Starting phenix.real_space_refine on Thu Jul 2 08:06:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xji_33228/07_2026/7xji_33228.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xji_33228/07_2026/7xji_33228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7xji_33228/07_2026/7xji_33228.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xji_33228/07_2026/7xji_33228.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xji_33228/07_2026/7xji_33228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xji_33228/07_2026/7xji_33228.map" model { file = "/net/cci-nas-00/data/ceres_data/7xji_33228/07_2026/7xji_33228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xji_33228/07_2026/7xji_33228.cif" } resolution = 3.9 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= 0.001 sd= 0.008 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: 5 Type Number sf(0) Gaussians S 46 5.16 5 Cl 1 4.86 5 C 4977 2.51 5 N 1381 2.21 5 O 1446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7851 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: "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: "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: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'EI5': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.01, per 1000 atoms: 0.26 Number of scatterers: 7851 At special positions: 0 Unit cell: (101.592, 77.688, 132.667, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 46 16.00 O 1446 8.00 N 1381 7.00 C 4977 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=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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=2.04 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: 0.43 Conformation dependent library (CDL) restraints added in 348.3 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: 27 helices and 10 sheets defined 40.5% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.513A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 removed outlier: 3.702A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 52 through 57' Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.886A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.375A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 306 removed outlier: 3.547A 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: 3.553A pdb=" N ILE A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 3.899A pdb=" N ASP A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP A 371 " --> pdb=" O ASN A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.683A pdb=" N GLN B 6 " --> pdb=" O SER B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.750A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.625A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.640A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 64 removed outlier: 3.951A pdb=" N ALA R 50 " --> pdb=" O LEU R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 69 removed outlier: 3.560A pdb=" N GLN R 69 " --> pdb=" O PRO R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 90 removed outlier: 3.880A pdb=" N VAL R 76 " --> pdb=" O THR R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 100 Processing helix chain 'R' and resid 106 through 141 Processing helix chain 'R' and resid 150 through 170 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: 4.493A 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 removed outlier: 3.521A pdb=" N LEU R 328 " --> pdb=" O PRO R 324 " (cutoff:3.500A) Proline residue: R 343 - end of helix Processing helix chain 'R' and resid 349 through 360 Processing helix chain 'G' and resid 11 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.510A pdb=" N TYR G 40 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.792A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.586A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.496A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.612A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.222A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 150 removed outlier: 3.820A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 191 removed outlier: 3.674A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.722A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.341A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.531A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.615A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1122 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: 0.84 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2590 1.34 - 1.46: 1911 1.46 - 1.58: 3445 1.58 - 1.70: 0 1.70 - 1.82: 62 Bond restraints: 8008 Sorted by residual: bond pdb=" C6 EI5 R 401 " pdb=" O1 EI5 R 401 " ideal model delta sigma weight residual 1.246 1.306 -0.060 2.00e-02 2.50e+03 8.95e+00 bond pdb=" C4 EI5 R 401 " pdb=" C6 EI5 R 401 " ideal model delta sigma weight residual 1.528 1.488 0.040 2.00e-02 2.50e+03 4.04e+00 bond pdb=" CB PRO R 320 " pdb=" CG PRO R 320 " ideal model delta sigma weight residual 1.492 1.567 -0.075 5.00e-02 4.00e+02 2.26e+00 bond pdb=" CA ASN R 192 " pdb=" CB ASN R 192 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.37e+00 bond pdb=" C16 EI5 R 401 " pdb=" O2 EI5 R 401 " ideal model delta sigma weight residual 1.401 1.423 -0.022 2.00e-02 2.50e+03 1.25e+00 ... (remaining 8003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 10638 1.64 - 3.28: 197 3.28 - 4.92: 35 4.92 - 6.56: 14 6.56 - 8.20: 3 Bond angle restraints: 10887 Sorted by residual: angle pdb=" N VAL A 357 " pdb=" CA VAL A 357 " pdb=" C VAL A 357 " ideal model delta sigma weight residual 112.43 108.30 4.13 9.20e-01 1.18e+00 2.02e+01 angle pdb=" N VAL R 37 " pdb=" CA VAL R 37 " pdb=" C VAL R 37 " ideal model delta sigma weight residual 113.71 110.07 3.64 9.50e-01 1.11e+00 1.47e+01 angle pdb=" C LEU R 221 " pdb=" N PHE R 222 " pdb=" CA PHE R 222 " ideal model delta sigma weight residual 120.68 114.20 6.48 1.70e+00 3.46e-01 1.45e+01 angle pdb=" CA CYS R 195 " pdb=" CB CYS R 195 " pdb=" SG CYS R 195 " ideal model delta sigma weight residual 114.40 122.04 -7.64 2.30e+00 1.89e-01 1.10e+01 angle pdb=" C VAL R 90 " pdb=" N VAL R 91 " pdb=" CA VAL R 91 " ideal model delta sigma weight residual 120.33 122.49 -2.16 8.00e-01 1.56e+00 7.28e+00 ... (remaining 10882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.75: 4392 19.75 - 39.50: 317 39.50 - 59.25: 36 59.25 - 79.00: 9 79.00 - 98.75: 6 Dihedral angle restraints: 4760 sinusoidal: 1784 harmonic: 2976 Sorted by residual: dihedral pdb=" CB CYS R 110 " pdb=" SG CYS R 110 " pdb=" SG CYS R 196 " pdb=" CB CYS R 196 " ideal model delta sinusoidal sigma weight residual 93.00 -177.52 -89.48 1 1.00e+01 1.00e-02 9.51e+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 93.00 4.82 88.18 1 1.00e+01 1.00e-02 9.30e+01 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 93.00 147.93 -54.93 1 1.00e+01 1.00e-02 4.08e+01 ... (remaining 4757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 878 0.039 - 0.078: 281 0.078 - 0.117: 85 0.117 - 0.155: 13 0.155 - 0.194: 1 Chirality restraints: 1258 Sorted by residual: chirality pdb=" CB THR A 315 " pdb=" CA THR A 315 " pdb=" OG1 THR A 315 " pdb=" CG2 THR A 315 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CA ILE R 202 " pdb=" N ILE R 202 " pdb=" C ILE R 202 " pdb=" CB ILE R 202 " both_signs ideal model delta sigma weight residual False 2.43 2.29 0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" CA PRO R 320 " pdb=" N PRO R 320 " pdb=" C PRO R 320 " pdb=" CB PRO R 320 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 1255 not shown) Planarity restraints: 1394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 342 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO R 343 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO R 343 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 343 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 341 " 0.013 2.00e-02 2.50e+03 1.31e-02 3.02e+00 pdb=" CG PHE R 341 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE R 341 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE R 341 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE R 341 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 341 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE R 341 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY R 319 " 0.027 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO R 320 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO R 320 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 320 " 0.022 5.00e-02 4.00e+02 ... (remaining 1391 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 265 2.71 - 3.26: 7821 3.26 - 3.81: 12399 3.81 - 4.35: 15240 4.35 - 4.90: 26286 Nonbonded interactions: 62011 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.165 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.251 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.267 3.040 nonbonded pdb=" O ARG B 314 " pdb=" OG SER B 331 " model vdw 2.278 3.040 nonbonded pdb=" OD2 ASP B 258 " pdb=" NH1 ARG G 27 " model vdw 2.289 3.120 ... (remaining 62006 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: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.070 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 0.075 8012 Z= 0.156 Angle : 0.608 8.196 10895 Z= 0.325 Chirality : 0.042 0.194 1258 Planarity : 0.004 0.048 1394 Dihedral : 13.856 98.747 2822 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -0.25 (0.27), residues: 1011 helix: 0.90 (0.27), residues: 391 sheet: -0.97 (0.35), residues: 221 loop : -0.61 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 255 TYR 0.012 0.001 TYR R 204 PHE 0.031 0.002 PHE R 341 TRP 0.006 0.001 TRP A 271 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 8008) covalent geometry : angle 0.60431 / 0.32 (10887) SS BOND : bond 0.00280 / 0.13 ( 4) SS BOND : angle 2.40302 / 1.43 ( 8) hydrogen bonds : bond 0.19658 / 12.74 ( 390) hydrogen bonds : angle 7.35435 / 5.27 ( 1122) *********************** 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 173 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 205 SER cc_start: 0.7508 (p) cc_final: 0.7221 (t) REVERT: A 252 ASP cc_start: 0.8546 (t0) cc_final: 0.8223 (t0) REVERT: A 304 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7615 (mm-30) REVERT: A 344 ASP cc_start: 0.6738 (m-30) cc_final: 0.6388 (p0) REVERT: B 145 TYR cc_start: 0.8429 (p90) cc_final: 0.8203 (p90) REVERT: B 156 GLN cc_start: 0.8681 (mm110) cc_final: 0.8090 (mm-40) REVERT: B 175 GLN cc_start: 0.7788 (pt0) cc_final: 0.7255 (mt0) REVERT: B 188 MET cc_start: 0.8138 (mmm) cc_final: 0.7211 (mmm) REVERT: B 262 MET cc_start: 0.7888 (mmm) cc_final: 0.7617 (mmp) REVERT: N 82 GLN cc_start: 0.8071 (tm-30) cc_final: 0.7857 (tm-30) REVERT: N 84 ASN cc_start: 0.7227 (m-40) cc_final: 0.7004 (m-40) REVERT: R 235 LEU cc_start: 0.8159 (tt) cc_final: 0.7909 (tt) REVERT: G 19 LEU cc_start: 0.7467 (tp) cc_final: 0.6859 (tp) REVERT: G 21 MET cc_start: 0.6481 (ttm) cc_final: 0.6185 (ttp) REVERT: G 22 GLU cc_start: 0.5603 (mp0) cc_final: 0.4871 (mp0) REVERT: G 32 LYS cc_start: 0.8459 (ptpt) cc_final: 0.7588 (mmtt) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.0575 time to fit residues: 14.2495 Evaluate side-chains 129 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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: 6.9990 chunk 97 optimal weight: 30.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.128549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.106156 restraints weight = 11386.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.108281 restraints weight = 7705.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.109539 restraints weight = 5924.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.110720 restraints weight = 5010.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.111276 restraints weight = 4458.707| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8012 Z= 0.240 Angle : 0.672 7.753 10895 Z= 0.349 Chirality : 0.046 0.226 1258 Planarity : 0.005 0.045 1394 Dihedral : 5.495 91.353 1122 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.33 % Allowed : 11.15 % Favored : 86.52 % 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: 1.06 (0.26), residues: 392 sheet: -0.95 (0.37), residues: 196 loop : -0.81 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 49 TYR 0.018 0.002 TYR N 60 PHE 0.039 0.003 PHE R 222 TRP 0.011 0.002 TRP B 297 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.24 ( 8008) covalent geometry : angle 0.66883 / 0.35 (10887) SS BOND : bond 0.00228 / 0.09 ( 4) SS BOND : angle 2.33639 / 1.40 ( 8) hydrogen bonds : bond 0.04920 / 3.22 ( 390) hydrogen bonds : angle 5.33805 / 3.84 ( 1122) *********************** 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 146 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.257 Fit side-chains REVERT: A 205 SER cc_start: 0.7993 (p) cc_final: 0.7626 (t) REVERT: A 304 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7485 (mm-30) REVERT: B 57 LYS cc_start: 0.8409 (mtmm) cc_final: 0.7967 (mtmm) REVERT: B 145 TYR cc_start: 0.8712 (p90) cc_final: 0.8298 (p90) REVERT: B 175 GLN cc_start: 0.7489 (pt0) cc_final: 0.7246 (mt0) REVERT: B 188 MET cc_start: 0.8450 (mmm) cc_final: 0.7979 (mmm) REVERT: B 331 SER cc_start: 0.8723 (t) cc_final: 0.8157 (t) REVERT: B 333 ASP cc_start: 0.8217 (p0) cc_final: 0.7383 (p0) REVERT: R 207 LEU cc_start: 0.8972 (tt) cc_final: 0.8764 (tt) outliers start: 19 outliers final: 15 residues processed: 140 average time/residue: 0.0578 time to fit residues: 11.6278 Evaluate side-chains 132 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain R residue 312 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 13 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 6 optimal weight: 0.0870 chunk 18 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.132233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.109916 restraints weight = 11064.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.112113 restraints weight = 7394.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.113443 restraints weight = 5661.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.114588 restraints weight = 4768.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.115070 restraints weight = 4227.507| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8012 Z= 0.130 Angle : 0.570 8.497 10895 Z= 0.292 Chirality : 0.042 0.163 1258 Planarity : 0.004 0.047 1394 Dihedral : 5.217 89.456 1122 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.82 % Allowed : 11.64 % Favored : 85.54 % 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: 0.07 (0.27), residues: 1011 helix: 1.45 (0.27), residues: 387 sheet: -0.79 (0.38), residues: 190 loop : -0.80 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 38 TYR 0.014 0.001 TYR R 204 PHE 0.023 0.002 PHE R 222 TRP 0.013 0.001 TRP N 47 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 8008) covalent geometry : angle 0.56754 / 0.29 (10887) SS BOND : bond 0.00282 / 0.11 ( 4) SS BOND : angle 1.85871 / 1.12 ( 8) hydrogen bonds : bond 0.04080 / 2.67 ( 390) hydrogen bonds : angle 4.95715 / 3.59 ( 1122) *********************** 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 158 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.232 Fit side-chains REVERT: A 205 SER cc_start: 0.7912 (p) cc_final: 0.7607 (t) REVERT: A 304 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7135 (mm-30) REVERT: B 57 LYS cc_start: 0.8381 (mtmm) cc_final: 0.8139 (mtmt) REVERT: B 145 TYR cc_start: 0.8700 (p90) cc_final: 0.8288 (p90) REVERT: B 188 MET cc_start: 0.8417 (mmm) cc_final: 0.7569 (mmm) outliers start: 23 outliers final: 15 residues processed: 152 average time/residue: 0.0553 time to fit residues: 12.3208 Evaluate side-chains 136 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 242 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 98 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 92 optimal weight: 0.4980 chunk 88 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.126408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.103061 restraints weight = 11483.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.105451 restraints weight = 7379.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.107028 restraints weight = 5514.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.107935 restraints weight = 4558.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.108608 restraints weight = 4044.897| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8012 Z= 0.203 Angle : 0.612 8.135 10895 Z= 0.317 Chirality : 0.044 0.229 1258 Planarity : 0.004 0.051 1394 Dihedral : 5.345 88.262 1122 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.66 % Allowed : 13.24 % Favored : 82.11 % 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: -0.04 (0.27), residues: 1011 helix: 1.30 (0.27), residues: 394 sheet: -0.84 (0.37), residues: 193 loop : -0.82 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 379 TYR 0.015 0.002 TYR N 80 PHE 0.031 0.002 PHE R 222 TRP 0.011 0.002 TRP B 297 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 ( 8008) covalent geometry : angle 0.61051 / 0.32 (10887) SS BOND : bond 0.00125 / 0.06 ( 4) SS BOND : angle 1.90992 / 1.14 ( 8) hydrogen bonds : bond 0.04187 / 2.74 ( 390) hydrogen bonds : angle 4.88974 / 3.53 ( 1122) *********************** 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 163 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 0.189 Fit side-chains REVERT: A 20 ARG cc_start: 0.7187 (tpt170) cc_final: 0.6981 (tpt170) REVERT: A 304 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7244 (mm-30) REVERT: B 57 LYS cc_start: 0.8487 (mtmm) cc_final: 0.8002 (mtmm) REVERT: B 93 ILE cc_start: 0.8982 (mt) cc_final: 0.8776 (mt) REVERT: B 188 MET cc_start: 0.8478 (mmm) cc_final: 0.7917 (mmm) outliers start: 38 outliers final: 26 residues processed: 150 average time/residue: 0.0564 time to fit residues: 12.2441 Evaluate side-chains 142 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 9 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.127412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.104026 restraints weight = 11339.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.106410 restraints weight = 7285.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.107814 restraints weight = 5433.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.109025 restraints weight = 4538.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.109638 restraints weight = 3993.092| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8012 Z= 0.165 Angle : 0.584 8.320 10895 Z= 0.301 Chirality : 0.043 0.210 1258 Planarity : 0.004 0.052 1394 Dihedral : 5.265 87.531 1122 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.90 % Allowed : 14.46 % Favored : 80.64 % 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: 0.04 (0.27), residues: 1011 helix: 1.36 (0.27), residues: 397 sheet: -0.80 (0.38), residues: 193 loop : -0.78 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.015 0.002 TYR N 80 PHE 0.024 0.002 PHE R 222 TRP 0.010 0.001 TRP B 99 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 8008) covalent geometry : angle 0.58236 / 0.30 (10887) SS BOND : bond 0.00163 / 0.07 ( 4) SS BOND : angle 1.74467 / 1.04 ( 8) hydrogen bonds : bond 0.03953 / 2.58 ( 390) hydrogen bonds : angle 4.75727 / 3.44 ( 1122) *********************** 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 163 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.239 Fit side-chains REVERT: A 304 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7197 (mm-30) REVERT: B 57 LYS cc_start: 0.8383 (mtmm) cc_final: 0.7982 (mtmm) REVERT: B 93 ILE cc_start: 0.8974 (mt) cc_final: 0.8735 (mt) REVERT: B 188 MET cc_start: 0.8503 (mmm) cc_final: 0.8065 (mmm) outliers start: 40 outliers final: 29 residues processed: 151 average time/residue: 0.0605 time to fit residues: 13.4124 Evaluate side-chains 144 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 20 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 20.0000 chunk 83 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.128967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.105711 restraints weight = 11133.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.108109 restraints weight = 7179.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.109516 restraints weight = 5356.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.110811 restraints weight = 4458.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.111434 restraints weight = 3887.382| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8012 Z= 0.134 Angle : 0.568 8.399 10895 Z= 0.288 Chirality : 0.042 0.185 1258 Planarity : 0.004 0.053 1394 Dihedral : 5.100 85.960 1122 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.53 % Allowed : 15.56 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.17 (0.27), residues: 1011 helix: 1.57 (0.27), residues: 393 sheet: -0.86 (0.37), residues: 200 loop : -0.73 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.016 0.001 TYR N 80 PHE 0.018 0.001 PHE R 222 TRP 0.010 0.001 TRP B 99 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 8008) covalent geometry : angle 0.56620 / 0.29 (10887) SS BOND : bond 0.00175 / 0.08 ( 4) SS BOND : angle 1.57729 / 0.94 ( 8) hydrogen bonds : bond 0.03704 / 2.42 ( 390) hydrogen bonds : angle 4.63938 / 3.35 ( 1122) *********************** 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 168 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7153 (mm-30) REVERT: B 93 ILE cc_start: 0.8876 (mt) cc_final: 0.8618 (mt) REVERT: B 188 MET cc_start: 0.8422 (mmm) cc_final: 0.8081 (mmm) REVERT: B 266 HIS cc_start: 0.6956 (OUTLIER) cc_final: 0.6593 (t-170) REVERT: B 321 THR cc_start: 0.8088 (p) cc_final: 0.7888 (p) outliers start: 37 outliers final: 27 residues processed: 157 average time/residue: 0.0564 time to fit residues: 13.0917 Evaluate side-chains 151 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain R residue 220 MET 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 61 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 29 optimal weight: 0.0870 chunk 68 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 92 optimal weight: 40.0000 chunk 70 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.129638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.107322 restraints weight = 11255.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.109504 restraints weight = 7458.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.111024 restraints weight = 5676.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.111883 restraints weight = 4724.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.112694 restraints weight = 4219.888| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8012 Z= 0.174 Angle : 0.599 8.894 10895 Z= 0.304 Chirality : 0.043 0.184 1258 Planarity : 0.004 0.053 1394 Dihedral : 5.211 85.825 1122 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.90 % Allowed : 15.81 % Favored : 79.29 % 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: 0.15 (0.27), residues: 1011 helix: 1.48 (0.27), residues: 397 sheet: -0.84 (0.37), residues: 207 loop : -0.70 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 379 TYR 0.014 0.002 TYR N 80 PHE 0.020 0.002 PHE R 222 TRP 0.010 0.001 TRP A 271 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 ( 8008) covalent geometry : angle 0.59789 / 0.30 (10887) SS BOND : bond 0.00167 / 0.08 ( 4) SS BOND : angle 1.68708 / 1.00 ( 8) hydrogen bonds : bond 0.03869 / 2.53 ( 390) hydrogen bonds : angle 4.63560 / 3.35 ( 1122) *********************** 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 166 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 126 time to evaluate : 0.272 Fit side-chains REVERT: A 304 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7161 (mm-30) REVERT: B 57 LYS cc_start: 0.8103 (mtmm) cc_final: 0.7883 (mtmt) REVERT: B 75 GLN cc_start: 0.7789 (mt0) cc_final: 0.7416 (mt0) REVERT: B 188 MET cc_start: 0.8420 (mmm) cc_final: 0.8215 (mmm) REVERT: B 226 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8185 (mm-30) REVERT: B 266 HIS cc_start: 0.7029 (OUTLIER) cc_final: 0.6624 (t-170) REVERT: B 321 THR cc_start: 0.8085 (p) cc_final: 0.7858 (p) REVERT: N 117 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.6323 (m-80) REVERT: R 52 VAL cc_start: 0.7902 (t) cc_final: 0.7510 (p) outliers start: 40 outliers final: 31 residues processed: 154 average time/residue: 0.0516 time to fit residues: 11.8432 Evaluate side-chains 153 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 220 MET Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 303 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 79 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.129335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.106109 restraints weight = 11177.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.108512 restraints weight = 7166.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.110093 restraints weight = 5342.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.111225 restraints weight = 4387.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.111865 restraints weight = 3858.978| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8012 Z= 0.132 Angle : 0.570 7.798 10895 Z= 0.288 Chirality : 0.042 0.181 1258 Planarity : 0.004 0.055 1394 Dihedral : 5.055 84.369 1122 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.41 % Allowed : 16.67 % Favored : 78.92 % 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: 0.23 (0.27), residues: 1011 helix: 1.62 (0.27), residues: 394 sheet: -0.79 (0.37), residues: 207 loop : -0.72 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 314 TYR 0.016 0.001 TYR N 80 PHE 0.015 0.001 PHE B 235 TRP 0.010 0.001 TRP B 99 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 8008) covalent geometry : angle 0.56754 / 0.29 (10887) SS BOND : bond 0.00132 / 0.06 ( 4) SS BOND : angle 2.04010 / 1.23 ( 8) hydrogen bonds : bond 0.03666 / 2.39 ( 390) hydrogen bonds : angle 4.57447 / 3.29 ( 1122) *********************** 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 166 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: A 304 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7158 (mm-30) REVERT: B 45 MET cc_start: 0.7814 (tpp) cc_final: 0.7135 (mmm) REVERT: B 57 LYS cc_start: 0.8147 (mtmm) cc_final: 0.7880 (mtmt) REVERT: B 188 MET cc_start: 0.8388 (mmm) cc_final: 0.8129 (mmm) REVERT: B 226 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8150 (mm-30) REVERT: B 266 HIS cc_start: 0.7006 (OUTLIER) cc_final: 0.6581 (t-170) REVERT: B 301 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.6761 (mmmt) REVERT: B 321 THR cc_start: 0.8065 (p) cc_final: 0.7809 (p) REVERT: N 117 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.6235 (m-80) REVERT: R 52 VAL cc_start: 0.7742 (t) cc_final: 0.7316 (p) outliers start: 36 outliers final: 29 residues processed: 154 average time/residue: 0.0519 time to fit residues: 11.6872 Evaluate side-chains 158 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain R residue 220 MET 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 31 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 8 optimal weight: 0.2980 chunk 85 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 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 = 0.3549 r_free = 0.3549 target = 0.130947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.107866 restraints weight = 11076.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.110340 restraints weight = 7054.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.111984 restraints weight = 5204.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.112980 restraints weight = 4258.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.113841 restraints weight = 3744.718| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8012 Z= 0.121 Angle : 0.567 7.828 10895 Z= 0.286 Chirality : 0.041 0.176 1258 Planarity : 0.004 0.057 1394 Dihedral : 4.975 82.718 1122 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.53 % Allowed : 16.79 % 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: 0.33 (0.27), residues: 1011 helix: 1.71 (0.27), residues: 394 sheet: -0.67 (0.37), residues: 201 loop : -0.71 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 27 TYR 0.016 0.001 TYR N 80 PHE 0.015 0.001 PHE B 235 TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 8008) covalent geometry : angle 0.56549 / 0.29 (10887) SS BOND : bond 0.00192 / 0.09 ( 4) SS BOND : angle 1.80262 / 1.09 ( 8) hydrogen bonds : bond 0.03540 / 2.31 ( 390) hydrogen bonds : angle 4.53996 / 3.26 ( 1122) *********************** 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 168 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: A 304 GLU cc_start: 0.7332 (mm-30) cc_final: 0.7111 (mm-30) REVERT: B 45 MET cc_start: 0.7827 (tpp) cc_final: 0.7200 (mmm) REVERT: B 188 MET cc_start: 0.8267 (mmm) cc_final: 0.8027 (mmm) REVERT: B 226 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8007 (mm-30) REVERT: B 266 HIS cc_start: 0.6953 (OUTLIER) cc_final: 0.6605 (t-170) REVERT: B 301 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.6803 (mmmt) REVERT: B 321 THR cc_start: 0.8144 (p) cc_final: 0.7913 (p) REVERT: N 83 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6849 (mtm) REVERT: N 117 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.6234 (m-80) REVERT: R 52 VAL cc_start: 0.7774 (t) cc_final: 0.7317 (p) outliers start: 37 outliers final: 28 residues processed: 156 average time/residue: 0.0516 time to fit residues: 11.8969 Evaluate side-chains 161 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain R residue 220 MET 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 56 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.127328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.104260 restraints weight = 11261.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.106593 restraints weight = 7271.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.108179 restraints weight = 5443.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.109084 restraints weight = 4498.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.109792 restraints weight = 3989.280| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8012 Z= 0.196 Angle : 0.617 7.751 10895 Z= 0.315 Chirality : 0.044 0.264 1258 Planarity : 0.004 0.056 1394 Dihedral : 5.207 83.967 1122 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.04 % Allowed : 17.89 % Favored : 78.06 % 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: 0.26 (0.27), residues: 1011 helix: 1.59 (0.27), residues: 401 sheet: -0.84 (0.36), residues: 207 loop : -0.64 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 379 TYR 0.014 0.002 TYR N 80 PHE 0.018 0.002 PHE B 235 TRP 0.011 0.002 TRP A 271 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 ( 8008) covalent geometry : angle 0.61524 / 0.31 (10887) SS BOND : bond 0.00128 / 0.06 ( 4) SS BOND : angle 1.91565 / 1.15 ( 8) hydrogen bonds : bond 0.03909 / 2.55 ( 390) hydrogen bonds : angle 4.60246 / 3.29 ( 1122) ********************** 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 159 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.300 Fit side-chains REVERT: A 304 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7213 (mm-30) REVERT: B 45 MET cc_start: 0.7828 (tpp) cc_final: 0.7219 (mmm) REVERT: B 156 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8361 (mt0) REVERT: B 188 MET cc_start: 0.8315 (mmm) cc_final: 0.8067 (mmm) REVERT: B 226 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8177 (mm-30) REVERT: B 266 HIS cc_start: 0.7189 (OUTLIER) cc_final: 0.6718 (t-170) REVERT: B 321 THR cc_start: 0.8129 (p) cc_final: 0.7862 (p) REVERT: N 117 TYR cc_start: 0.8232 (OUTLIER) cc_final: 0.6374 (m-80) REVERT: R 52 VAL cc_start: 0.7795 (t) cc_final: 0.7345 (p) outliers start: 33 outliers final: 27 residues processed: 147 average time/residue: 0.0564 time to fit residues: 12.4108 Evaluate side-chains 154 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 348 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 202 ILE Chi-restraints excluded: chain R residue 220 MET 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 100 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 0.1980 chunk 82 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 269 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 = 0.3562 r_free = 0.3562 target = 0.131982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.108912 restraints weight = 11052.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.111352 restraints weight = 6990.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.113036 restraints weight = 5177.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.114010 restraints weight = 4231.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.114711 restraints weight = 3726.832| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8012 Z= 0.110 Angle : 0.564 7.817 10895 Z= 0.283 Chirality : 0.041 0.241 1258 Planarity : 0.004 0.056 1394 Dihedral : 4.913 80.860 1122 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.19 % Allowed : 19.00 % Favored : 77.82 % 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: 0.34 (0.27), residues: 1011 helix: 1.75 (0.27), residues: 394 sheet: -0.76 (0.36), residues: 207 loop : -0.68 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 27 TYR 0.016 0.001 TYR N 80 PHE 0.014 0.001 PHE B 235 TRP 0.011 0.001 TRP B 99 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 8008) covalent geometry : angle 0.56243 / 0.28 (10887) SS BOND : bond 0.00193 / 0.09 ( 4) SS BOND : angle 1.69894 / 1.03 ( 8) hydrogen bonds : bond 0.03467 / 2.27 ( 390) hydrogen bonds : angle 4.49523 / 3.22 ( 1122) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 936.15 seconds wall clock time: 16 minutes 56.56 seconds (1016.56 seconds total)