Starting phenix.real_space_refine on Sun Jun 8 19:23:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zep_60042/06_2025/8zep_60042_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zep_60042/06_2025/8zep_60042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zep_60042/06_2025/8zep_60042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zep_60042/06_2025/8zep_60042.map" model { file = "/net/cci-nas-00/data/ceres_data/8zep_60042/06_2025/8zep_60042_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zep_60042/06_2025/8zep_60042_trim.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.035 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 12 5.49 5 S 58 5.16 5 C 6180 2.51 5 N 1689 2.21 5 O 1919 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9860 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1162 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "C" Number of atoms: 3729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3729 Classifications: {'peptide': 476} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 457} Chain: "D" Number of atoms: 3729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3729 Classifications: {'peptide': 476} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 457} Chain: "E" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1166 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 145} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' ZN': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' ZN': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2943 SG CYS C 244 53.724 65.585 52.280 1.00115.39 S ATOM 3404 SG CYS C 305 56.255 66.590 51.583 1.00 65.57 S ATOM 6672 SG CYS D 244 66.158 65.663 84.090 1.00 79.61 S ATOM 7133 SG CYS D 305 65.930 65.304 87.714 1.00 75.59 S Time building chain proxies: 6.48, per 1000 atoms: 0.66 Number of scatterers: 9860 At special positions: 0 Unit cell: (106.875, 124.83, 137.655, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 58 16.00 P 12 15.00 O 1919 8.00 N 1689 7.00 C 6180 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 305 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 244 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 191 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" SG CYS D 305 " pdb="ZN ZN D 502 " - pdb=" ND1 HIS D 191 " pdb="ZN ZN D 502 " - pdb=" SG CYS D 244 " 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2366 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 13 sheets defined 45.7% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'B' and resid 69 through 84 removed outlier: 3.879A pdb=" N GLN B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLN B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.644A pdb=" N GLN B 119 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 120 " --> pdb=" O VAL B 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 116 through 120' Processing helix chain 'B' and resid 123 through 130 Processing helix chain 'B' and resid 159 through 168 removed outlier: 3.618A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 191 Processing helix chain 'B' and resid 192 through 211 Processing helix chain 'B' and resid 211 through 216 Processing helix chain 'C' and resid 23 through 34 removed outlier: 3.803A pdb=" N LYS C 27 " --> pdb=" O PRO C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 49 Processing helix chain 'C' and resid 87 through 104 Processing helix chain 'C' and resid 104 through 109 removed outlier: 3.502A pdb=" N GLU C 109 " --> pdb=" O LYS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 142 removed outlier: 3.867A pdb=" N MET C 126 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 127 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 180 removed outlier: 3.514A pdb=" N LYS C 179 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE C 180 " --> pdb=" O GLY C 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 176 through 180' Processing helix chain 'C' and resid 191 through 214 removed outlier: 3.714A pdb=" N LEU C 195 " --> pdb=" O HIS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 263 Processing helix chain 'C' and resid 290 through 297 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 321 through 325 removed outlier: 3.614A pdb=" N HIS C 324 " --> pdb=" O ILE C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 350 Processing helix chain 'C' and resid 351 through 354 Processing helix chain 'C' and resid 428 through 443 Processing helix chain 'C' and resid 453 through 459 Processing helix chain 'C' and resid 460 through 477 Processing helix chain 'C' and resid 486 through 491 removed outlier: 3.772A pdb=" N MET C 491 " --> pdb=" O GLU C 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 34 removed outlier: 3.628A pdb=" N LYS D 27 " --> pdb=" O PRO D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 49 Processing helix chain 'D' and resid 87 through 105 removed outlier: 3.667A pdb=" N ALA D 91 " --> pdb=" O LYS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 142 removed outlier: 3.573A pdb=" N LEU D 127 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 146 Processing helix chain 'D' and resid 176 through 180 removed outlier: 3.529A pdb=" N ILE D 180 " --> pdb=" O GLY D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 214 removed outlier: 3.848A pdb=" N ARG D 197 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 249 Processing helix chain 'D' and resid 257 through 265 Processing helix chain 'D' and resid 290 through 296 Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 342 through 350 removed outlier: 3.599A pdb=" N ALA D 348 " --> pdb=" O ARG D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 354 Processing helix chain 'D' and resid 428 through 443 Processing helix chain 'D' and resid 452 through 459 Processing helix chain 'D' and resid 460 through 477 Processing helix chain 'D' and resid 486 through 491 removed outlier: 3.517A pdb=" N MET D 491 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 84 Processing helix chain 'E' and resid 104 through 109 removed outlier: 4.731A pdb=" N GLN E 109 " --> pdb=" O THR E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 120 Processing helix chain 'E' and resid 123 through 129 removed outlier: 3.591A pdb=" N LEU E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 131 No H-bonds generated for 'chain 'E' and resid 130 through 131' Processing helix chain 'E' and resid 132 through 136 removed outlier: 3.844A pdb=" N LYS E 135 " --> pdb=" O ASP E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 170 Processing helix chain 'E' and resid 177 through 191 removed outlier: 3.616A pdb=" N ARG E 190 " --> pdb=" O ASN E 186 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS E 191 " --> pdb=" O VAL E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 211 Processing helix chain 'E' and resid 211 through 216 removed outlier: 3.948A pdb=" N VAL E 215 " --> pdb=" O ALA E 211 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.360A pdb=" N VAL C 155 " --> pdb=" O ILE C 166 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU C 168 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA C 153 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE C 152 " --> pdb=" O ASN C 240 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER C 333 " --> pdb=" O PHE C 235 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR C 241 " --> pdb=" O ALA C 337 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE C 334 " --> pdb=" O GLY C 370 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 87 through 89 removed outlier: 4.678A pdb=" N MET C 392 " --> pdb=" O THR C 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 55 through 61 Processing sheet with id=AA4, first strand: chain 'C' and resid 220 through 221 Processing sheet with id=AA5, first strand: chain 'C' and resid 277 through 279 removed outlier: 3.552A pdb=" N PHE C 269 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR C 302 " --> pdb=" O LYS C 270 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 410 through 415 removed outlier: 5.662A pdb=" N ASP C 415 " --> pdb=" O ALA C 419 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA C 419 " --> pdb=" O ASP C 415 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 451 through 452 removed outlier: 4.397A pdb=" N ILE C 451 " --> pdb=" O ILE C 494 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 74 through 75 removed outlier: 4.217A pdb=" N LEU D 75 " --> pdb=" O GLU D 78 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 368 through 371 removed outlier: 3.729A pdb=" N VAL D 336 " --> pdb=" O GLY D 370 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER D 333 " --> pdb=" O PHE D 235 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA D 153 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU D 168 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL D 155 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET D 392 " --> pdb=" O THR D 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 368 through 371 removed outlier: 3.729A pdb=" N VAL D 336 " --> pdb=" O GLY D 370 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER D 333 " --> pdb=" O PHE D 235 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA D 153 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU D 168 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL D 155 " --> pdb=" O ILE D 166 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 220 through 222 Processing sheet with id=AB3, first strand: chain 'D' and resid 278 through 279 Processing sheet with id=AB4, first strand: chain 'D' and resid 411 through 414 removed outlier: 3.765A pdb=" N VAL D 411 " --> pdb=" O THR D 423 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR D 423 " --> pdb=" O VAL D 411 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1674 1.31 - 1.44: 2413 1.44 - 1.56: 5826 1.56 - 1.69: 13 1.69 - 1.82: 92 Bond restraints: 10018 Sorted by residual: bond pdb=" CA CYS C 244 " pdb=" C CYS C 244 " ideal model delta sigma weight residual 1.527 1.455 0.072 1.34e-02 5.57e+03 2.87e+01 bond pdb=" O12 IHP D 501 " pdb=" P2 IHP D 501 " ideal model delta sigma weight residual 1.675 1.589 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" O14 IHP D 501 " pdb=" P4 IHP D 501 " ideal model delta sigma weight residual 1.671 1.587 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" O16 IHP D 501 " pdb=" P6 IHP D 501 " ideal model delta sigma weight residual 1.672 1.592 0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" CA HIS C 191 " pdb=" CB HIS C 191 " ideal model delta sigma weight residual 1.529 1.467 0.062 1.59e-02 3.96e+03 1.52e+01 ... (remaining 10013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 13452 3.58 - 7.16: 78 7.16 - 10.74: 11 10.74 - 14.32: 1 14.32 - 17.90: 2 Bond angle restraints: 13544 Sorted by residual: angle pdb=" C HIS C 191 " pdb=" N ALA C 192 " pdb=" CA ALA C 192 " ideal model delta sigma weight residual 120.29 130.25 -9.96 1.42e+00 4.96e-01 4.92e+01 angle pdb=" CA HIS C 191 " pdb=" C HIS C 191 " pdb=" N ALA C 192 " ideal model delta sigma weight residual 115.30 123.72 -8.42 1.33e+00 5.65e-01 4.01e+01 angle pdb=" C4 IHP C 501 " pdb=" C5 IHP C 501 " pdb=" O15 IHP C 501 " ideal model delta sigma weight residual 111.56 129.46 -17.90 3.00e+00 1.11e-01 3.56e+01 angle pdb=" C4 IHP C 501 " pdb=" C5 IHP C 501 " pdb=" C6 IHP C 501 " ideal model delta sigma weight residual 109.60 92.22 17.38 3.00e+00 1.11e-01 3.36e+01 angle pdb=" CA HIS C 191 " pdb=" C HIS C 191 " pdb=" O HIS C 191 " ideal model delta sigma weight residual 121.87 116.97 4.90 1.10e+00 8.26e-01 1.99e+01 ... (remaining 13539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.24: 5962 33.24 - 66.48: 218 66.48 - 99.72: 19 99.72 - 132.95: 8 132.95 - 166.19: 5 Dihedral angle restraints: 6212 sinusoidal: 2567 harmonic: 3645 Sorted by residual: dihedral pdb=" CA GLN E 152 " pdb=" C GLN E 152 " pdb=" N ILE E 153 " pdb=" CA ILE E 153 " ideal model delta harmonic sigma weight residual 180.00 -150.36 -29.64 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" C CYS C 244 " pdb=" N CYS C 244 " pdb=" CA CYS C 244 " pdb=" CB CYS C 244 " ideal model delta harmonic sigma weight residual -122.60 -110.95 -11.65 0 2.50e+00 1.60e-01 2.17e+01 dihedral pdb=" C6 IHP C 501 " pdb=" C1 IHP C 501 " pdb=" C2 IHP C 501 " pdb=" O12 IHP C 501 " ideal model delta sinusoidal sigma weight residual 61.05 -132.76 -166.19 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 6209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.977: 1543 0.977 - 1.955: 0 1.955 - 2.932: 0 2.932 - 3.909: 0 3.909 - 4.887: 8 Chirality restraints: 1551 Sorted by residual: chirality pdb=" C2 IHP D 501 " pdb=" C1 IHP D 501 " pdb=" C3 IHP D 501 " pdb=" O12 IHP D 501 " both_signs ideal model delta sigma weight residual False -2.52 2.37 -4.89 2.00e-01 2.50e+01 5.97e+02 chirality pdb=" C2 IHP C 501 " pdb=" C1 IHP C 501 " pdb=" C3 IHP C 501 " pdb=" O12 IHP C 501 " both_signs ideal model delta sigma weight residual False -2.52 2.31 -4.83 2.00e-01 2.50e+01 5.83e+02 chirality pdb=" C5 IHP C 501 " pdb=" C4 IHP C 501 " pdb=" C6 IHP C 501 " pdb=" O15 IHP C 501 " both_signs ideal model delta sigma weight residual False -2.42 2.39 -4.81 2.00e-01 2.50e+01 5.78e+02 ... (remaining 1548 not shown) Planarity restraints: 1735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS C 190 " -0.022 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C CYS C 190 " 0.073 2.00e-02 2.50e+03 pdb=" O CYS C 190 " -0.027 2.00e-02 2.50e+03 pdb=" N HIS C 191 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 154 " -0.026 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO E 155 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO E 155 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 155 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 350 " 0.007 2.00e-02 2.50e+03 1.02e-02 2.08e+00 pdb=" CG TYR D 350 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR D 350 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR D 350 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR D 350 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 350 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR D 350 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 350 " -0.000 2.00e-02 2.50e+03 ... (remaining 1732 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 374 2.72 - 3.27: 9941 3.27 - 3.81: 15274 3.81 - 4.36: 18169 4.36 - 4.90: 31259 Nonbonded interactions: 75017 Sorted by model distance: nonbonded pdb=" OG SER C 304 " pdb=" OD1 ASP C 307 " model vdw 2.179 3.040 nonbonded pdb=" NZ LYS D 457 " pdb=" O21 IHP D 501 " model vdw 2.248 3.120 nonbonded pdb=" OG1 THR B 116 " pdb=" OD1 ASN B 118 " model vdw 2.266 3.040 nonbonded pdb=" OD2 ASP C 292 " pdb=" OG1 THR D 277 " model vdw 2.281 3.040 nonbonded pdb=" OD2 ASP E 132 " pdb=" NZ LYS E 135 " model vdw 2.284 3.120 ... (remaining 75012 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 67 through 98 or (resid 99 and (name N or name CA or name \ C or name O or name CB )) or resid 100 through 148 or (resid 149 and (name N or \ name CA or name C or name O or name CB )) or resid 150 through 217)) selection = (chain 'E' and resid 67 through 217) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 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: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 27.850 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 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 : 0.011 0.702 10025 Z= 0.485 Angle : 0.701 17.904 13544 Z= 0.342 Chirality : 0.343 4.887 1551 Planarity : 0.004 0.042 1735 Dihedral : 18.013 166.193 3846 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.01 % Favored : 95.67 % Rotamer: Outliers : 0.09 % Allowed : 18.84 % Favored : 81.07 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.24), residues: 1247 helix: 1.45 (0.24), residues: 488 sheet: 1.41 (0.47), residues: 134 loop : 0.09 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 482 HIS 0.010 0.001 HIS C 191 PHE 0.013 0.001 PHE D 362 TYR 0.025 0.001 TYR D 350 ARG 0.007 0.000 ARG E 156 Details of bonding type rmsd hydrogen bonds : bond 0.20371 ( 423) hydrogen bonds : angle 6.10674 ( 1251) metal coordination : bond 0.41383 ( 6) covalent geometry : bond 0.00481 (10018) covalent geometry : angle 0.70096 (13544) Misc. bond : bond 0.24493 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: B 84 THR cc_start: 0.7370 (m) cc_final: 0.6955 (t) REVERT: C 126 MET cc_start: 0.7396 (mmm) cc_final: 0.7109 (mmp) REVERT: C 295 MET cc_start: 0.7334 (tpt) cc_final: 0.6559 (mtm) REVERT: C 344 ARG cc_start: 0.7572 (ttm-80) cc_final: 0.6723 (ttm-80) REVERT: C 416 MET cc_start: 0.5723 (mmm) cc_final: 0.5351 (mmt) REVERT: D 67 MET cc_start: 0.3067 (ttp) cc_final: 0.2855 (tmm) REVERT: D 149 GLU cc_start: 0.6484 (mp0) cc_final: 0.6113 (mt-10) REVERT: D 221 THR cc_start: 0.8227 (t) cc_final: 0.7766 (p) REVERT: D 222 LYS cc_start: 0.8695 (ttpp) cc_final: 0.8297 (ttmm) REVERT: D 224 LYS cc_start: 0.8092 (tppp) cc_final: 0.7504 (tmmt) REVERT: D 475 ARG cc_start: 0.6877 (tpp80) cc_final: 0.6559 (tpp-160) REVERT: E 157 GLN cc_start: 0.6606 (tm-30) cc_final: 0.5891 (pm20) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.2630 time to fit residues: 49.0747 Evaluate side-chains 110 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 52 optimal weight: 0.0980 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN C 191 HIS C 431 ASN ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.206734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.139615 restraints weight = 11004.435| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.38 r_work: 0.3359 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.939 10025 Z= 0.338 Angle : 0.654 14.943 13544 Z= 0.302 Chirality : 0.045 0.401 1551 Planarity : 0.004 0.044 1735 Dihedral : 8.468 61.650 1423 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.33 % Favored : 95.43 % Rotamer: Outliers : 2.59 % Allowed : 17.36 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.24), residues: 1247 helix: 1.64 (0.23), residues: 502 sheet: 1.28 (0.45), residues: 139 loop : -0.03 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 473 HIS 0.003 0.001 HIS D 130 PHE 0.012 0.001 PHE C 148 TYR 0.012 0.001 TYR D 453 ARG 0.006 0.000 ARG E 156 Details of bonding type rmsd hydrogen bonds : bond 0.04237 ( 423) hydrogen bonds : angle 4.34537 ( 1251) metal coordination : bond 0.38342 ( 6) covalent geometry : bond 0.00287 (10018) covalent geometry : angle 0.65369 (13544) Misc. bond : bond 0.00093 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: B 84 THR cc_start: 0.7750 (m) cc_final: 0.7352 (t) REVERT: C 126 MET cc_start: 0.7815 (mmm) cc_final: 0.7612 (mmp) REVERT: C 295 MET cc_start: 0.7461 (tpt) cc_final: 0.7102 (ttp) REVERT: C 344 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7435 (mtp85) REVERT: C 484 ARG cc_start: 0.8455 (mtm180) cc_final: 0.8186 (mtp180) REVERT: D 67 MET cc_start: 0.2959 (ttp) cc_final: 0.2753 (tmm) REVERT: D 80 ILE cc_start: -0.2031 (OUTLIER) cc_final: -0.2238 (mt) REVERT: D 221 THR cc_start: 0.8453 (t) cc_final: 0.8006 (p) REVERT: D 222 LYS cc_start: 0.8757 (ttpp) cc_final: 0.8387 (ttmm) REVERT: D 224 LYS cc_start: 0.8208 (tppp) cc_final: 0.7705 (tmmt) REVERT: D 357 LYS cc_start: 0.8388 (ttpt) cc_final: 0.7716 (tppt) REVERT: D 475 ARG cc_start: 0.7132 (tpp80) cc_final: 0.6896 (tpp-160) REVERT: E 157 GLN cc_start: 0.6923 (tm-30) cc_final: 0.5746 (tp40) REVERT: E 167 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6696 (mp) outliers start: 28 outliers final: 13 residues processed: 142 average time/residue: 0.2534 time to fit residues: 48.6730 Evaluate side-chains 116 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 449 TYR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 167 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 0.0470 chunk 94 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN E 170 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.197746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.138211 restraints weight = 11135.615| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.39 r_work: 0.3227 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10025 Z= 0.150 Angle : 0.589 11.886 13544 Z= 0.292 Chirality : 0.047 0.406 1551 Planarity : 0.004 0.045 1735 Dihedral : 7.597 61.933 1423 Min Nonbonded Distance : 1.520 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.81 % Favored : 94.95 % Rotamer: Outliers : 3.51 % Allowed : 17.27 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.24), residues: 1247 helix: 1.76 (0.23), residues: 496 sheet: 1.17 (0.48), residues: 127 loop : -0.19 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 394 HIS 0.008 0.001 HIS C 191 PHE 0.018 0.002 PHE C 148 TYR 0.011 0.001 TYR D 453 ARG 0.006 0.000 ARG E 156 Details of bonding type rmsd hydrogen bonds : bond 0.04391 ( 423) hydrogen bonds : angle 4.12325 ( 1251) metal coordination : bond 0.01547 ( 6) covalent geometry : bond 0.00360 (10018) covalent geometry : angle 0.58928 (13544) Misc. bond : bond 0.00070 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 97 time to evaluate : 1.025 Fit side-chains REVERT: B 72 LYS cc_start: 0.7267 (mmtm) cc_final: 0.6996 (ttmt) REVERT: B 165 GLU cc_start: 0.6324 (OUTLIER) cc_final: 0.6095 (pm20) REVERT: C 295 MET cc_start: 0.7473 (tpt) cc_final: 0.7185 (ttp) REVERT: C 299 ARG cc_start: 0.7639 (mtt180) cc_final: 0.7339 (mtt90) REVERT: C 343 ASP cc_start: 0.7722 (t0) cc_final: 0.7473 (t0) REVERT: C 344 ARG cc_start: 0.8114 (ttm-80) cc_final: 0.7423 (mtp85) REVERT: C 484 ARG cc_start: 0.8387 (mtm180) cc_final: 0.8182 (mtp180) REVERT: D 67 MET cc_start: 0.3005 (ttp) cc_final: 0.2773 (tmm) REVERT: D 80 ILE cc_start: -0.2025 (OUTLIER) cc_final: -0.2227 (mt) REVERT: D 222 LYS cc_start: 0.8833 (ttpp) cc_final: 0.8551 (ttmm) REVERT: D 224 LYS cc_start: 0.8354 (tppp) cc_final: 0.7861 (tmmt) REVERT: D 284 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7833 (tt0) REVERT: D 357 LYS cc_start: 0.8412 (ttpt) cc_final: 0.7767 (tppt) REVERT: D 475 ARG cc_start: 0.7256 (tpp80) cc_final: 0.6978 (tpp-160) REVERT: E 146 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7132 (tptp) REVERT: E 157 GLN cc_start: 0.6978 (tm-30) cc_final: 0.6130 (pm20) REVERT: E 167 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6902 (mp) REVERT: E 168 LYS cc_start: 0.7187 (OUTLIER) cc_final: 0.6587 (ttpp) outliers start: 38 outliers final: 17 residues processed: 127 average time/residue: 0.2663 time to fit residues: 46.2827 Evaluate side-chains 114 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 449 TYR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 146 LYS Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 168 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 70 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 113 optimal weight: 0.0470 chunk 8 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.197932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.126556 restraints weight = 11095.708| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.80 r_work: 0.3202 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10025 Z= 0.130 Angle : 0.549 11.353 13544 Z= 0.272 Chirality : 0.045 0.409 1551 Planarity : 0.004 0.045 1735 Dihedral : 7.501 61.806 1423 Min Nonbonded Distance : 1.598 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.49 % Favored : 95.27 % Rotamer: Outliers : 3.42 % Allowed : 17.82 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.24), residues: 1247 helix: 1.80 (0.23), residues: 499 sheet: 1.19 (0.48), residues: 127 loop : -0.26 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 394 HIS 0.003 0.001 HIS D 130 PHE 0.013 0.001 PHE C 148 TYR 0.009 0.001 TYR D 453 ARG 0.005 0.000 ARG D 344 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 423) hydrogen bonds : angle 4.01123 ( 1251) metal coordination : bond 0.00603 ( 6) covalent geometry : bond 0.00309 (10018) covalent geometry : angle 0.54906 (13544) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 95 time to evaluate : 1.121 Fit side-chains REVERT: B 148 SER cc_start: 0.7359 (p) cc_final: 0.7130 (t) REVERT: C 269 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7665 (m-10) REVERT: C 295 MET cc_start: 0.7468 (tpt) cc_final: 0.7163 (ttp) REVERT: C 343 ASP cc_start: 0.7753 (t0) cc_final: 0.7497 (t0) REVERT: C 344 ARG cc_start: 0.8091 (ttm-80) cc_final: 0.7237 (ttt90) REVERT: D 67 MET cc_start: 0.3069 (ttp) cc_final: 0.2842 (tmm) REVERT: D 80 ILE cc_start: -0.1719 (OUTLIER) cc_final: -0.1944 (mt) REVERT: D 222 LYS cc_start: 0.8766 (ttpp) cc_final: 0.8469 (ttmm) REVERT: D 224 LYS cc_start: 0.8417 (tppp) cc_final: 0.7948 (tmmt) REVERT: D 284 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: D 303 MET cc_start: 0.8738 (mmt) cc_final: 0.8508 (mmt) REVERT: D 357 LYS cc_start: 0.8408 (ttpt) cc_final: 0.7768 (tppt) REVERT: D 475 ARG cc_start: 0.7262 (tpp80) cc_final: 0.6439 (tpm170) REVERT: E 146 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7221 (tptp) REVERT: E 167 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6976 (mp) REVERT: E 168 LYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6625 (ttpp) outliers start: 37 outliers final: 25 residues processed: 125 average time/residue: 0.2467 time to fit residues: 42.6714 Evaluate side-chains 120 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 146 LYS Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 206 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 49 optimal weight: 0.0470 chunk 42 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 106 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 105 optimal weight: 0.3980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 GLN ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.199959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.129343 restraints weight = 11075.102| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.74 r_work: 0.3260 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10025 Z= 0.099 Angle : 0.507 9.541 13544 Z= 0.250 Chirality : 0.043 0.375 1551 Planarity : 0.003 0.045 1735 Dihedral : 7.213 60.046 1423 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.49 % Favored : 95.27 % Rotamer: Outliers : 2.40 % Allowed : 19.11 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.24), residues: 1247 helix: 1.97 (0.23), residues: 499 sheet: 1.67 (0.50), residues: 117 loop : -0.27 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 473 HIS 0.002 0.000 HIS C 191 PHE 0.009 0.001 PHE C 148 TYR 0.007 0.001 TYR D 205 ARG 0.004 0.000 ARG E 156 Details of bonding type rmsd hydrogen bonds : bond 0.03085 ( 423) hydrogen bonds : angle 3.82305 ( 1251) metal coordination : bond 0.00398 ( 6) covalent geometry : bond 0.00222 (10018) covalent geometry : angle 0.50654 (13544) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 1.143 Fit side-chains REVERT: B 87 ARG cc_start: 0.8550 (ttm-80) cc_final: 0.8322 (ttm-80) REVERT: B 148 SER cc_start: 0.7416 (p) cc_final: 0.7177 (t) REVERT: C 269 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7643 (m-10) REVERT: C 295 MET cc_start: 0.7397 (tpt) cc_final: 0.7174 (ttp) REVERT: C 343 ASP cc_start: 0.7690 (t0) cc_final: 0.7438 (t0) REVERT: C 344 ARG cc_start: 0.8106 (ttm-80) cc_final: 0.7396 (ttm-80) REVERT: D 67 MET cc_start: 0.3059 (ttp) cc_final: 0.2841 (tmm) REVERT: D 80 ILE cc_start: -0.1782 (OUTLIER) cc_final: -0.2005 (mt) REVERT: D 222 LYS cc_start: 0.8729 (ttpp) cc_final: 0.8441 (ttmm) REVERT: D 224 LYS cc_start: 0.8450 (tppp) cc_final: 0.7952 (tmmt) REVERT: D 475 ARG cc_start: 0.7220 (tpp80) cc_final: 0.6449 (tpm170) REVERT: E 167 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.7007 (mp) outliers start: 26 outliers final: 16 residues processed: 113 average time/residue: 0.2669 time to fit residues: 41.5799 Evaluate side-chains 107 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 167 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 37 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 49 optimal weight: 0.0270 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 47 optimal weight: 0.0470 chunk 60 optimal weight: 1.9990 overall best weight: 1.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.194616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.123010 restraints weight = 11101.327| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.80 r_work: 0.3154 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10025 Z= 0.158 Angle : 0.588 11.851 13544 Z= 0.287 Chirality : 0.046 0.436 1551 Planarity : 0.004 0.043 1735 Dihedral : 7.495 60.495 1423 Min Nonbonded Distance : 1.538 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.73 % Favored : 95.03 % Rotamer: Outliers : 3.69 % Allowed : 19.11 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.24), residues: 1247 helix: 1.86 (0.23), residues: 500 sheet: 1.10 (0.47), residues: 127 loop : -0.44 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 394 HIS 0.003 0.001 HIS D 130 PHE 0.016 0.001 PHE C 148 TYR 0.009 0.001 TYR D 453 ARG 0.004 0.000 ARG E 156 Details of bonding type rmsd hydrogen bonds : bond 0.04316 ( 423) hydrogen bonds : angle 4.01448 ( 1251) metal coordination : bond 0.00453 ( 6) covalent geometry : bond 0.00387 (10018) covalent geometry : angle 0.58750 (13544) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 87 time to evaluate : 1.116 Fit side-chains REVERT: B 148 SER cc_start: 0.7626 (p) cc_final: 0.7418 (t) REVERT: C 269 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7718 (m-10) REVERT: C 295 MET cc_start: 0.7466 (tpt) cc_final: 0.7231 (ttp) REVERT: C 343 ASP cc_start: 0.7730 (t0) cc_final: 0.7477 (t0) REVERT: C 344 ARG cc_start: 0.8108 (ttm-80) cc_final: 0.7270 (ttt90) REVERT: D 67 MET cc_start: 0.3084 (ttm) cc_final: 0.2846 (tmm) REVERT: D 80 ILE cc_start: -0.1640 (OUTLIER) cc_final: -0.1863 (mt) REVERT: D 222 LYS cc_start: 0.8776 (ttpp) cc_final: 0.8436 (ttmm) REVERT: D 224 LYS cc_start: 0.8489 (tppp) cc_final: 0.7958 (tmmt) REVERT: D 357 LYS cc_start: 0.8434 (ttpt) cc_final: 0.7799 (tppt) REVERT: D 475 ARG cc_start: 0.7271 (tpp80) cc_final: 0.6472 (tpm170) REVERT: E 146 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7300 (tptp) REVERT: E 167 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7038 (mp) REVERT: E 168 LYS cc_start: 0.7145 (OUTLIER) cc_final: 0.6523 (ttpp) REVERT: E 200 THR cc_start: 0.7740 (m) cc_final: 0.7522 (m) outliers start: 40 outliers final: 29 residues processed: 120 average time/residue: 0.2488 time to fit residues: 41.0606 Evaluate side-chains 118 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 84 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 476 GLN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 146 LYS Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 168 LYS Chi-restraints excluded: chain E residue 206 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 6 optimal weight: 0.9980 chunk 85 optimal weight: 0.0170 chunk 102 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 0.3980 chunk 70 optimal weight: 0.9980 chunk 75 optimal weight: 0.0770 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.199515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.129130 restraints weight = 11186.222| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.73 r_work: 0.3259 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10025 Z= 0.095 Angle : 0.499 9.015 13544 Z= 0.248 Chirality : 0.042 0.359 1551 Planarity : 0.004 0.078 1735 Dihedral : 7.031 59.130 1423 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.17 % Favored : 95.59 % Rotamer: Outliers : 2.40 % Allowed : 20.31 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.24), residues: 1247 helix: 2.05 (0.23), residues: 499 sheet: 1.58 (0.50), residues: 117 loop : -0.34 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 482 HIS 0.002 0.000 HIS C 130 PHE 0.008 0.001 PHE C 123 TYR 0.006 0.001 TYR D 110 ARG 0.004 0.000 ARG E 156 Details of bonding type rmsd hydrogen bonds : bond 0.02842 ( 423) hydrogen bonds : angle 3.72999 ( 1251) metal coordination : bond 0.00314 ( 6) covalent geometry : bond 0.00209 (10018) covalent geometry : angle 0.49942 (13544) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: B 87 ARG cc_start: 0.8520 (ttm-80) cc_final: 0.8304 (ttm-80) REVERT: B 148 SER cc_start: 0.7590 (p) cc_final: 0.7362 (t) REVERT: C 343 ASP cc_start: 0.7622 (t0) cc_final: 0.7415 (t0) REVERT: C 344 ARG cc_start: 0.8076 (ttm-80) cc_final: 0.7411 (ttm-80) REVERT: D 67 MET cc_start: 0.3174 (ttm) cc_final: 0.2944 (tmm) REVERT: D 80 ILE cc_start: -0.1533 (OUTLIER) cc_final: -0.1781 (mt) REVERT: D 222 LYS cc_start: 0.8667 (ttpp) cc_final: 0.8397 (ttmm) REVERT: D 224 LYS cc_start: 0.8513 (tppp) cc_final: 0.7962 (tmmt) REVERT: D 475 ARG cc_start: 0.7211 (tpp80) cc_final: 0.6470 (tpm170) REVERT: E 146 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7326 (tptp) REVERT: E 159 ASP cc_start: 0.5342 (m-30) cc_final: 0.5047 (m-30) REVERT: E 167 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7026 (mp) REVERT: E 168 LYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6551 (ttpp) REVERT: E 200 THR cc_start: 0.7743 (m) cc_final: 0.7511 (m) outliers start: 26 outliers final: 16 residues processed: 110 average time/residue: 0.2721 time to fit residues: 40.9119 Evaluate side-chains 107 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 146 LYS Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 168 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 85 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 104 optimal weight: 0.0060 chunk 31 optimal weight: 0.9980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 HIS C 191 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.197876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.126998 restraints weight = 11172.970| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.76 r_work: 0.3213 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.659 10025 Z= 0.244 Angle : 0.508 8.943 13544 Z= 0.252 Chirality : 0.043 0.380 1551 Planarity : 0.004 0.058 1735 Dihedral : 6.945 57.291 1423 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.65 % Favored : 95.11 % Rotamer: Outliers : 2.77 % Allowed : 19.85 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.24), residues: 1247 helix: 2.08 (0.23), residues: 500 sheet: 1.58 (0.50), residues: 117 loop : -0.37 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 473 HIS 0.005 0.001 HIS C 47 PHE 0.009 0.001 PHE C 123 TYR 0.008 0.001 TYR D 205 ARG 0.003 0.000 ARG E 156 Details of bonding type rmsd hydrogen bonds : bond 0.03152 ( 423) hydrogen bonds : angle 3.73395 ( 1251) metal coordination : bond 0.26919 ( 6) covalent geometry : bond 0.00248 (10018) covalent geometry : angle 0.50758 (13544) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 1.054 Fit side-chains REVERT: B 87 ARG cc_start: 0.8524 (ttm-80) cc_final: 0.8305 (ttm-80) REVERT: B 148 SER cc_start: 0.7634 (p) cc_final: 0.7395 (t) REVERT: C 269 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7747 (m-10) REVERT: C 343 ASP cc_start: 0.7620 (t0) cc_final: 0.7403 (t0) REVERT: C 344 ARG cc_start: 0.8086 (ttm-80) cc_final: 0.7423 (ttm-80) REVERT: D 67 MET cc_start: 0.3165 (ttm) cc_final: 0.2935 (tmm) REVERT: D 80 ILE cc_start: -0.1589 (OUTLIER) cc_final: -0.1821 (mt) REVERT: D 222 LYS cc_start: 0.8677 (ttpp) cc_final: 0.8414 (ttmm) REVERT: D 224 LYS cc_start: 0.8543 (tppp) cc_final: 0.7970 (tmmt) REVERT: D 475 ARG cc_start: 0.7228 (tpp80) cc_final: 0.6465 (tpm170) REVERT: E 146 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7283 (tptp) REVERT: E 159 ASP cc_start: 0.5279 (m-30) cc_final: 0.4990 (m-30) REVERT: E 167 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7050 (mp) REVERT: E 168 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6468 (ttpp) REVERT: E 200 THR cc_start: 0.7693 (m) cc_final: 0.7470 (m) outliers start: 30 outliers final: 22 residues processed: 111 average time/residue: 0.2546 time to fit residues: 38.7744 Evaluate side-chains 115 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 146 LYS Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 168 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 69 optimal weight: 0.9990 chunk 89 optimal weight: 0.0570 chunk 117 optimal weight: 7.9990 chunk 41 optimal weight: 0.0270 chunk 72 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN C 47 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.199373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.142638 restraints weight = 11107.511| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.77 r_work: 0.3283 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10025 Z= 0.096 Angle : 0.503 9.766 13544 Z= 0.249 Chirality : 0.042 0.361 1551 Planarity : 0.004 0.048 1735 Dihedral : 6.802 56.166 1423 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.65 % Favored : 95.19 % Rotamer: Outliers : 2.40 % Allowed : 20.41 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.24), residues: 1247 helix: 2.11 (0.23), residues: 499 sheet: 1.63 (0.50), residues: 117 loop : -0.31 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 473 HIS 0.004 0.001 HIS C 47 PHE 0.007 0.001 PHE C 123 TYR 0.007 0.001 TYR D 205 ARG 0.003 0.000 ARG E 156 Details of bonding type rmsd hydrogen bonds : bond 0.02872 ( 423) hydrogen bonds : angle 3.66821 ( 1251) metal coordination : bond 0.00359 ( 6) covalent geometry : bond 0.00211 (10018) covalent geometry : angle 0.50334 (13544) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 1.024 Fit side-chains REVERT: B 87 ARG cc_start: 0.8416 (ttm-80) cc_final: 0.8180 (ttm-80) REVERT: B 148 SER cc_start: 0.7526 (p) cc_final: 0.7299 (t) REVERT: B 165 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.6164 (pm20) REVERT: C 38 MET cc_start: 0.5668 (mmt) cc_final: 0.5343 (ptp) REVERT: C 116 LYS cc_start: 0.6446 (mmtm) cc_final: 0.6175 (mmmt) REVERT: C 269 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7649 (m-10) REVERT: C 343 ASP cc_start: 0.7534 (t0) cc_final: 0.7328 (t0) REVERT: C 344 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7296 (ttm-80) REVERT: D 67 MET cc_start: 0.2985 (ttm) cc_final: 0.2776 (tmm) REVERT: D 80 ILE cc_start: -0.1539 (OUTLIER) cc_final: -0.1758 (mt) REVERT: D 222 LYS cc_start: 0.8657 (ttpp) cc_final: 0.8372 (ttmm) REVERT: D 224 LYS cc_start: 0.8553 (tppp) cc_final: 0.7946 (tmmt) REVERT: D 475 ARG cc_start: 0.7160 (tpp80) cc_final: 0.6342 (tpm170) REVERT: E 146 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7164 (tptp) REVERT: E 167 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6934 (mp) REVERT: E 200 THR cc_start: 0.7551 (m) cc_final: 0.7335 (m) outliers start: 26 outliers final: 19 residues processed: 107 average time/residue: 0.2653 time to fit residues: 39.0442 Evaluate side-chains 110 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 47 HIS Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 146 LYS Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 167 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 69 optimal weight: 30.0000 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 123 optimal weight: 8.9990 chunk 76 optimal weight: 0.0970 chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 8 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.195801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.124897 restraints weight = 11160.233| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.69 r_work: 0.3182 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10025 Z= 0.140 Angle : 0.550 9.678 13544 Z= 0.273 Chirality : 0.045 0.406 1551 Planarity : 0.004 0.046 1735 Dihedral : 7.039 57.244 1423 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.73 % Favored : 95.11 % Rotamer: Outliers : 2.49 % Allowed : 19.94 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.24), residues: 1247 helix: 1.93 (0.23), residues: 501 sheet: 1.53 (0.50), residues: 117 loop : -0.43 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 394 HIS 0.006 0.001 HIS C 47 PHE 0.014 0.001 PHE C 148 TYR 0.008 0.001 TYR D 205 ARG 0.002 0.000 ARG E 156 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 423) hydrogen bonds : angle 3.82991 ( 1251) metal coordination : bond 0.00731 ( 6) covalent geometry : bond 0.00338 (10018) covalent geometry : angle 0.55036 (13544) Misc. bond : bond 0.00042 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 1.151 Fit side-chains REVERT: B 148 SER cc_start: 0.7705 (p) cc_final: 0.7492 (t) REVERT: C 116 LYS cc_start: 0.6513 (mmtm) cc_final: 0.6193 (mmmt) REVERT: C 269 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7787 (m-10) REVERT: C 343 ASP cc_start: 0.7610 (t0) cc_final: 0.7402 (t0) REVERT: C 344 ARG cc_start: 0.8100 (ttm-80) cc_final: 0.7436 (ttm-80) REVERT: D 67 MET cc_start: 0.3010 (ttm) cc_final: 0.2783 (tmm) REVERT: D 80 ILE cc_start: -0.1745 (OUTLIER) cc_final: -0.1947 (mt) REVERT: D 222 LYS cc_start: 0.8663 (ttpp) cc_final: 0.8396 (ttmm) REVERT: D 224 LYS cc_start: 0.8512 (tppp) cc_final: 0.7951 (tmmt) REVERT: D 475 ARG cc_start: 0.7217 (tpp80) cc_final: 0.6509 (tpm170) REVERT: E 146 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7266 (tptp) REVERT: E 167 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7109 (mp) outliers start: 27 outliers final: 18 residues processed: 107 average time/residue: 0.2541 time to fit residues: 37.5825 Evaluate side-chains 108 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 146 TYR Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 146 LYS Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 167 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 0.0980 chunk 90 optimal weight: 3.9990 chunk 21 optimal weight: 0.0270 chunk 97 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.198336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.140312 restraints weight = 11074.579| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.93 r_work: 0.3275 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 10025 Z= 0.101 Angle : 0.505 8.681 13544 Z= 0.252 Chirality : 0.043 0.368 1551 Planarity : 0.004 0.042 1735 Dihedral : 6.815 56.291 1423 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.25 % Favored : 95.59 % Rotamer: Outliers : 2.31 % Allowed : 20.13 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.24), residues: 1247 helix: 2.12 (0.24), residues: 500 sheet: 1.59 (0.50), residues: 117 loop : -0.34 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 482 HIS 0.002 0.000 HIS C 47 PHE 0.008 0.001 PHE C 148 TYR 0.007 0.001 TYR D 205 ARG 0.003 0.000 ARG D 344 Details of bonding type rmsd hydrogen bonds : bond 0.03003 ( 423) hydrogen bonds : angle 3.70358 ( 1251) metal coordination : bond 0.00377 ( 6) covalent geometry : bond 0.00228 (10018) covalent geometry : angle 0.50528 (13544) Misc. bond : bond 0.00018 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5645.56 seconds wall clock time: 98 minutes 14.57 seconds (5894.57 seconds total)