Starting phenix.real_space_refine on Fri Sep 11 10:46:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rxd_24729/09_2026/7rxd_24729.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rxd_24729/09_2026/7rxd_24729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rxd_24729/09_2026/7rxd_24729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rxd_24729/09_2026/7rxd_24729.map" model { file = "/net/cci-nas-00/data/ceres_data/7rxd_24729/09_2026/7rxd_24729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rxd_24729/09_2026/7rxd_24729.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7rxd_24729/09_2026/7rxd_24729.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rxd_24729/09_2026/7rxd_24729.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 31 5.16 5 C 5749 2.51 5 N 1490 2.21 5 O 1737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9007 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3433 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 24, 'TRANS': 414} Chain breaks: 4 Chain: "H" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1582 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 192} Chain breaks: 2 Chain: "L" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1588 Classifications: {'peptide': 204} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 194} Chain breaks: 2 Chain: "N" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 990 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 121} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1391 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 9, 'TRANS': 163} Chain breaks: 2 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.87, per 1000 atoms: 0.21 Number of scatterers: 9007 At special positions: 0 Unit cell: (118.72, 133.56, 111.3, 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 31 16.00 O 1737 8.00 N 1490 7.00 C 5749 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.05 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " 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 Links applied ALPHA1-4 " GLC A 1 " - " GLC A 2 " Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 236.4 milliseconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 22 sheets defined 27.9% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'B' and resid 17 through 28 Processing helix chain 'B' and resid 43 through 52 Proline residue: B 49 - end of helix Processing helix chain 'B' and resid 64 through 74 removed outlier: 4.055A pdb=" N PHE B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY B 69 " --> pdb=" O HIS B 65 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 89 Processing helix chain 'B' and resid 91 through 98 removed outlier: 3.553A pdb=" N TRP B 95 " --> pdb=" O TYR B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 141 removed outlier: 4.490A pdb=" N ALA B 135 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 164 removed outlier: 3.923A pdb=" N THR B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Proline residue: B 160 - end of helix Processing helix chain 'B' and resid 182 through 185 removed outlier: 4.399A pdb=" N ASP B 185 " --> pdb=" O VAL B 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 182 through 185' Processing helix chain 'B' and resid 186 through 202 Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 287 through 298 removed outlier: 3.640A pdb=" N ASP B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 313 Processing helix chain 'B' and resid 315 through 328 Processing helix chain 'B' and resid 336 through 353 removed outlier: 3.913A pdb=" N PHE B 340 " --> pdb=" O GLN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 370 removed outlier: 3.610A pdb=" N MET B 370 " --> pdb=" O GLN B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 388 Processing helix chain 'B' and resid 391 through 406 Processing helix chain 'B' and resid 502 through 517 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.568A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.798A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 89 Processing helix chain 'L' and resid 126 through 133 Processing helix chain 'L' and resid 188 through 194 removed outlier: 3.722A pdb=" N HIS L 194 " --> pdb=" O ASP L 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.531A pdb=" N LYS N 65 " --> pdb=" O ASP N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 337 through 343 removed outlier: 3.748A pdb=" N VAL R 341 " --> pdb=" O PRO R 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 383 through 387 removed outlier: 3.798A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 410 removed outlier: 4.935A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 438 through 443 Processing helix chain 'R' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'B' and resid 37 through 39 removed outlier: 5.958A pdb=" N ILE B 10 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL B 9 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE B 62 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TRP B 11 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ALA B 265 " --> pdb=" O PRO B 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 37 through 39 removed outlier: 5.958A pdb=" N ILE B 10 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL B 9 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE B 62 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TRP B 11 " --> pdb=" O PHE B 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 99 through 100 Processing sheet with id=AA4, first strand: chain 'B' and resid 225 through 228 Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 173 removed outlier: 4.055A pdb=" N LYS B 171 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 250 through 251 Processing sheet with id=AA7, first strand: chain 'B' and resid 522 through 526 Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.770A pdb=" N GLY H 33 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 130 through 134 removed outlier: 4.043A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 130 through 134 removed outlier: 4.043A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.835A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LYS L 112 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL L 13 " --> pdb=" O LYS L 112 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.835A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LYS L 112 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL L 13 " --> pdb=" O LYS L 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.682A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 150 through 154 Processing sheet with id=AB8, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB9, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.299A pdb=" N GLY N 10 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N SER N 120 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL N 12 " --> pdb=" O SER N 120 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LYS N 99 " --> pdb=" O ARG N 33 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG N 33 " --> pdb=" O LYS N 99 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N MET N 34 " --> pdb=" O ALA N 50 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.299A pdb=" N GLY N 10 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N SER N 120 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL N 12 " --> pdb=" O SER N 120 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.921A pdb=" N VAL R 395 " --> pdb=" O ILE R 358 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'R' and resid 473 through 474 423 hydrogen bonds defined for protein. 1116 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2864 1.35 - 1.48: 2471 1.48 - 1.61: 3844 1.61 - 1.74: 0 1.74 - 1.87: 47 Bond restraints: 9226 Sorted by residual: bond pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " ideal model delta sigma weight residual 1.808 1.875 -0.067 3.30e-02 9.18e+02 4.09e+00 bond pdb=" CB VAL N 48 " pdb=" CG2 VAL N 48 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.68e+00 bond pdb=" CB CYS R 432 " pdb=" SG CYS R 432 " ideal model delta sigma weight residual 1.808 1.768 0.040 3.30e-02 9.18e+02 1.48e+00 bond pdb=" C ILE B 133 " pdb=" N PRO B 134 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.00e-01 bond pdb=" C GLY R 431 " pdb=" N CYS R 432 " ideal model delta sigma weight residual 1.328 1.340 -0.012 1.35e-02 5.49e+03 8.27e-01 ... (remaining 9221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 12440 2.65 - 5.31: 82 5.31 - 7.96: 3 7.96 - 10.62: 0 10.62 - 13.27: 2 Bond angle restraints: 12527 Sorted by residual: angle pdb=" N CYS R 432 " pdb=" CA CYS R 432 " pdb=" C CYS R 432 " ideal model delta sigma weight residual 107.88 119.63 -11.75 1.41e+00 5.03e-01 6.95e+01 angle pdb=" CA CYS R 432 " pdb=" CB CYS R 432 " pdb=" SG CYS R 432 " ideal model delta sigma weight residual 114.40 127.67 -13.27 2.30e+00 1.89e-01 3.33e+01 angle pdb=" C GLY R 431 " pdb=" N CYS R 432 " pdb=" CA CYS R 432 " ideal model delta sigma weight residual 122.45 118.44 4.01 1.78e+00 3.16e-01 5.07e+00 angle pdb=" N GLU B 23 " pdb=" CA GLU B 23 " pdb=" CB GLU B 23 " ideal model delta sigma weight residual 110.16 113.37 -3.21 1.48e+00 4.57e-01 4.70e+00 angle pdb=" C GLU B 173 " pdb=" N ASN B 174 " pdb=" CA ASN B 174 " ideal model delta sigma weight residual 121.54 125.58 -4.04 1.91e+00 2.74e-01 4.47e+00 ... (remaining 12522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4945 17.94 - 35.87: 421 35.87 - 53.81: 73 53.81 - 71.75: 14 71.75 - 89.68: 11 Dihedral angle restraints: 5464 sinusoidal: 2137 harmonic: 3327 Sorted by residual: dihedral pdb=" CA GLU H 158 " pdb=" C GLU H 158 " pdb=" N PRO H 159 " pdb=" CA PRO H 159 " ideal model delta harmonic sigma weight residual 180.00 144.49 35.51 0 5.00e+00 4.00e-02 5.04e+01 dihedral pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " pdb=" SG CYS R 432 " pdb=" CB CYS R 432 " ideal model delta sinusoidal sigma weight residual 93.00 34.17 58.83 1 1.00e+01 1.00e-02 4.63e+01 dihedral pdb=" CB CYS H 150 " pdb=" SG CYS H 150 " pdb=" SG CYS H 206 " pdb=" CB CYS H 206 " ideal model delta sinusoidal sigma weight residual 93.00 140.09 -47.09 1 1.00e+01 1.00e-02 3.06e+01 ... (remaining 5461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.935: 1366 0.935 - 1.870: 0 1.870 - 2.806: 0 2.806 - 3.741: 0 3.741 - 4.676: 1 Chirality restraints: 1367 Sorted by residual: chirality pdb=" C1 GLC A 1 " pdb=" C2 GLC A 1 " pdb=" O1 GLC A 1 " pdb=" O5 GLC A 1 " both_signs ideal model delta sigma weight residual False 2.33 -2.34 4.68 2.00e-01 2.50e+01 5.47e+02 chirality pdb=" C1 GLC A 2 " pdb=" O4 GLC A 1 " pdb=" C2 GLC A 2 " pdb=" O5 GLC A 2 " both_signs ideal model delta sigma weight residual False 2.40 2.32 0.08 2.00e-02 2.50e+03 1.72e+01 chirality pdb=" CA CYS R 432 " pdb=" N CYS R 432 " pdb=" C CYS R 432 " pdb=" CB CYS R 432 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 1364 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 158 " 0.076 5.00e-02 4.00e+02 1.17e-01 2.19e+01 pdb=" N PRO H 159 " -0.203 5.00e-02 4.00e+02 pdb=" CA PRO H 159 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO H 159 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER R 383 " -0.053 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO R 384 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO R 384 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO R 384 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 123 " 0.050 5.00e-02 4.00e+02 7.68e-02 9.43e+00 pdb=" N PRO B 124 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " 0.042 5.00e-02 4.00e+02 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 200 2.69 - 3.24: 8625 3.24 - 3.80: 14199 3.80 - 4.35: 18927 4.35 - 4.90: 31721 Nonbonded interactions: 73672 Sorted by model distance: nonbonded pdb=" OD1 ASP R 442 " pdb=" OH TYR R 451 " model vdw 2.138 3.040 nonbonded pdb=" O MET H 110 " pdb=" OH TYR L 42 " model vdw 2.140 3.040 nonbonded pdb=" ND2 ASN H 207 " pdb=" OD1 ASP H 218 " model vdw 2.145 3.120 nonbonded pdb=" OE1 GLN L 27 " pdb=" OG1 THR N 118 " model vdw 2.204 3.040 nonbonded pdb=" OD2 ASP R 398 " pdb=" OH TYR R 423 " model vdw 2.208 3.040 ... (remaining 73667 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.170 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 9234 Z= 0.139 Angle : 0.573 13.271 12544 Z= 0.303 Chirality : 0.133 4.676 1367 Planarity : 0.005 0.117 1604 Dihedral : 13.877 89.685 3317 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.21 % Allowed : 0.21 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.25), residues: 1118 helix: 0.60 (0.33), residues: 261 sheet: 0.60 (0.27), residues: 346 loop : 0.11 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 38 TYR 0.015 0.001 TYR R 505 PHE 0.020 0.002 PHE B 259 TRP 0.016 0.001 TRP L 56 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 9226) covalent geometry : angle 0.56424 / 0.30 (12527) SS BOND : bond 0.00845 / 0.42 ( 7) SS BOND : angle 1.87767 / 1.30 ( 14) hydrogen bonds : bond 0.13486 / 8.28 ( 401) hydrogen bonds : angle 6.96838 / 4.82 ( 1116) link_ALPHA1-4 : bond 0.02745 / 1.44 ( 1) link_ALPHA1-4 : angle 5.24159 / 2.78 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 0.272 Fit side-chains REVERT: B 327 LYS cc_start: 0.8157 (mttt) cc_final: 0.7643 (tptt) REVERT: B 405 HIS cc_start: 0.8620 (t-90) cc_final: 0.8062 (t-170) REVERT: B 485 LEU cc_start: 0.8913 (tp) cc_final: 0.8316 (tp) REVERT: H 6 GLU cc_start: 0.7247 (mp0) cc_final: 0.6941 (mp0) REVERT: H 153 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8255 (mmtp) outliers start: 2 outliers final: 0 residues processed: 143 average time/residue: 0.0873 time to fit residues: 17.8669 Evaluate side-chains 111 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 125 ASN B 204 HIS ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 143 ASN ** R 422 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 = 0.4304 r_free = 0.4304 target = 0.194480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.163050 restraints weight = 11775.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.159785 restraints weight = 11079.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.157491 restraints weight = 12011.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.158693 restraints weight = 9995.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.159248 restraints weight = 7295.111| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 9234 Z= 0.196 Angle : 0.603 14.695 12544 Z= 0.314 Chirality : 0.043 0.170 1367 Planarity : 0.005 0.103 1604 Dihedral : 4.512 33.940 1250 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.24 % Allowed : 7.97 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.25), residues: 1118 helix: 1.07 (0.32), residues: 263 sheet: 0.64 (0.27), residues: 344 loop : 0.03 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 147 TYR 0.035 0.002 TYR R 505 PHE 0.023 0.002 PHE B 510 TRP 0.018 0.002 TRP N 47 HIS 0.003 0.001 HIS L 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 ( 9226) covalent geometry : angle 0.59849 / 0.31 (12527) SS BOND : bond 0.00754 / 0.39 ( 7) SS BOND : angle 2.23476 / 1.55 ( 14) hydrogen bonds : bond 0.03514 / 2.22 ( 401) hydrogen bonds : angle 5.53453 / 3.89 ( 1116) link_ALPHA1-4 : bond 0.00200 / 0.11 ( 1) link_ALPHA1-4 : angle 1.80920 / 1.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.334 Fit side-chains REVERT: B 318 ILE cc_start: 0.8707 (mm) cc_final: 0.8373 (mp) REVERT: B 405 HIS cc_start: 0.8672 (t-90) cc_final: 0.8159 (t-170) REVERT: B 532 PHE cc_start: 0.7631 (m-80) cc_final: 0.7181 (m-80) REVERT: H 6 GLU cc_start: 0.7246 (mp0) cc_final: 0.6978 (mp0) REVERT: H 219 LYS cc_start: 0.7540 (tppt) cc_final: 0.7300 (tppt) REVERT: R 357 ARG cc_start: 0.6722 (ttp-170) cc_final: 0.6502 (ttp-170) outliers start: 12 outliers final: 10 residues processed: 139 average time/residue: 0.0830 time to fit residues: 16.6637 Evaluate side-chains 128 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain R residue 392 PHE Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 11 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 89 optimal weight: 0.4980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 ASN B 125 ASN B 204 HIS ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.190546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.160659 restraints weight = 11518.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.159694 restraints weight = 16571.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.162060 restraints weight = 15027.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.162282 restraints weight = 9117.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.163189 restraints weight = 7969.322| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 9234 Z= 0.169 Angle : 0.567 13.752 12544 Z= 0.296 Chirality : 0.043 0.276 1367 Planarity : 0.005 0.093 1604 Dihedral : 4.442 32.308 1250 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.66 % Allowed : 12.32 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.25), residues: 1118 helix: 1.16 (0.32), residues: 265 sheet: 0.56 (0.26), residues: 354 loop : 0.03 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 147 TYR 0.027 0.001 TYR R 505 PHE 0.017 0.002 PHE R 374 TRP 0.020 0.001 TRP N 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 9226) covalent geometry : angle 0.56201 / 0.29 (12527) SS BOND : bond 0.00873 / 0.47 ( 7) SS BOND : angle 2.14795 / 1.44 ( 14) hydrogen bonds : bond 0.03114 / 1.97 ( 401) hydrogen bonds : angle 5.28331 / 3.73 ( 1116) link_ALPHA1-4 : bond 0.00065 / 0.03 ( 1) link_ALPHA1-4 : angle 1.59323 / 0.86 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.349 Fit side-chains REVERT: B 405 HIS cc_start: 0.8652 (t-90) cc_final: 0.8177 (t-170) REVERT: H 219 LYS cc_start: 0.7590 (tppt) cc_final: 0.7372 (tppt) REVERT: L 87 GLU cc_start: 0.8195 (pp20) cc_final: 0.7946 (pp20) REVERT: R 357 ARG cc_start: 0.6908 (ttp-170) cc_final: 0.6556 (ttp-170) outliers start: 16 outliers final: 12 residues processed: 140 average time/residue: 0.0843 time to fit residues: 17.4061 Evaluate side-chains 133 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 15 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 0.0000 chunk 65 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 104 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 54.9108 > 50:) chunk 85 optimal weight: 0.0870 overall best weight: 0.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 204 HIS ** R 422 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 = 0.4332 r_free = 0.4332 target = 0.194068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.164400 restraints weight = 11632.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.162888 restraints weight = 16817.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.165280 restraints weight = 14536.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.165762 restraints weight = 9171.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.167383 restraints weight = 8750.595| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 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 : 0.003 0.069 9234 Z= 0.106 Angle : 0.528 11.485 12544 Z= 0.273 Chirality : 0.041 0.132 1367 Planarity : 0.004 0.081 1604 Dihedral : 4.205 30.348 1250 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.04 % Allowed : 14.18 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.25), residues: 1118 helix: 1.45 (0.33), residues: 259 sheet: 0.60 (0.27), residues: 359 loop : 0.11 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 147 TYR 0.019 0.001 TYR R 505 PHE 0.022 0.001 PHE L 144 TRP 0.017 0.001 TRP N 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 9226) covalent geometry : angle 0.52412 / 0.27 (12527) SS BOND : bond 0.00666 / 0.33 ( 7) SS BOND : angle 1.93272 / 1.31 ( 14) hydrogen bonds : bond 0.02744 / 1.73 ( 401) hydrogen bonds : angle 4.99110 / 3.51 ( 1116) link_ALPHA1-4 : bond 0.00137 / 0.07 ( 1) link_ALPHA1-4 : angle 1.34121 / 0.71 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.337 Fit side-chains REVERT: B 327 LYS cc_start: 0.8126 (mttt) cc_final: 0.7625 (tptt) REVERT: B 405 HIS cc_start: 0.8627 (t-90) cc_final: 0.8188 (t-170) REVERT: B 485 LEU cc_start: 0.8953 (tp) cc_final: 0.8500 (tp) REVERT: L 87 GLU cc_start: 0.8144 (pp20) cc_final: 0.7913 (pp20) REVERT: R 357 ARG cc_start: 0.6938 (ttp-170) cc_final: 0.6633 (ttp-170) outliers start: 10 outliers final: 7 residues processed: 141 average time/residue: 0.0789 time to fit residues: 16.4299 Evaluate side-chains 129 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 102 optimal weight: 0.0870 chunk 39 optimal weight: 5.9990 chunk 99 optimal weight: 0.0870 chunk 93 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 ASN B 204 HIS ** R 422 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 = 0.4332 r_free = 0.4332 target = 0.194041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.165607 restraints weight = 11595.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.166000 restraints weight = 18613.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.168425 restraints weight = 14564.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.168438 restraints weight = 8624.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.169643 restraints weight = 7795.014| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9234 Z= 0.108 Angle : 0.536 14.651 12544 Z= 0.276 Chirality : 0.041 0.169 1367 Planarity : 0.004 0.062 1604 Dihedral : 4.115 30.577 1250 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.55 % Allowed : 15.53 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.25), residues: 1118 helix: 1.61 (0.33), residues: 252 sheet: 0.62 (0.27), residues: 361 loop : 0.12 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 19 TYR 0.016 0.001 TYR B 100 PHE 0.022 0.001 PHE B 510 TRP 0.014 0.001 TRP N 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 9226) covalent geometry : angle 0.53126 / 0.27 (12527) SS BOND : bond 0.00392 / 0.20 ( 7) SS BOND : angle 2.17847 / 1.42 ( 14) hydrogen bonds : bond 0.02714 / 1.72 ( 401) hydrogen bonds : angle 4.84791 / 3.43 ( 1116) link_ALPHA1-4 : bond 0.00141 / 0.07 ( 1) link_ALPHA1-4 : angle 1.32387 / 0.70 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: B 327 LYS cc_start: 0.8122 (mttt) cc_final: 0.7649 (tptt) REVERT: B 405 HIS cc_start: 0.8608 (t-90) cc_final: 0.8177 (t-170) REVERT: L 69 THR cc_start: 0.8080 (t) cc_final: 0.7850 (p) REVERT: L 87 GLU cc_start: 0.8168 (pp20) cc_final: 0.7922 (pp20) REVERT: R 357 ARG cc_start: 0.7020 (ttp-170) cc_final: 0.6789 (ttp-170) outliers start: 15 outliers final: 14 residues processed: 140 average time/residue: 0.0823 time to fit residues: 17.0256 Evaluate side-chains 137 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 5 optimal weight: 0.1980 chunk 46 optimal weight: 7.9990 chunk 6 optimal weight: 0.0980 chunk 32 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 422 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 = 0.4314 r_free = 0.4314 target = 0.192068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.161705 restraints weight = 11612.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.160870 restraints weight = 18267.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.163043 restraints weight = 15718.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.163671 restraints weight = 9608.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.164414 restraints weight = 8484.426| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9234 Z= 0.147 Angle : 0.558 14.712 12544 Z= 0.287 Chirality : 0.042 0.171 1367 Planarity : 0.004 0.058 1604 Dihedral : 4.182 29.751 1250 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.07 % Allowed : 16.36 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.25), residues: 1118 helix: 1.56 (0.33), residues: 251 sheet: 0.66 (0.27), residues: 359 loop : 0.04 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 38 TYR 0.018 0.001 TYR B 100 PHE 0.020 0.002 PHE B 532 TRP 0.014 0.001 TRP N 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 9226) covalent geometry : angle 0.55232 / 0.28 (12527) SS BOND : bond 0.00986 / 0.50 ( 7) SS BOND : angle 2.41508 / 1.57 ( 14) hydrogen bonds : bond 0.02846 / 1.81 ( 401) hydrogen bonds : angle 4.87041 / 3.44 ( 1116) link_ALPHA1-4 : bond 0.00044 / 0.02 ( 1) link_ALPHA1-4 : angle 1.32367 / 0.71 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 327 LYS cc_start: 0.8129 (mttt) cc_final: 0.7622 (tptt) REVERT: B 405 HIS cc_start: 0.8643 (t-90) cc_final: 0.8227 (t-170) REVERT: L 69 THR cc_start: 0.8099 (t) cc_final: 0.7857 (p) REVERT: R 351 TYR cc_start: 0.8034 (p90) cc_final: 0.7752 (p90) REVERT: R 481 ASN cc_start: 0.6803 (t0) cc_final: 0.6570 (t0) outliers start: 20 outliers final: 16 residues processed: 140 average time/residue: 0.0794 time to fit residues: 16.2633 Evaluate side-chains 137 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 101 optimal weight: 0.4980 chunk 110 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 ASN H 174 HIS ** R 422 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 = 0.4323 r_free = 0.4323 target = 0.192811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.165685 restraints weight = 11635.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.165286 restraints weight = 17079.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.167615 restraints weight = 13981.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.167007 restraints weight = 8522.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.168022 restraints weight = 7053.848| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9234 Z= 0.115 Angle : 0.545 14.846 12544 Z= 0.279 Chirality : 0.042 0.179 1367 Planarity : 0.004 0.052 1604 Dihedral : 4.122 29.963 1250 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.97 % Allowed : 16.77 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.25), residues: 1118 helix: 1.53 (0.33), residues: 252 sheet: 0.61 (0.27), residues: 361 loop : 0.05 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 38 TYR 0.017 0.001 TYR B 100 PHE 0.018 0.001 PHE B 532 TRP 0.015 0.001 TRP N 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 ( 9226) covalent geometry : angle 0.53949 / 0.28 (12527) SS BOND : bond 0.00633 / 0.32 ( 7) SS BOND : angle 2.32652 / 1.53 ( 14) hydrogen bonds : bond 0.02715 / 1.72 ( 401) hydrogen bonds : angle 4.82249 / 3.40 ( 1116) link_ALPHA1-4 : bond 0.00168 / 0.09 ( 1) link_ALPHA1-4 : angle 1.26208 / 0.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.351 Fit side-chains REVERT: B 327 LYS cc_start: 0.8123 (mttt) cc_final: 0.7640 (tptt) REVERT: L 69 THR cc_start: 0.8052 (t) cc_final: 0.7807 (p) REVERT: R 351 TYR cc_start: 0.7968 (p90) cc_final: 0.7667 (p90) REVERT: R 481 ASN cc_start: 0.6839 (t0) cc_final: 0.6511 (t0) outliers start: 19 outliers final: 15 residues processed: 135 average time/residue: 0.0781 time to fit residues: 15.5624 Evaluate side-chains 133 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 96 optimal weight: 0.0070 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 0.0010 chunk 70 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 overall best weight: 0.9808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 ASN ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 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 = 0.4324 r_free = 0.4324 target = 0.195624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.163321 restraints weight = 11930.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 176)---------------| | r_work = 0.3885 r_free = 0.3885 target = 0.152785 restraints weight = 12932.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.154151 restraints weight = 9105.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.155805 restraints weight = 7019.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.156605 restraints weight = 5862.014| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9234 Z= 0.130 Angle : 0.568 17.139 12544 Z= 0.290 Chirality : 0.042 0.217 1367 Planarity : 0.004 0.051 1604 Dihedral : 4.149 29.678 1250 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.59 % Allowed : 16.56 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.25), residues: 1118 helix: 1.55 (0.33), residues: 252 sheet: 0.64 (0.27), residues: 361 loop : 0.02 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 38 TYR 0.019 0.001 TYR B 100 PHE 0.017 0.001 PHE B 532 TRP 0.014 0.001 TRP N 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 9226) covalent geometry : angle 0.56266 / 0.29 (12527) SS BOND : bond 0.00783 / 0.39 ( 7) SS BOND : angle 2.38392 / 1.56 ( 14) hydrogen bonds : bond 0.02774 / 1.76 ( 401) hydrogen bonds : angle 4.83146 / 3.41 ( 1116) link_ALPHA1-4 : bond 0.00010 / 0.01 ( 1) link_ALPHA1-4 : angle 1.27461 / 0.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.347 Fit side-chains REVERT: L 69 THR cc_start: 0.8068 (t) cc_final: 0.7816 (p) REVERT: R 351 TYR cc_start: 0.8004 (p90) cc_final: 0.7678 (p90) REVERT: R 481 ASN cc_start: 0.6980 (t0) cc_final: 0.6740 (t0) outliers start: 25 outliers final: 17 residues processed: 134 average time/residue: 0.0790 time to fit residues: 15.7534 Evaluate side-chains 136 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain R residue 461 LEU Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 15 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 0.0030 chunk 39 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 ASN ** R 422 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 = 0.4331 r_free = 0.4331 target = 0.193725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.164837 restraints weight = 11572.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.163066 restraints weight = 15795.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.165402 restraints weight = 11774.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.165378 restraints weight = 8234.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.165949 restraints weight = 8491.012| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9234 Z= 0.110 Angle : 0.565 16.410 12544 Z= 0.286 Chirality : 0.042 0.208 1367 Planarity : 0.004 0.052 1604 Dihedral : 4.106 29.558 1250 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.48 % Allowed : 16.46 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.25), residues: 1118 helix: 1.62 (0.33), residues: 252 sheet: 0.60 (0.27), residues: 361 loop : 0.04 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 457 TYR 0.019 0.001 TYR B 100 PHE 0.015 0.001 PHE B 532 TRP 0.015 0.001 TRP N 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 9226) covalent geometry : angle 0.56069 / 0.28 (12527) SS BOND : bond 0.00738 / 0.37 ( 7) SS BOND : angle 2.16177 / 1.42 ( 14) hydrogen bonds : bond 0.02694 / 1.70 ( 401) hydrogen bonds : angle 4.77593 / 3.37 ( 1116) link_ALPHA1-4 : bond 0.00195 / 0.10 ( 1) link_ALPHA1-4 : angle 1.21804 / 0.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.330 Fit side-chains REVERT: L 69 THR cc_start: 0.8035 (t) cc_final: 0.7794 (p) REVERT: R 351 TYR cc_start: 0.7902 (p90) cc_final: 0.7595 (p90) REVERT: R 481 ASN cc_start: 0.6992 (t0) cc_final: 0.6770 (t0) outliers start: 24 outliers final: 20 residues processed: 142 average time/residue: 0.0803 time to fit residues: 17.0542 Evaluate side-chains 139 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 94 CYS Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 461 LEU Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 1.9990 chunk 42 optimal weight: 0.0060 chunk 21 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 ASN B 125 ASN ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 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 = 0.4098 r_free = 0.4098 target = 0.175651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.143287 restraints weight = 11223.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.140968 restraints weight = 14250.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.138059 restraints weight = 12700.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.138253 restraints weight = 12776.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.139081 restraints weight = 9730.317| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9234 Z= 0.192 Angle : 0.624 16.413 12544 Z= 0.317 Chirality : 0.043 0.201 1367 Planarity : 0.004 0.050 1604 Dihedral : 4.337 29.930 1250 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.48 % Allowed : 16.56 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.25), residues: 1118 helix: 1.57 (0.33), residues: 252 sheet: 0.63 (0.27), residues: 359 loop : -0.12 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 38 TYR 0.019 0.002 TYR L 97 PHE 0.020 0.002 PHE B 532 TRP 0.014 0.001 TRP N 47 HIS 0.003 0.001 HIS L 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 ( 9226) covalent geometry : angle 0.61918 / 0.31 (12527) SS BOND : bond 0.00801 / 0.41 ( 7) SS BOND : angle 2.33073 / 1.47 ( 14) hydrogen bonds : bond 0.02987 / 1.90 ( 401) hydrogen bonds : angle 4.92854 / 3.48 ( 1116) link_ALPHA1-4 : bond 0.00052 / 0.03 ( 1) link_ALPHA1-4 : angle 1.31525 / 0.71 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.361 Fit side-chains REVERT: R 351 TYR cc_start: 0.8111 (p90) cc_final: 0.7787 (p90) REVERT: R 481 ASN cc_start: 0.7063 (t0) cc_final: 0.6788 (t0) outliers start: 24 outliers final: 19 residues processed: 132 average time/residue: 0.0858 time to fit residues: 16.5428 Evaluate side-chains 135 residues out of total 967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 94 CYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 461 LEU Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 83 optimal weight: 0.0980 chunk 30 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 ASN B 125 ASN ** R 422 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 = 0.4328 r_free = 0.4328 target = 0.194896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.167367 restraints weight = 11491.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.166415 restraints weight = 16428.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.168672 restraints weight = 12298.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.168512 restraints weight = 8669.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.169346 restraints weight = 8947.164| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9234 Z= 0.118 Angle : 0.584 15.928 12544 Z= 0.296 Chirality : 0.042 0.192 1367 Planarity : 0.004 0.098 1604 Dihedral : 4.204 31.122 1250 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.38 % Allowed : 16.56 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.25), residues: 1118 helix: 1.66 (0.33), residues: 252 sheet: 0.59 (0.27), residues: 356 loop : -0.06 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 457 TYR 0.018 0.001 TYR B 100 PHE 0.015 0.001 PHE B 532 TRP 0.016 0.001 TRP N 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 9226) covalent geometry : angle 0.57972 / 0.29 (12527) SS BOND : bond 0.00748 / 0.37 ( 7) SS BOND : angle 2.08285 / 1.36 ( 14) hydrogen bonds : bond 0.02741 / 1.74 ( 401) hydrogen bonds : angle 4.84486 / 3.42 ( 1116) link_ALPHA1-4 : bond 0.00179 / 0.09 ( 1) link_ALPHA1-4 : angle 1.19808 / 0.63 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1533.10 seconds wall clock time: 27 minutes 18.95 seconds (1638.95 seconds total)