Starting phenix.real_space_refine on Tue Mar 3 17:49:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dh5_30678/03_2026/7dh5_30678.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dh5_30678/03_2026/7dh5_30678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dh5_30678/03_2026/7dh5_30678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dh5_30678/03_2026/7dh5_30678.map" model { file = "/net/cci-nas-00/data/ceres_data/7dh5_30678/03_2026/7dh5_30678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dh5_30678/03_2026/7dh5_30678.cif" } resolution = 3.16 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= 0.009 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 47 5.16 5 C 4975 2.51 5 N 1383 2.21 5 O 1445 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7850 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1884 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2543 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'ASP:plan': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "G" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 393 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 950 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2052 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 259} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 4, 'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'H6U': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.80, per 1000 atoms: 0.23 Number of scatterers: 7850 At special positions: 0 Unit cell: (98.5625, 79.8875, 132.8, 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 47 16.00 O 1445 8.00 N 1383 7.00 C 4975 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 110 " - pdb=" SG CYS R 196 " distance=2.03 Simple disulfide: pdb=" SG CYS R 189 " - pdb=" SG CYS R 195 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 326.3 milliseconds 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 41.3% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.649A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 283 through 294 removed outlier: 3.508A pdb=" N GLY A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.249A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 306 removed outlier: 3.957A pdb=" N ALA A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 306' Processing helix chain 'A' and resid 321 through 341 removed outlier: 3.614A pdb=" N ARG A 326 " --> pdb=" O PRO A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 3.638A pdb=" N ASP A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A 371 " --> pdb=" O ASN A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.693A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 11 through 23 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 'N' and resid 28 through 32 removed outlier: 3.627A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.536A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 64 Processing helix chain 'R' and resid 72 through 90 Processing helix chain 'R' and resid 90 through 100 Processing helix chain 'R' and resid 106 through 141 removed outlier: 3.564A pdb=" N THR R 122 " --> pdb=" O VAL R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 170 Processing helix chain 'R' and resid 188 through 192 Processing helix chain 'R' and resid 201 through 213 Processing helix chain 'R' and resid 213 through 241 Processing helix chain 'R' and resid 289 through 318 removed outlier: 4.314A pdb=" N CYS R 304 " --> pdb=" O THR R 300 " (cutoff:3.500A) Proline residue: R 307 - end of helix Processing helix chain 'R' and resid 324 through 346 Proline residue: R 343 - end of helix removed outlier: 3.560A pdb=" N TYR R 346 " --> pdb=" O ASN R 342 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 358 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.236A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL A 277 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N HIS A 352 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU A 279 " --> pdb=" O HIS A 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.667A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.672A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 5.866A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 150 removed outlier: 3.652A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.521A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.010A 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: 3.676A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.659A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.012A 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 removed outlier: 3.648A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'N' and resid 49 through 50 removed outlier: 3.600A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1119 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: 1.25 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1277 1.31 - 1.44: 2179 1.44 - 1.56: 4488 1.56 - 1.69: 2 1.69 - 1.81: 61 Bond restraints: 8007 Sorted by residual: bond pdb=" C27 H6U R 401 " pdb=" S28 H6U R 401 " ideal model delta sigma weight residual 1.731 1.589 0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" C02 H6U R 401 " pdb=" S28 H6U R 401 " ideal model delta sigma weight residual 1.742 1.616 0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" C06 H6U R 401 " pdb=" N08 H6U R 401 " ideal model delta sigma weight residual 1.353 1.464 -0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C ARG N 98 " pdb=" N CYS N 99 " ideal model delta sigma weight residual 1.333 1.209 0.124 2.74e-02 1.33e+03 2.03e+01 bond pdb=" C02 H6U R 401 " pdb=" N01 H6U R 401 " ideal model delta sigma weight residual 1.348 1.438 -0.090 2.00e-02 2.50e+03 2.01e+01 ... (remaining 8002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 10653 2.28 - 4.56: 199 4.56 - 6.84: 29 6.84 - 9.12: 2 9.12 - 11.40: 2 Bond angle restraints: 10885 Sorted by residual: angle pdb=" N ILE A 365 " pdb=" CA ILE A 365 " pdb=" C ILE A 365 " ideal model delta sigma weight residual 112.35 106.61 5.74 1.41e+00 5.03e-01 1.66e+01 angle pdb=" C LEU R 221 " pdb=" N PHE R 222 " pdb=" CA PHE R 222 " ideal model delta sigma weight residual 120.31 114.26 6.05 1.52e+00 4.33e-01 1.58e+01 angle pdb=" N VAL R 37 " pdb=" CA VAL R 37 " pdb=" C VAL R 37 " ideal model delta sigma weight residual 113.16 107.84 5.32 1.49e+00 4.50e-01 1.27e+01 angle pdb=" C02 H6U R 401 " pdb=" S28 H6U R 401 " pdb=" C27 H6U R 401 " ideal model delta sigma weight residual 89.03 98.94 -9.91 3.00e+00 1.11e-01 1.09e+01 angle pdb=" C ARG N 98 " pdb=" N CYS N 99 " pdb=" CA CYS N 99 " ideal model delta sigma weight residual 122.15 110.75 11.40 3.47e+00 8.31e-02 1.08e+01 ... (remaining 10880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 4310 18.01 - 36.03: 376 36.03 - 54.04: 59 54.04 - 72.06: 14 72.06 - 90.07: 5 Dihedral angle restraints: 4764 sinusoidal: 1788 harmonic: 2976 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 158.35 -65.35 1 1.00e+01 1.00e-02 5.60e+01 dihedral pdb=" CA LEU A 281 " pdb=" C LEU A 281 " pdb=" N ASN A 282 " pdb=" CA ASN A 282 " ideal model delta harmonic sigma weight residual 180.00 -146.23 -33.77 0 5.00e+00 4.00e-02 4.56e+01 dihedral pdb=" CB CYS R 189 " pdb=" SG CYS R 189 " pdb=" SG CYS R 195 " pdb=" CB CYS R 195 " ideal model delta sinusoidal sigma weight residual -86.00 -122.50 36.50 1 1.00e+01 1.00e-02 1.88e+01 ... (remaining 4761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 708 0.036 - 0.072: 386 0.072 - 0.109: 124 0.109 - 0.145: 37 0.145 - 0.181: 3 Chirality restraints: 1258 Sorted by residual: chirality pdb=" CA PHE R 222 " pdb=" N PHE R 222 " pdb=" C PHE R 222 " pdb=" CB PHE R 222 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" CB VAL A 357 " pdb=" CA VAL A 357 " pdb=" CG1 VAL A 357 " pdb=" CG2 VAL A 357 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.97e-01 chirality pdb=" CA ILE A 244 " pdb=" N ILE A 244 " pdb=" C ILE A 244 " pdb=" CB ILE A 244 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.52e-01 ... (remaining 1255 not shown) Planarity restraints: 1394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE N 108 " -0.023 2.00e-02 2.50e+03 2.69e-02 1.26e+01 pdb=" CG PHE N 108 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE N 108 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE N 108 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 PHE N 108 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE N 108 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE N 108 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 308 " -0.018 2.00e-02 2.50e+03 1.35e-02 3.21e+00 pdb=" CG PHE R 308 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE R 308 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE R 308 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 308 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE R 308 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE R 308 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 321 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO A 322 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " 0.024 5.00e-02 4.00e+02 ... (remaining 1391 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 83 2.58 - 3.16: 6554 3.16 - 3.74: 12116 3.74 - 4.32: 17285 4.32 - 4.90: 29426 Nonbonded interactions: 65464 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.005 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.056 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.066 3.040 nonbonded pdb=" OG SER B 275 " pdb=" O SER B 316 " model vdw 2.240 3.040 nonbonded pdb=" OD1 ASP R 117 " pdb=" N VAL R 118 " model vdw 2.245 3.120 ... (remaining 65459 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 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: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.580 Find NCS groups from input model: 0.030 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 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 : 0.008 0.142 8011 Z= 0.363 Angle : 0.801 11.404 10893 Z= 0.443 Chirality : 0.049 0.181 1258 Planarity : 0.005 0.044 1394 Dihedral : 14.096 90.073 2826 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.78 (0.22), residues: 1011 helix: -1.82 (0.22), residues: 378 sheet: -3.37 (0.28), residues: 201 loop : -2.54 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 98 TYR 0.017 0.002 TYR B 59 PHE 0.061 0.003 PHE N 108 TRP 0.025 0.003 TRP B 99 HIS 0.012 0.002 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00837 ( 8007) covalent geometry : angle 0.79802 (10885) SS BOND : bond 0.00491 ( 4) SS BOND : angle 2.47552 ( 8) hydrogen bonds : bond 0.18028 ( 398) hydrogen bonds : angle 7.75481 ( 1119) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8301 (tttm) cc_final: 0.7973 (tttt) REVERT: A 323 ARG cc_start: 0.6958 (mtp180) cc_final: 0.6752 (mtm180) REVERT: B 61 MET cc_start: 0.8785 (ppp) cc_final: 0.8464 (ppp) REVERT: B 111 TYR cc_start: 0.8725 (m-80) cc_final: 0.8494 (m-80) REVERT: B 219 ARG cc_start: 0.7515 (mmt-90) cc_final: 0.7147 (mtp-110) REVERT: R 238 LEU cc_start: 0.8186 (tt) cc_final: 0.7864 (tp) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1301 time to fit residues: 22.7924 Evaluate side-chains 115 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 213 GLN A 261 ASN A 268 ASN B 239 ASN B 268 ASN N 1 GLN N 84 ASN R 338 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.145154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.117228 restraints weight = 8768.633| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.51 r_work: 0.3096 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8011 Z= 0.133 Angle : 0.599 7.135 10893 Z= 0.316 Chirality : 0.043 0.186 1258 Planarity : 0.005 0.061 1394 Dihedral : 6.066 74.513 1126 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.72 % Allowed : 12.38 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.25), residues: 1011 helix: 0.14 (0.26), residues: 378 sheet: -2.73 (0.31), residues: 203 loop : -1.97 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 137 TYR 0.010 0.001 TYR A 329 PHE 0.035 0.002 PHE R 222 TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8007) covalent geometry : angle 0.59817 (10885) SS BOND : bond 0.00207 ( 4) SS BOND : angle 1.06347 ( 8) hydrogen bonds : bond 0.04779 ( 398) hydrogen bonds : angle 5.11249 ( 1119) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.251 Fit side-chains REVERT: A 16 GLU cc_start: 0.7594 (mp0) cc_final: 0.7205 (mp0) REVERT: A 17 LYS cc_start: 0.8577 (tttm) cc_final: 0.8297 (tttt) REVERT: A 209 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6898 (mm-30) REVERT: A 249 ASP cc_start: 0.8062 (p0) cc_final: 0.7832 (p0) REVERT: B 33 ILE cc_start: 0.7434 (OUTLIER) cc_final: 0.7030 (mp) REVERT: B 219 ARG cc_start: 0.7862 (mmt-90) cc_final: 0.7642 (mtp-110) REVERT: R 238 LEU cc_start: 0.8357 (tt) cc_final: 0.8117 (tp) REVERT: R 242 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8387 (tt) outliers start: 14 outliers final: 8 residues processed: 139 average time/residue: 0.1239 time to fit residues: 21.8465 Evaluate side-chains 123 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 242 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 26 optimal weight: 0.0670 chunk 39 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 overall best weight: 2.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.143137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.113343 restraints weight = 8761.140| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.51 r_work: 0.3124 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8011 Z= 0.181 Angle : 0.602 7.952 10893 Z= 0.314 Chirality : 0.045 0.214 1258 Planarity : 0.004 0.052 1394 Dihedral : 5.828 72.237 1126 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.55 % Allowed : 14.71 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.26), residues: 1011 helix: 0.64 (0.27), residues: 384 sheet: -2.22 (0.31), residues: 220 loop : -1.74 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 98 TYR 0.015 0.001 TYR A 37 PHE 0.033 0.002 PHE R 222 TRP 0.014 0.002 TRP B 99 HIS 0.008 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 8007) covalent geometry : angle 0.60134 (10885) SS BOND : bond 0.00199 ( 4) SS BOND : angle 1.14881 ( 8) hydrogen bonds : bond 0.04653 ( 398) hydrogen bonds : angle 4.88253 ( 1119) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.290 Fit side-chains REVERT: A 16 GLU cc_start: 0.7522 (mp0) cc_final: 0.7122 (mp0) REVERT: A 17 LYS cc_start: 0.8514 (tttm) cc_final: 0.8233 (tttt) REVERT: A 209 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6845 (mm-30) REVERT: A 211 LYS cc_start: 0.8934 (mttp) cc_final: 0.8280 (mtpt) REVERT: A 299 GLU cc_start: 0.8213 (pm20) cc_final: 0.7880 (pm20) REVERT: B 33 ILE cc_start: 0.7276 (OUTLIER) cc_final: 0.6828 (mp) REVERT: B 219 ARG cc_start: 0.7928 (mmt-90) cc_final: 0.7604 (mtp-110) REVERT: N 108 PHE cc_start: 0.9183 (OUTLIER) cc_final: 0.8570 (t80) REVERT: R 238 LEU cc_start: 0.8423 (tt) cc_final: 0.8154 (tp) REVERT: R 242 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8458 (tt) outliers start: 29 outliers final: 23 residues processed: 142 average time/residue: 0.1151 time to fit residues: 20.8841 Evaluate side-chains 143 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 134 ASP Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 303 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 9 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 88 optimal weight: 30.0000 chunk 35 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 88 ASN B 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.147497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.117838 restraints weight = 8801.801| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.52 r_work: 0.3179 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8011 Z= 0.114 Angle : 0.532 7.565 10893 Z= 0.278 Chirality : 0.041 0.139 1258 Planarity : 0.004 0.046 1394 Dihedral : 5.373 69.429 1126 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.82 % Allowed : 17.52 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.26), residues: 1011 helix: 1.22 (0.27), residues: 378 sheet: -2.26 (0.31), residues: 216 loop : -1.52 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 256 TYR 0.009 0.001 TYR A 37 PHE 0.030 0.002 PHE R 341 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8007) covalent geometry : angle 0.53210 (10885) SS BOND : bond 0.00131 ( 4) SS BOND : angle 0.78372 ( 8) hydrogen bonds : bond 0.04032 ( 398) hydrogen bonds : angle 4.61627 ( 1119) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.237 Fit side-chains REVERT: A 16 GLU cc_start: 0.7472 (mp0) cc_final: 0.6980 (mp0) REVERT: A 17 LYS cc_start: 0.8471 (tttm) cc_final: 0.8224 (tttt) REVERT: A 211 LYS cc_start: 0.8844 (mttp) cc_final: 0.8234 (mtpt) REVERT: A 307 ARG cc_start: 0.8133 (ptp-110) cc_final: 0.7771 (mtm-85) REVERT: B 33 ILE cc_start: 0.7302 (OUTLIER) cc_final: 0.6866 (mp) REVERT: B 217 MET cc_start: 0.8065 (ttt) cc_final: 0.7509 (ppp) REVERT: B 234 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.8425 (m-80) REVERT: N 94 TYR cc_start: 0.8760 (m-80) cc_final: 0.8480 (m-80) REVERT: R 238 LEU cc_start: 0.8375 (tt) cc_final: 0.8169 (tp) REVERT: R 242 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8402 (tt) REVERT: R 357 ARG cc_start: 0.8142 (mtp85) cc_final: 0.7227 (ttp80) outliers start: 23 outliers final: 13 residues processed: 143 average time/residue: 0.1098 time to fit residues: 20.3518 Evaluate side-chains 133 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 134 ASP Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 242 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 47 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 60 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN N 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.145071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.115228 restraints weight = 8807.604| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.52 r_work: 0.3108 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8011 Z= 0.160 Angle : 0.561 9.150 10893 Z= 0.292 Chirality : 0.043 0.158 1258 Planarity : 0.004 0.044 1394 Dihedral : 5.523 68.715 1126 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.17 % Allowed : 17.16 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.73 (0.27), residues: 1011 helix: 1.42 (0.27), residues: 372 sheet: -2.05 (0.31), residues: 228 loop : -1.24 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 19 TYR 0.014 0.001 TYR A 37 PHE 0.029 0.002 PHE R 222 TRP 0.012 0.001 TRP B 99 HIS 0.007 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 8007) covalent geometry : angle 0.56068 (10885) SS BOND : bond 0.00075 ( 4) SS BOND : angle 0.98140 ( 8) hydrogen bonds : bond 0.04214 ( 398) hydrogen bonds : angle 4.63187 ( 1119) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 0.297 Fit side-chains REVERT: A 16 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: A 17 LYS cc_start: 0.8478 (tttm) cc_final: 0.8247 (tttt) REVERT: A 211 LYS cc_start: 0.8807 (mttp) cc_final: 0.8233 (mtpt) REVERT: B 33 ILE cc_start: 0.7321 (OUTLIER) cc_final: 0.6846 (mp) REVERT: B 153 ASP cc_start: 0.8476 (m-30) cc_final: 0.8212 (m-30) REVERT: B 217 MET cc_start: 0.8032 (ttt) cc_final: 0.7598 (ppp) REVERT: B 234 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.8434 (m-80) REVERT: R 238 LEU cc_start: 0.8412 (tt) cc_final: 0.8195 (tp) REVERT: R 242 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8418 (tt) REVERT: R 357 ARG cc_start: 0.8140 (mtp85) cc_final: 0.7272 (ttp80) outliers start: 34 outliers final: 21 residues processed: 142 average time/residue: 0.1086 time to fit residues: 20.0641 Evaluate side-chains 140 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 134 ASP Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 242 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 23 optimal weight: 8.9990 chunk 8 optimal weight: 0.1980 chunk 69 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 20.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.144270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.114534 restraints weight = 8737.414| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.51 r_work: 0.3122 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8011 Z= 0.177 Angle : 0.576 11.489 10893 Z= 0.299 Chirality : 0.043 0.168 1258 Planarity : 0.004 0.044 1394 Dihedral : 5.565 68.684 1126 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.78 % Allowed : 17.77 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.27), residues: 1011 helix: 1.47 (0.27), residues: 372 sheet: -1.94 (0.31), residues: 228 loop : -1.18 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 98 TYR 0.015 0.002 TYR R 346 PHE 0.028 0.002 PHE R 222 TRP 0.014 0.002 TRP B 99 HIS 0.007 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 8007) covalent geometry : angle 0.57559 (10885) SS BOND : bond 0.00076 ( 4) SS BOND : angle 1.01771 ( 8) hydrogen bonds : bond 0.04295 ( 398) hydrogen bonds : angle 4.62959 ( 1119) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 0.296 Fit side-chains REVERT: A 16 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: A 17 LYS cc_start: 0.8476 (tttm) cc_final: 0.8253 (tttt) REVERT: A 211 LYS cc_start: 0.8814 (mttp) cc_final: 0.8230 (mtpt) REVERT: B 33 ILE cc_start: 0.7393 (OUTLIER) cc_final: 0.6915 (mp) REVERT: B 234 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8425 (m-80) REVERT: N 98 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8285 (ppt170) REVERT: R 148 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7834 (tt) REVERT: R 238 LEU cc_start: 0.8383 (tt) cc_final: 0.8145 (tp) REVERT: R 242 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8397 (tt) REVERT: R 357 ARG cc_start: 0.8111 (mtp85) cc_final: 0.7254 (ttp80) outliers start: 39 outliers final: 27 residues processed: 142 average time/residue: 0.1101 time to fit residues: 20.1833 Evaluate side-chains 145 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 134 ASP Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 242 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 63 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 97 optimal weight: 0.0870 chunk 72 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.145779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.116016 restraints weight = 8738.856| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.51 r_work: 0.3120 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8011 Z= 0.138 Angle : 0.563 15.357 10893 Z= 0.288 Chirality : 0.042 0.173 1258 Planarity : 0.004 0.042 1394 Dihedral : 5.451 68.465 1126 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.04 % Allowed : 18.63 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.27), residues: 1011 helix: 1.64 (0.27), residues: 371 sheet: -1.99 (0.32), residues: 225 loop : -1.09 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 19 TYR 0.014 0.001 TYR R 346 PHE 0.026 0.002 PHE R 222 TRP 0.013 0.001 TRP B 99 HIS 0.005 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8007) covalent geometry : angle 0.56288 (10885) SS BOND : bond 0.00083 ( 4) SS BOND : angle 0.95851 ( 8) hydrogen bonds : bond 0.04097 ( 398) hydrogen bonds : angle 4.54117 ( 1119) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.282 Fit side-chains REVERT: A 16 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: A 17 LYS cc_start: 0.8477 (tttm) cc_final: 0.8257 (tttt) REVERT: A 211 LYS cc_start: 0.8784 (mttp) cc_final: 0.8242 (mtpt) REVERT: A 307 ARG cc_start: 0.8059 (ptp-110) cc_final: 0.7770 (mtm-85) REVERT: B 33 ILE cc_start: 0.7387 (OUTLIER) cc_final: 0.6904 (mp) REVERT: B 152 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8220 (tt) REVERT: B 234 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8357 (m-80) REVERT: N 98 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8127 (ppt170) REVERT: R 148 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7843 (tt) REVERT: R 238 LEU cc_start: 0.8354 (tt) cc_final: 0.8114 (tp) REVERT: R 242 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8401 (tt) REVERT: R 357 ARG cc_start: 0.8095 (mtp85) cc_final: 0.7251 (ttp80) outliers start: 33 outliers final: 20 residues processed: 141 average time/residue: 0.1075 time to fit residues: 19.5894 Evaluate side-chains 140 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 134 ASP Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 242 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 21 optimal weight: 0.3980 chunk 19 optimal weight: 10.0000 chunk 74 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 88 optimal weight: 30.0000 chunk 26 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.145189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.115398 restraints weight = 8710.351| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.51 r_work: 0.3092 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8011 Z= 0.163 Angle : 0.571 13.887 10893 Z= 0.293 Chirality : 0.043 0.185 1258 Planarity : 0.004 0.042 1394 Dihedral : 5.509 68.937 1126 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.78 % Allowed : 18.26 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.27), residues: 1011 helix: 1.59 (0.27), residues: 376 sheet: -1.96 (0.32), residues: 221 loop : -1.11 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 67 TYR 0.015 0.001 TYR R 346 PHE 0.026 0.002 PHE R 222 TRP 0.014 0.001 TRP B 99 HIS 0.006 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 8007) covalent geometry : angle 0.57064 (10885) SS BOND : bond 0.00073 ( 4) SS BOND : angle 1.02658 ( 8) hydrogen bonds : bond 0.04182 ( 398) hydrogen bonds : angle 4.53200 ( 1119) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 0.278 Fit side-chains REVERT: A 16 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: A 211 LYS cc_start: 0.8786 (mttp) cc_final: 0.8249 (mtpt) REVERT: A 307 ARG cc_start: 0.8174 (ptp-110) cc_final: 0.7873 (mtm-85) REVERT: B 33 ILE cc_start: 0.7352 (OUTLIER) cc_final: 0.6880 (mp) REVERT: B 152 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8245 (tt) REVERT: B 234 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8339 (m-80) REVERT: N 98 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8223 (ppt170) REVERT: R 148 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7869 (tt) REVERT: R 238 LEU cc_start: 0.8369 (tt) cc_final: 0.8126 (tp) REVERT: R 240 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7278 (ttp-170) REVERT: R 242 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8400 (tt) REVERT: R 357 ARG cc_start: 0.8124 (mtp85) cc_final: 0.7279 (ttp80) outliers start: 39 outliers final: 27 residues processed: 145 average time/residue: 0.1154 time to fit residues: 21.5001 Evaluate side-chains 149 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 134 ASP Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 240 ARG Chi-restraints excluded: chain R residue 242 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 53 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** 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 = 0.3572 r_free = 0.3572 target = 0.139811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.108876 restraints weight = 8592.731| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.55 r_work: 0.3097 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8011 Z= 0.154 Angle : 0.567 13.613 10893 Z= 0.291 Chirality : 0.043 0.192 1258 Planarity : 0.004 0.041 1394 Dihedral : 5.491 68.934 1126 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.78 % Allowed : 19.12 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.27), residues: 1011 helix: 1.66 (0.27), residues: 376 sheet: -1.92 (0.32), residues: 221 loop : -1.10 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 364 TYR 0.015 0.001 TYR R 346 PHE 0.025 0.002 PHE R 222 TRP 0.014 0.001 TRP B 99 HIS 0.006 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 8007) covalent geometry : angle 0.56661 (10885) SS BOND : bond 0.00075 ( 4) SS BOND : angle 1.00939 ( 8) hydrogen bonds : bond 0.04126 ( 398) hydrogen bonds : angle 4.50576 ( 1119) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 0.293 Fit side-chains REVERT: A 16 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: A 211 LYS cc_start: 0.8781 (mttp) cc_final: 0.8203 (mtpt) REVERT: A 307 ARG cc_start: 0.8153 (ptp-110) cc_final: 0.7817 (mtm-85) REVERT: B 33 ILE cc_start: 0.7260 (OUTLIER) cc_final: 0.6791 (mp) REVERT: B 152 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8184 (tt) REVERT: B 234 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8319 (m-80) REVERT: N 98 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8141 (ppt170) REVERT: R 148 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7844 (tt) REVERT: R 238 LEU cc_start: 0.8312 (tt) cc_final: 0.8069 (tp) REVERT: R 240 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7221 (ttp-170) REVERT: R 242 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8405 (tt) REVERT: R 357 ARG cc_start: 0.8087 (mtp85) cc_final: 0.7215 (ttp80) outliers start: 39 outliers final: 25 residues processed: 143 average time/residue: 0.1110 time to fit residues: 20.5004 Evaluate side-chains 147 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 134 ASP Chi-restraints excluded: chain R residue 148 LEU Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 223 VAL Chi-restraints excluded: chain R residue 240 ARG Chi-restraints excluded: chain R residue 242 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 47 optimal weight: 3.9990 chunk 68 optimal weight: 0.3980 chunk 84 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 97 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 74 optimal weight: 0.0020 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.143933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.113534 restraints weight = 8559.115| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.55 r_work: 0.3198 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8011 Z= 0.105 Angle : 0.531 14.817 10893 Z= 0.270 Chirality : 0.041 0.178 1258 Planarity : 0.004 0.040 1394 Dihedral : 5.105 67.245 1126 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.94 % Allowed : 21.08 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.27), residues: 1011 helix: 1.95 (0.27), residues: 375 sheet: -1.94 (0.31), residues: 223 loop : -1.00 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 256 TYR 0.011 0.001 TYR R 346 PHE 0.023 0.001 PHE R 222 TRP 0.014 0.001 TRP A 271 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 8007) covalent geometry : angle 0.53072 (10885) SS BOND : bond 0.00142 ( 4) SS BOND : angle 0.73575 ( 8) hydrogen bonds : bond 0.03691 ( 398) hydrogen bonds : angle 4.36281 ( 1119) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.304 Fit side-chains REVERT: A 307 ARG cc_start: 0.8059 (ptp-110) cc_final: 0.7712 (mtm-85) REVERT: B 33 ILE cc_start: 0.7274 (OUTLIER) cc_final: 0.6796 (mp) REVERT: B 234 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8295 (m-80) REVERT: N 98 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7974 (ppt170) REVERT: R 238 LEU cc_start: 0.8307 (tt) cc_final: 0.8083 (tp) REVERT: R 357 ARG cc_start: 0.8062 (mtp85) cc_final: 0.7178 (ttp80) outliers start: 24 outliers final: 15 residues processed: 135 average time/residue: 0.1157 time to fit residues: 20.1168 Evaluate side-chains 130 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 134 ASP Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 223 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 44 optimal weight: 0.0060 chunk 53 optimal weight: 2.9990 chunk 7 optimal weight: 0.0070 chunk 2 optimal weight: 1.9990 overall best weight: 0.9818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.148759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.118934 restraints weight = 8552.278| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.52 r_work: 0.3211 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8011 Z= 0.117 Angle : 0.541 14.964 10893 Z= 0.276 Chirality : 0.042 0.178 1258 Planarity : 0.004 0.040 1394 Dihedral : 5.121 66.379 1126 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.70 % Allowed : 21.20 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.27), residues: 1011 helix: 2.00 (0.27), residues: 376 sheet: -1.91 (0.31), residues: 225 loop : -0.93 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 256 TYR 0.013 0.001 TYR R 346 PHE 0.023 0.001 PHE R 222 TRP 0.013 0.001 TRP B 99 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8007) covalent geometry : angle 0.54125 (10885) SS BOND : bond 0.00096 ( 4) SS BOND : angle 0.80717 ( 8) hydrogen bonds : bond 0.03731 ( 398) hydrogen bonds : angle 4.35122 ( 1119) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2023.80 seconds wall clock time: 35 minutes 15.44 seconds (2115.44 seconds total)