 9697.283| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.82 r_work: 0.3585 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9041 Z= 0.139 Angle : 0.462 6.735 12279 Z= 0.248 Chirality : 0.040 0.250 1379 Planarity : 0.003 0.050 1563 Dihedral : 4.101 46.222 1246 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.66 % Allowed : 13.65 % Favored : 84.68 % 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: 1.66 (0.26), residues: 1119 helix: 3.02 (0.25), residues: 425 sheet: -0.42 (0.33), residues: 220 loop : 0.14 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.005 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 *********************** 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 135 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.997 Fit side-chains REVERT: A 58 LYS cc_start: 0.7563 (mtpt) cc_final: 0.7240 (ttpp) REVERT: A 278 ASN cc_start: 0.8387 (m110) cc_final: 0.8157 (m110) REVERT: B 137 ARG cc_start: 0.6327 (tpt90) cc_final: 0.5850 (ttm-80) REVERT: N 38 ARG cc_start: 0.8298 (ptt180) cc_final: 0.8005 (ptp90) REVERT: R 335 PHE cc_start: 0.6168 (p90) cc_final: 0.5840 (p90) REVERT: R 447 PHE cc_start: 0.5561 (OUTLIER) cc_final: 0.4789 (m-10) outliers start: 15 outliers final: 9 residues processed: 129 average time/residue: 0.2803 time to fit residues: 50.5874 Evaluate side-chains 131 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 1.839 ------------------------------------------------------------------------------- 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 308 ILE Chi-restraints excluded: chain A residue 325 THR 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 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: 0.0370 chunk 83 optimal weight: 50.0000 chunk 28 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 49 optimal weight: 0.0570 chunk 55 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- 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 = 0.4135 r_free = 0.4135 target = 0.193923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.155433 restraints weight = 9611.889| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.81 r_work: 0.3592 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9041 Z= 0.139 Angle : 0.461 6.773 12279 Z= 0.247 Chirality : 0.040 0.252 1379 Planarity : 0.004 0.050 1563 Dihedral : 3.830 20.458 1244 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.33 % Allowed : 13.87 % 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 (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: 1.71 (0.26), residues: 1119 helix: 3.05 (0.25), residues: 426 sheet: -0.47 (0.32), residues: 223 loop : 0.23 (0.31), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.005 0.001 HIS A 220 PHE 0.028 0.001 PHE R 335 TYR 0.025 0.001 TYR R 191 ARG 0.007 0.000 ARG B 42 *********************** 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 135 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 1.033 Fit side-chains REVERT: A 58 LYS cc_start: 0.7617 (mtpt) cc_final: 0.7275 (ttpp) REVERT: A 278 ASN cc_start: 0.8378 (m110) cc_final: 0.8149 (m110) REVERT: B 137 ARG cc_start: 0.6339 (tpt90) cc_final: 0.5885 (ttm-80) REVERT: N 38 ARG cc_start: 0.8327 (ptt180) cc_final: 0.8055 (ptp90) REVERT: R 317 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7329 (tm-30) REVERT: R 335 PHE cc_start: 0.6157 (p90) cc_final: 0.5830 (p90) REVERT: R 447 PHE cc_start: 0.5580 (OUTLIER) cc_final: 0.4841 (m-10) outliers start: 12 outliers final: 9 residues processed: 131 average time/residue: 0.2429 time to fit residues: 43.2548 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 : 0.895 ------------------------------------------------------------------------------- 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 308 ILE Chi-restraints excluded: chain A residue 325 THR 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 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: 10.0000 chunk 77 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 81 optimal weight: 0.0770 chunk 109 optimal weight: 0.7980 overall best weight: 0.7540 ------------------------------------------------------------------------------- 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 = 0.4107 r_free = 0.4107 target = 0.191296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.152899 restraints weight = 9627.184| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.82 r_work: 0.3609 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9041 Z= 0.171 Angle : 0.480 6.867 12279 Z= 0.256 Chirality : 0.041 0.269 1379 Planarity : 0.004 0.051 1563 Dihedral : 3.932 21.258 1244 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.33 % Allowed : 13.76 % 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: 1.66 (0.26), residues: 1119 helix: 3.01 (0.24), residues: 426 sheet: -0.51 (0.33), residues: 223 loop : 0.21 (0.31), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 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 ********************** 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 134 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.972 Fit side-chains REVERT: A 58 LYS cc_start: 0.7583 (mtpt) cc_final: 0.7259 (ttpp) REVERT: A 278 ASN cc_start: 0.8431 (m110) cc_final: 0.8179 (m110) REVERT: B 137 ARG cc_start: 0.6335 (tpt90) cc_final: 0.5862 (ttm-80) REVERT: N 38 ARG cc_start: 0.8360 (ptt180) cc_final: 0.8077 (ptp90) REVERT: R 317 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7390 (tm-30) REVERT: R 335 PHE cc_start: 0.6171 (p90) cc_final: 0.5813 (p90) REVERT: R 447 PHE cc_start: 0.5569 (OUTLIER) cc_final: 0.4900 (m-10) outliers start: 12 outliers final: 10 residues processed: 130 average time/residue: 0.2692 time to fit residues: 47.5366 Evaluate side-chains 132 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 1.590 ------------------------------------------------------------------------------- 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 308 ILE Chi-restraints excluded: chain A residue 325 THR 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 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: 0.8980 chunk 81 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN R 225 HIS ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.188060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.151647 restraints weight = 9651.019| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.77 r_work: 0.3522 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9041 Z= 0.291 Angle : 0.564 7.889 12279 Z= 0.298 Chirality : 0.043 0.273 1379 Planarity : 0.004 0.057 1563 Dihedral : 4.330 23.780 1244 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.33 % Allowed : 14.32 % 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: 1.39 (0.26), residues: 1119 helix: 2.71 (0.25), residues: 425 sheet: -0.67 (0.32), residues: 230 loop : 0.18 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.008 0.001 HIS A 357 PHE 0.027 0.002 PHE R 335 TYR 0.028 0.002 TYR R 191 ARG 0.006 0.000 ARG B 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5676.12 seconds wall clock time: 100 minutes 26.31 seconds (6026.31 seconds total)