Starting phenix.real_space_refine on Wed Sep 17 16:54:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zep_60042/09_2025/8zep_60042_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zep_60042/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zep_60042/09_2025/8zep_60042_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zep_60042/09_2025/8zep_60042_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zep_60042/09_2025/8zep_60042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zep_60042/09_2025/8zep_60042.map" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.035 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.48, per 1000 atoms: 0.25 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: 0.93 Conformation dependent library (CDL) restraints added in 381.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.37 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: 1.44 Time building geometry restraints manager: 1.21 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: 1.840 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.470 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.870 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.000 ARG E 156 TYR 0.025 0.001 TYR D 350 PHE 0.013 0.001 PHE D 362 TRP 0.003 0.000 TRP D 482 HIS 0.010 0.001 HIS C 191 Details of bonding type rmsd covalent geometry : bond 0.00481 (10018) covalent geometry : angle 0.70096 (13544) hydrogen bonds : bond 0.20371 ( 423) hydrogen bonds : angle 6.10674 ( 1251) metal coordination : bond 0.41383 ( 6) 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 : 0.373 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: 0.1245 time to fit residues: 23.0617 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 : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 123 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 D 373 GLN E 170 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.197348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.137452 restraints weight = 11099.769| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 3.54 r_work: 0.3223 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.862 10025 Z= 0.354 Angle : 0.735 20.568 13544 Z= 0.347 Chirality : 0.050 0.469 1551 Planarity : 0.004 0.044 1735 Dihedral : 8.422 63.640 1423 Min Nonbonded Distance : 1.534 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.73 % Favored : 95.03 % Rotamer: Outliers : 3.60 % Allowed : 16.53 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 0.88 (0.24), residues: 1247 helix: 1.46 (0.23), residues: 496 sheet: 1.10 (0.47), residues: 127 loop : -0.20 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 156 TYR 0.016 0.002 TYR D 453 PHE 0.021 0.002 PHE C 148 TRP 0.011 0.002 TRP D 394 HIS 0.003 0.001 HIS C 412 Details of bonding type rmsd covalent geometry : bond 0.00509 (10018) covalent geometry : angle 0.73472 (13544) hydrogen bonds : bond 0.05338 ( 423) hydrogen bonds : angle 4.48753 ( 1251) metal coordination : bond 0.35212 ( 6) Misc. bond : bond 0.00231 ( 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 146 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 107 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: B 72 LYS cc_start: 0.7482 (mmtm) cc_final: 0.7059 (ttmt) REVERT: B 84 THR cc_start: 0.8126 (m) cc_final: 0.7724 (t) REVERT: C 295 MET cc_start: 0.7366 (tpt) cc_final: 0.7003 (ttp) REVERT: C 298 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7167 (mt-10) REVERT: C 343 ASP cc_start: 0.7776 (t0) cc_final: 0.7552 (t0) REVERT: C 344 ARG cc_start: 0.8121 (ttm-80) cc_final: 0.7452 (mtp85) REVERT: D 222 LYS cc_start: 0.8845 (ttpp) cc_final: 0.8526 (ttmm) REVERT: D 224 LYS cc_start: 0.8294 (tppp) cc_final: 0.7798 (tmmt) REVERT: D 357 LYS cc_start: 0.8401 (ttpt) cc_final: 0.7774 (tppt) REVERT: D 475 ARG cc_start: 0.7242 (tpp80) cc_final: 0.6958 (tpp-160) REVERT: E 157 GLN cc_start: 0.6849 (tm-30) cc_final: 0.5647 (tp40) REVERT: E 167 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6850 (mp) REVERT: E 168 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6863 (ttpp) outliers start: 39 outliers final: 20 residues processed: 138 average time/residue: 0.1182 time to fit residues: 21.8313 Evaluate side-chains 112 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 ILE 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 302 THR Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 355 THR Chi-restraints excluded: chain C residue 407 SER Chi-restraints excluded: chain C residue 474 LEU 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 234 SER 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 106 SER Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 168 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 97 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.197356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.137954 restraints weight = 11028.803| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 3.44 r_work: 0.3220 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10025 Z= 0.144 Angle : 0.576 11.982 13544 Z= 0.285 Chirality : 0.045 0.388 1551 Planarity : 0.004 0.046 1735 Dihedral : 7.616 62.320 1423 Min Nonbonded Distance : 1.556 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.73 % Favored : 95.03 % Rotamer: Outliers : 3.23 % Allowed : 17.36 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 0.87 (0.24), residues: 1247 helix: 1.64 (0.23), residues: 496 sheet: 0.99 (0.47), residues: 127 loop : -0.35 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 156 TYR 0.020 0.001 TYR B 180 PHE 0.015 0.001 PHE C 148 TRP 0.006 0.001 TRP C 394 HIS 0.004 0.001 HIS D 130 Details of bonding type rmsd covalent geometry : bond 0.00346 (10018) covalent geometry : angle 0.57639 (13544) hydrogen bonds : bond 0.04259 ( 423) hydrogen bonds : angle 4.18557 ( 1251) metal coordination : bond 0.00318 ( 6) Misc. bond : bond 0.00154 ( 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 127 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 0.256 Fit side-chains REVERT: B 72 LYS cc_start: 0.7388 (mmtm) cc_final: 0.7090 (ttmt) REVERT: C 269 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.7793 (m-10) REVERT: C 295 MET cc_start: 0.7463 (tpt) cc_final: 0.7168 (ttp) REVERT: C 298 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7211 (mt-10) REVERT: C 343 ASP cc_start: 0.7771 (t0) cc_final: 0.7498 (t0) REVERT: C 344 ARG cc_start: 0.8108 (ttm-80) cc_final: 0.7431 (mtp85) REVERT: D 222 LYS cc_start: 0.8799 (ttpp) cc_final: 0.8481 (ttmm) REVERT: D 224 LYS cc_start: 0.8425 (tppp) cc_final: 0.7938 (tmmt) REVERT: D 357 LYS cc_start: 0.8422 (ttpt) cc_final: 0.7767 (tppt) REVERT: D 475 ARG cc_start: 0.7229 (tpp80) cc_final: 0.6384 (tpm170) REVERT: E 146 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7144 (tptp) REVERT: E 167 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6982 (mp) REVERT: E 168 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6674 (ttpp) outliers start: 35 outliers final: 19 residues processed: 120 average time/residue: 0.1064 time to fit residues: 17.6791 Evaluate side-chains 109 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 ILE 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 333 SER Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 404 VAL 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 234 SER 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 106 SER Chi-restraints excluded: chain E residue 111 VAL 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 59 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 91 optimal weight: 0.1980 chunk 3 optimal weight: 0.0670 chunk 112 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 overall best weight: 0.7922 ------------------------------------------------------------------------------- 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 = 0.4213 r_free = 0.4213 target = 0.198021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.127296 restraints weight = 11159.527| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.74 r_work: 0.3246 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2636 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= 0.115 Angle : 0.528 10.380 13544 Z= 0.262 Chirality : 0.044 0.401 1551 Planarity : 0.004 0.045 1735 Dihedral : 7.341 61.248 1423 Min Nonbonded Distance : 1.616 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.81 % Favored : 94.95 % Rotamer: Outliers : 2.59 % Allowed : 18.10 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 0.99 (0.24), residues: 1247 helix: 1.83 (0.23), residues: 498 sheet: 0.96 (0.47), residues: 127 loop : -0.35 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 156 TYR 0.008 0.001 TYR D 453 PHE 0.012 0.001 PHE C 148 TRP 0.005 0.001 TRP D 473 HIS 0.002 0.001 HIS D 130 Details of bonding type rmsd covalent geometry : bond 0.00269 (10018) covalent geometry : angle 0.52810 (13544) hydrogen bonds : bond 0.03530 ( 423) hydrogen bonds : angle 3.93282 ( 1251) metal coordination : bond 0.00613 ( 6) Misc. bond : bond 0.00036 ( 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 120 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: B 148 SER cc_start: 0.7370 (p) cc_final: 0.7121 (t) REVERT: C 269 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7689 (m-10) REVERT: C 295 MET cc_start: 0.7447 (tpt) cc_final: 0.7208 (ttp) REVERT: C 298 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7215 (mt-10) REVERT: C 343 ASP cc_start: 0.7645 (t0) cc_final: 0.7363 (t0) REVERT: C 344 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7421 (ttm-80) REVERT: D 222 LYS cc_start: 0.8740 (ttpp) cc_final: 0.8448 (ttmm) REVERT: D 224 LYS cc_start: 0.8434 (tppp) cc_final: 0.7968 (tmmt) REVERT: D 475 ARG cc_start: 0.7183 (tpp80) cc_final: 0.6405 (tpm170) REVERT: E 146 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7189 (tptp) REVERT: E 167 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6994 (mp) REVERT: E 200 THR cc_start: 0.7715 (m) cc_final: 0.7490 (m) outliers start: 28 outliers final: 15 residues processed: 111 average time/residue: 0.1228 time to fit residues: 18.9816 Evaluate side-chains 106 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 406 THR 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 372 CYS 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 106 SER Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 146 LYS Chi-restraints excluded: chain E residue 167 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 119 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.4157 r_free = 0.4157 target = 0.192023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.120338 restraints weight = 11178.692| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.81 r_work: 0.3098 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10025 Z= 0.203 Angle : 0.642 14.302 13544 Z= 0.314 Chirality : 0.048 0.472 1551 Planarity : 0.004 0.045 1735 Dihedral : 7.868 63.257 1423 Min Nonbonded Distance : 1.508 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.97 % Favored : 94.79 % Rotamer: Outliers : 4.25 % Allowed : 17.82 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 0.64 (0.24), residues: 1247 helix: 1.64 (0.23), residues: 498 sheet: 0.55 (0.46), residues: 131 loop : -0.61 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 301 TYR 0.010 0.002 TYR D 453 PHE 0.020 0.002 PHE C 148 TRP 0.010 0.002 TRP D 394 HIS 0.003 0.001 HIS D 130 Details of bonding type rmsd covalent geometry : bond 0.00507 (10018) covalent geometry : angle 0.64204 (13544) hydrogen bonds : bond 0.05109 ( 423) hydrogen bonds : angle 4.25695 ( 1251) metal coordination : bond 0.00664 ( 6) Misc. bond : bond 0.00071 ( 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 130 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 84 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: C 269 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.7758 (m-10) REVERT: C 295 MET cc_start: 0.7395 (tpt) cc_final: 0.7114 (ttp) REVERT: C 298 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7652 (mt-10) REVERT: C 344 ARG cc_start: 0.8153 (ttm-80) cc_final: 0.7233 (ttt180) REVERT: D 222 LYS cc_start: 0.8794 (ttpp) cc_final: 0.8447 (ttmm) REVERT: D 224 LYS cc_start: 0.8450 (tppp) cc_final: 0.8020 (tmmt) REVERT: D 475 ARG cc_start: 0.7252 (tpp80) cc_final: 0.6402 (tpm170) REVERT: E 146 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7418 (tptp) REVERT: E 167 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7108 (mp) REVERT: E 168 LYS cc_start: 0.7297 (OUTLIER) cc_final: 0.6823 (ttpp) outliers start: 46 outliers final: 33 residues processed: 121 average time/residue: 0.1139 time to fit residues: 19.3593 Evaluate side-chains 119 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 82 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 170 THR 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 303 MET 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 406 THR Chi-restraints excluded: chain C residue 474 LEU 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 234 SER Chi-restraints excluded: chain D residue 372 CYS 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 105 THR Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 117 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 187 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 17 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 28 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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** ** E 170 GLN ** 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 = 0.4187 r_free = 0.4187 target = 0.195341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.127804 restraints weight = 11117.566| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 3.62 r_work: 0.3191 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10025 Z= 0.125 Angle : 0.547 11.341 13544 Z= 0.269 Chirality : 0.044 0.395 1551 Planarity : 0.004 0.045 1735 Dihedral : 7.469 62.757 1423 Min Nonbonded Distance : 1.625 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.97 % Favored : 94.79 % Rotamer: Outliers : 3.60 % Allowed : 18.56 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 0.79 (0.24), residues: 1247 helix: 1.77 (0.23), residues: 500 sheet: 0.75 (0.47), residues: 127 loop : -0.55 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 156 TYR 0.007 0.001 TYR D 205 PHE 0.011 0.001 PHE C 148 TRP 0.006 0.001 TRP D 473 HIS 0.001 0.001 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00296 (10018) covalent geometry : angle 0.54685 (13544) hydrogen bonds : bond 0.03670 ( 423) hydrogen bonds : angle 3.96445 ( 1251) metal coordination : bond 0.00462 ( 6) Misc. bond : bond 0.00039 ( 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 125 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 86 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: B 158 MET cc_start: 0.5394 (OUTLIER) cc_final: 0.4353 (pmm) REVERT: C 116 LYS cc_start: 0.6554 (mmtm) cc_final: 0.6129 (mmmt) REVERT: C 269 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.7757 (m-10) REVERT: C 295 MET cc_start: 0.7365 (tpt) cc_final: 0.7094 (ttp) REVERT: C 298 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7438 (mt-10) REVERT: C 344 ARG cc_start: 0.8181 (ttm-80) cc_final: 0.7288 (ttt180) REVERT: C 368 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7447 (tt0) REVERT: D 222 LYS cc_start: 0.8696 (ttpp) cc_final: 0.8377 (ttmm) REVERT: D 224 LYS cc_start: 0.8520 (tppp) cc_final: 0.8033 (tmmt) REVERT: D 475 ARG cc_start: 0.7207 (tpp80) cc_final: 0.6393 (tpm170) REVERT: E 146 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7316 (tptp) REVERT: E 167 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7053 (mp) REVERT: E 168 LYS cc_start: 0.7214 (OUTLIER) cc_final: 0.6609 (ttpp) outliers start: 39 outliers final: 26 residues processed: 116 average time/residue: 0.1288 time to fit residues: 20.5601 Evaluate side-chains 114 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 MET 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 333 SER Chi-restraints excluded: chain C residue 368 GLU 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 146 TYR Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 154 SER 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 D residue 476 GLN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 106 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 63 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 48 optimal weight: 0.4980 chunk 46 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN C 191 HIS ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.196048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.129412 restraints weight = 11111.567| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 3.46 r_work: 0.3201 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.648 10025 Z= 0.245 Angle : 0.535 10.479 13544 Z= 0.264 Chirality : 0.044 0.402 1551 Planarity : 0.004 0.076 1735 Dihedral : 7.236 60.345 1423 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.97 % Favored : 94.79 % Rotamer: Outliers : 3.51 % Allowed : 18.65 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 0.90 (0.24), residues: 1247 helix: 1.87 (0.23), residues: 500 sheet: 1.17 (0.49), residues: 117 loop : -0.57 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 156 TYR 0.008 0.001 TYR D 205 PHE 0.010 0.001 PHE C 148 TRP 0.006 0.001 TRP D 473 HIS 0.002 0.001 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00272 (10018) covalent geometry : angle 0.53488 (13544) hydrogen bonds : bond 0.03446 ( 423) hydrogen bonds : angle 3.87766 ( 1251) metal coordination : bond 0.26458 ( 6) Misc. bond : bond 0.00027 ( 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 122 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 84 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: B 158 MET cc_start: 0.5323 (OUTLIER) cc_final: 0.4309 (pmm) REVERT: C 116 LYS cc_start: 0.6505 (mmtm) cc_final: 0.6237 (mmmt) REVERT: C 269 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.7855 (m-10) REVERT: C 295 MET cc_start: 0.7472 (tpt) cc_final: 0.7210 (ttp) REVERT: C 298 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7361 (mt-10) REVERT: C 343 ASP cc_start: 0.7693 (t0) cc_final: 0.7431 (t0) REVERT: C 344 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7288 (ttt180) REVERT: C 368 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7497 (tt0) REVERT: D 80 ILE cc_start: -0.1496 (OUTLIER) cc_final: -0.1715 (mp) REVERT: D 222 LYS cc_start: 0.8665 (ttpp) cc_final: 0.8361 (ttmm) REVERT: D 224 LYS cc_start: 0.8573 (tppp) cc_final: 0.8002 (tmmt) REVERT: D 475 ARG cc_start: 0.7194 (tpp80) cc_final: 0.6389 (tpm170) REVERT: E 146 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7304 (tptp) REVERT: E 159 ASP cc_start: 0.5786 (m-30) cc_final: 0.5405 (m-30) REVERT: E 167 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7153 (mp) REVERT: E 168 LYS cc_start: 0.7201 (OUTLIER) cc_final: 0.6635 (ttpp) outliers start: 38 outliers final: 27 residues processed: 113 average time/residue: 0.1208 time to fit residues: 18.8017 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 : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 MET 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 159 ILE 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 368 GLU 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 152 ILE Chi-restraints excluded: chain D residue 154 SER 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 D residue 476 GLN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 106 SER 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 7 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 64 optimal weight: 20.0000 chunk 26 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 170 GLN ** 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 = 0.4186 r_free = 0.4186 target = 0.194696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.136983 restraints weight = 11134.189| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.99 r_work: 0.3197 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10025 Z= 0.134 Angle : 0.559 11.138 13544 Z= 0.275 Chirality : 0.045 0.415 1551 Planarity : 0.004 0.062 1735 Dihedral : 7.271 60.261 1423 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.97 % Favored : 94.79 % Rotamer: Outliers : 3.60 % Allowed : 18.56 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 0.85 (0.24), residues: 1247 helix: 1.85 (0.23), residues: 500 sheet: 1.15 (0.48), residues: 117 loop : -0.62 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 156 TYR 0.009 0.001 TYR D 205 PHE 0.013 0.001 PHE C 148 TRP 0.006 0.001 TRP D 394 HIS 0.002 0.001 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00324 (10018) covalent geometry : angle 0.55924 (13544) hydrogen bonds : bond 0.03798 ( 423) hydrogen bonds : angle 3.92227 ( 1251) metal coordination : bond 0.00675 ( 6) Misc. bond : bond 0.00033 ( 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 123 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 84 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: B 158 MET cc_start: 0.5377 (OUTLIER) cc_final: 0.4446 (pmm) REVERT: C 269 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.7857 (m-10) REVERT: C 295 MET cc_start: 0.7451 (tpt) cc_final: 0.7164 (ttp) REVERT: C 298 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7463 (mt-10) REVERT: C 344 ARG cc_start: 0.8161 (ttm-80) cc_final: 0.7298 (ttt180) REVERT: C 368 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7567 (tt0) REVERT: D 80 ILE cc_start: -0.1424 (OUTLIER) cc_final: -0.1634 (mp) REVERT: D 222 LYS cc_start: 0.8675 (ttpp) cc_final: 0.8366 (ttmm) REVERT: D 224 LYS cc_start: 0.8574 (tppp) cc_final: 0.7992 (tmmt) REVERT: D 475 ARG cc_start: 0.7208 (tpp80) cc_final: 0.6368 (tpm170) REVERT: E 146 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7404 (tptp) REVERT: E 159 ASP cc_start: 0.5569 (m-30) cc_final: 0.5178 (m-30) REVERT: E 167 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7142 (mp) REVERT: E 168 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6578 (ttpp) outliers start: 39 outliers final: 26 residues processed: 115 average time/residue: 0.1234 time to fit residues: 19.5921 Evaluate side-chains 116 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 83 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 MET 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 303 MET Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 395 ASN 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 234 SER Chi-restraints excluded: chain D residue 372 CYS 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 105 THR Chi-restraints excluded: chain E residue 106 SER 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 53 optimal weight: 3.9990 chunk 95 optimal weight: 0.3980 chunk 6 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 113 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 HIS ** E 170 GLN ** 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 = 0.4203 r_free = 0.4203 target = 0.196547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.126118 restraints weight = 11073.812| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.70 r_work: 0.3198 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3385 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= 0.124 Angle : 0.547 10.760 13544 Z= 0.270 Chirality : 0.044 0.402 1551 Planarity : 0.004 0.053 1735 Dihedral : 7.179 59.917 1423 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.73 % Favored : 95.11 % Rotamer: Outliers : 3.60 % Allowed : 18.74 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 0.90 (0.24), residues: 1247 helix: 1.89 (0.23), residues: 500 sheet: 1.17 (0.49), residues: 117 loop : -0.59 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 156 TYR 0.008 0.001 TYR D 205 PHE 0.010 0.001 PHE C 148 TRP 0.005 0.001 TRP D 473 HIS 0.005 0.001 HIS C 47 Details of bonding type rmsd covalent geometry : bond 0.00294 (10018) covalent geometry : angle 0.54692 (13544) hydrogen bonds : bond 0.03535 ( 423) hydrogen bonds : angle 3.85593 ( 1251) metal coordination : bond 0.00525 ( 6) Misc. bond : bond 0.00035 ( 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 126 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 87 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8181 (mt0) REVERT: B 158 MET cc_start: 0.5409 (OUTLIER) cc_final: 0.4453 (pmm) REVERT: B 161 LYS cc_start: 0.7178 (mmtm) cc_final: 0.6799 (mmmm) REVERT: C 269 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.7861 (m-10) REVERT: C 298 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7424 (mt-10) REVERT: C 344 ARG cc_start: 0.8142 (ttm-80) cc_final: 0.7289 (ttt180) REVERT: C 368 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7540 (tt0) REVERT: D 80 ILE cc_start: -0.1310 (OUTLIER) cc_final: -0.1524 (mp) REVERT: D 222 LYS cc_start: 0.8644 (ttpp) cc_final: 0.8420 (ttmm) REVERT: D 224 LYS cc_start: 0.8603 (tppp) cc_final: 0.8013 (tmmt) REVERT: D 475 ARG cc_start: 0.7157 (tpp80) cc_final: 0.6390 (tpm170) REVERT: E 146 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7417 (tptp) REVERT: E 159 ASP cc_start: 0.5538 (m-30) cc_final: 0.5192 (m-30) REVERT: E 167 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7193 (mp) REVERT: E 168 LYS cc_start: 0.7227 (OUTLIER) cc_final: 0.6651 (ttpp) outliers start: 39 outliers final: 28 residues processed: 118 average time/residue: 0.1242 time to fit residues: 20.1230 Evaluate side-chains 123 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 87 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 158 MET 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 139 CYS Chi-restraints excluded: chain C residue 159 ILE 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 303 MET Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 395 ASN 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 234 SER Chi-restraints excluded: chain D residue 372 CYS 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 105 THR Chi-restraints excluded: chain E residue 106 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 116 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 98 optimal weight: 0.0970 chunk 34 optimal weight: 0.0070 chunk 14 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 HIS C 379 GLN D 490 GLN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.197307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.127087 restraints weight = 11051.556| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.71 r_work: 0.3226 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3377 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= 0.103 Angle : 0.535 10.106 13544 Z= 0.263 Chirality : 0.043 0.374 1551 Planarity : 0.004 0.048 1735 Dihedral : 6.951 58.649 1423 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.73 % Favored : 95.11 % Rotamer: Outliers : 2.77 % Allowed : 19.30 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 1.03 (0.24), residues: 1247 helix: 1.98 (0.24), residues: 500 sheet: 1.25 (0.49), residues: 117 loop : -0.51 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 156 TYR 0.007 0.001 TYR D 205 PHE 0.008 0.001 PHE C 148 TRP 0.005 0.001 TRP D 473 HIS 0.004 0.001 HIS C 47 Details of bonding type rmsd covalent geometry : bond 0.00231 (10018) covalent geometry : angle 0.53548 (13544) hydrogen bonds : bond 0.03031 ( 423) hydrogen bonds : angle 3.74509 ( 1251) metal coordination : bond 0.00243 ( 6) Misc. bond : bond 0.00014 ( 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 118 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: B 119 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8133 (mt0) REVERT: B 158 MET cc_start: 0.5330 (OUTLIER) cc_final: 0.4296 (pmm) REVERT: B 161 LYS cc_start: 0.7111 (mmtm) cc_final: 0.6738 (mmmm) REVERT: C 269 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.7894 (m-10) REVERT: C 298 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7278 (mt-10) REVERT: C 344 ARG cc_start: 0.8099 (ttm-80) cc_final: 0.7412 (ttm-80) REVERT: C 368 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: C 379 GLN cc_start: 0.1232 (OUTLIER) cc_final: 0.0855 (tp40) REVERT: D 222 LYS cc_start: 0.8633 (ttpp) cc_final: 0.8381 (ttmm) REVERT: D 224 LYS cc_start: 0.8603 (tppp) cc_final: 0.8005 (tmmt) REVERT: D 475 ARG cc_start: 0.7178 (tpp80) cc_final: 0.6423 (tpm170) REVERT: E 146 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7356 (tptp) REVERT: E 159 ASP cc_start: 0.5366 (m-30) cc_final: 0.5031 (m-30) REVERT: E 167 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7159 (mp) outliers start: 30 outliers final: 21 residues processed: 110 average time/residue: 0.1242 time to fit residues: 18.7261 Evaluate side-chains 114 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 158 MET 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 368 GLU Chi-restraints excluded: chain C residue 379 GLN 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 146 TYR 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 476 GLN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 106 SER 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 115 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 120 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 112 optimal weight: 0.4980 chunk 95 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 HIS ** E 170 GLN ** 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 = 0.4205 r_free = 0.4205 target = 0.196690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.130480 restraints weight = 11155.476| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.48 r_work: 0.3215 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3416 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= 0.111 Angle : 0.536 9.434 13544 Z= 0.264 Chirality : 0.044 0.381 1551 Planarity : 0.004 0.045 1735 Dihedral : 6.906 57.827 1423 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.49 % Favored : 95.35 % Rotamer: Outliers : 2.68 % Allowed : 19.21 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 aren not related in a simple way. whole: 1.05 (0.24), residues: 1247 helix: 2.03 (0.23), residues: 500 sheet: 1.24 (0.49), residues: 117 loop : -0.51 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 156 TYR 0.008 0.001 TYR D 205 PHE 0.009 0.001 PHE C 148 TRP 0.005 0.001 TRP D 473 HIS 0.005 0.001 HIS C 47 Details of bonding type rmsd covalent geometry : bond 0.00259 (10018) covalent geometry : angle 0.53597 (13544) hydrogen bonds : bond 0.03157 ( 423) hydrogen bonds : angle 3.74452 ( 1251) metal coordination : bond 0.00261 ( 6) Misc. bond : bond 0.00024 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2766.66 seconds wall clock time: 48 minutes 17.14 seconds (2897.14 seconds total)