Starting phenix.real_space_refine on Fri Feb 6 12:39:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lgy_63076/02_2026/9lgy_63076_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lgy_63076/02_2026/9lgy_63076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lgy_63076/02_2026/9lgy_63076_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lgy_63076/02_2026/9lgy_63076_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lgy_63076/02_2026/9lgy_63076.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lgy_63076/02_2026/9lgy_63076.map" } resolution = 2.4 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= 0.088 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 89 5.16 5 C 7892 2.51 5 N 2098 2.21 5 O 2258 1.98 5 H 12334 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24671 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5722 Classifications: {'peptide': 372} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 357} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 5746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 5746 Classifications: {'peptide': 372} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 357} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 6345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 6345 Classifications: {'peptide': 399} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Chain: "E" Number of atoms: 6830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 6830 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 2 Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'D12': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'R16': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.27, per 1000 atoms: 0.17 Number of scatterers: 24671 At special positions: 0 Unit cell: (140.08, 93.112, 139.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 89 16.00 O 2258 8.00 N 2098 7.00 C 7892 6.00 H 12334 1.00 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=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 669.9 milliseconds 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2928 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 13 sheets defined 43.8% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 56 through 68 Processing helix chain 'A' and resid 71 through 76 Processing helix chain 'A' and resid 105 through 111 Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 117 through 122 Processing helix chain 'A' and resid 131 through 135 Processing helix chain 'A' and resid 162 through 184 Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 259 through 273 Processing helix chain 'A' and resid 318 through 328 Processing helix chain 'A' and resid 334 through 345 Processing helix chain 'A' and resid 411 through 422 Processing helix chain 'C' and resid 30 through 36 Processing helix chain 'C' and resid 56 through 68 Processing helix chain 'C' and resid 71 through 76 Processing helix chain 'C' and resid 105 through 111 Processing helix chain 'C' and resid 117 through 123 Processing helix chain 'C' and resid 131 through 135 Processing helix chain 'C' and resid 162 through 184 Processing helix chain 'C' and resid 241 through 250 removed outlier: 4.333A pdb=" N SER C 246 " --> pdb=" O ASP C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 272 Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 334 through 345 Processing helix chain 'C' and resid 367 through 370 Processing helix chain 'C' and resid 411 through 421 removed outlier: 3.677A pdb=" N THR C 419 " --> pdb=" O LEU C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 424 No H-bonds generated for 'chain 'C' and resid 422 through 424' Processing helix chain 'B' and resid 73 through 84 removed outlier: 4.367A pdb=" N VAL B 79 " --> pdb=" O PHE B 75 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 103 Processing helix chain 'B' and resid 105 through 117 Processing helix chain 'B' and resid 120 through 133 removed outlier: 3.789A pdb=" N ARG B 133 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 148 removed outlier: 3.766A pdb=" N TYR B 148 " --> pdb=" O ALA B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 178 Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 199 through 209 Processing helix chain 'B' and resid 225 through 241 removed outlier: 3.593A pdb=" N ILE B 229 " --> pdb=" O SER B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 258 removed outlier: 3.858A pdb=" N ASN B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 273 removed outlier: 3.904A pdb=" N LEU B 268 " --> pdb=" O ARG B 264 " (cutoff:3.500A) Proline residue: B 269 - end of helix removed outlier: 3.558A pdb=" N LEU B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 289 Processing helix chain 'B' and resid 307 through 312 Processing helix chain 'B' and resid 331 through 352 Proline residue: B 349 - end of helix Processing helix chain 'B' and resid 380 through 384 removed outlier: 3.601A pdb=" N GLN B 383 " --> pdb=" O ASP B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 406 Processing helix chain 'B' and resid 412 through 423 Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 428 through 440 Processing helix chain 'E' and resid 16 through 26 removed outlier: 3.653A pdb=" N ASN E 26 " --> pdb=" O GLN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 82 removed outlier: 3.676A pdb=" N TYR E 80 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 103 Processing helix chain 'E' and resid 105 through 117 Processing helix chain 'E' and resid 120 through 133 removed outlier: 3.776A pdb=" N ARG E 133 " --> pdb=" O ARG E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 148 removed outlier: 3.829A pdb=" N TYR E 148 " --> pdb=" O ALA E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 178 Processing helix chain 'E' and resid 180 through 184 Processing helix chain 'E' and resid 199 through 209 Processing helix chain 'E' and resid 225 through 241 removed outlier: 3.610A pdb=" N ILE E 229 " --> pdb=" O SER E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 258 removed outlier: 3.790A pdb=" N ASN E 257 " --> pdb=" O ILE E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 266 Processing helix chain 'E' and resid 267 through 273 Processing helix chain 'E' and resid 287 through 292 removed outlier: 4.563A pdb=" N ARG E 291 " --> pdb=" O ARG E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 312 Processing helix chain 'E' and resid 331 through 352 Proline residue: E 349 - end of helix Processing helix chain 'E' and resid 353 through 363 Processing helix chain 'E' and resid 380 through 384 removed outlier: 3.665A pdb=" N GLN E 383 " --> pdb=" O ASP E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 406 Processing helix chain 'E' and resid 412 through 423 Processing helix chain 'E' and resid 428 through 440 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 15 removed outlier: 5.295A pdb=" N SER A 9 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLN A 101 " --> pdb=" O SER A 9 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ARG A 96 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL A 142 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL A 98 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N TRP A 144 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA A 100 " --> pdb=" O TRP A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 217 Processing sheet with id=AA4, first strand: chain 'A' and resid 233 through 240 removed outlier: 6.818A pdb=" N THR A 285 " --> pdb=" O PHE A 360 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ASN A 362 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N CYS A 287 " --> pdb=" O ASN A 362 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 7 through 15 removed outlier: 5.234A pdb=" N SER C 9 " --> pdb=" O GLN C 101 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN C 101 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ARG C 96 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL C 142 " --> pdb=" O ARG C 96 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL C 98 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N TRP C 144 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA C 100 " --> pdb=" O TRP C 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 26 through 28 Processing sheet with id=AA7, first strand: chain 'C' and resid 216 through 217 Processing sheet with id=AA8, first strand: chain 'C' and resid 233 through 238 removed outlier: 3.504A pdb=" N LEU C 358 " --> pdb=" O ASN C 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 372 through 373 Processing sheet with id=AB1, first strand: chain 'B' and resid 215 through 219 removed outlier: 3.692A pdb=" N ASP B 92 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N SER B 283 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LEU B 90 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LEU B 296 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LYS B 466 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 314 through 318 Processing sheet with id=AB3, first strand: chain 'E' and resid 215 through 219 removed outlier: 6.559A pdb=" N ILE E 186 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N VAL E 249 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE E 188 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N THR E 251 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASN E 190 " --> pdb=" O THR E 251 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP E 92 " --> pdb=" O LEU E 281 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER E 283 " --> pdb=" O LEU E 90 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LEU E 90 " --> pdb=" O SER E 283 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LEU E 296 " --> pdb=" O LYS E 466 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LYS E 466 " --> pdb=" O LEU E 296 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 314 through 318 612 hydrogen bonds defined for protein. 1677 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: 5.75 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12292 1.03 - 1.23: 110 1.23 - 1.42: 5142 1.42 - 1.62: 7250 1.62 - 1.82: 136 Bond restraints: 24930 Sorted by residual: bond pdb=" CA PHE E 458 " pdb=" CB PHE E 458 " ideal model delta sigma weight residual 1.530 1.511 0.019 1.69e-02 3.50e+03 1.26e+00 bond pdb=" CB PHE E 458 " pdb=" CG PHE E 458 " ideal model delta sigma weight residual 1.502 1.478 0.024 2.30e-02 1.89e+03 1.11e+00 bond pdb=" CB PHE B 458 " pdb=" CG PHE B 458 " ideal model delta sigma weight residual 1.502 1.481 0.021 2.30e-02 1.89e+03 7.96e-01 bond pdb=" CA PHE B 458 " pdb=" CB PHE B 458 " ideal model delta sigma weight residual 1.530 1.516 0.014 1.69e-02 3.50e+03 6.98e-01 bond pdb=" CB GLN A 53 " pdb=" CG GLN A 53 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.47e-01 ... (remaining 24925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 44574 1.68 - 3.36: 440 3.36 - 5.04: 57 5.04 - 6.71: 6 6.71 - 8.39: 7 Bond angle restraints: 45084 Sorted by residual: angle pdb=" N GLY E 457 " pdb=" CA GLY E 457 " pdb=" C GLY E 457 " ideal model delta sigma weight residual 115.47 108.06 7.41 1.31e+00 5.83e-01 3.20e+01 angle pdb=" CA GLY E 457 " pdb=" C GLY E 457 " pdb=" N PHE E 458 " ideal model delta sigma weight residual 118.62 112.58 6.04 1.29e+00 6.01e-01 2.19e+01 angle pdb=" CA TYR B 486 " pdb=" CB TYR B 486 " pdb=" CG TYR B 486 " ideal model delta sigma weight residual 113.90 105.51 8.39 1.80e+00 3.09e-01 2.17e+01 angle pdb=" CA TYR E 486 " pdb=" CB TYR E 486 " pdb=" CG TYR E 486 " ideal model delta sigma weight residual 113.90 105.92 7.98 1.80e+00 3.09e-01 1.96e+01 angle pdb=" CA PHE E 458 " pdb=" CB PHE E 458 " pdb=" CG PHE E 458 " ideal model delta sigma weight residual 113.80 109.46 4.34 1.00e+00 1.00e+00 1.88e+01 ... (remaining 45079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 10653 17.88 - 35.75: 721 35.75 - 53.63: 278 53.63 - 71.50: 69 71.50 - 89.38: 13 Dihedral angle restraints: 11734 sinusoidal: 6384 harmonic: 5350 Sorted by residual: dihedral pdb=" CA PHE B 458 " pdb=" C PHE B 458 " pdb=" N LYS B 459 " pdb=" CA LYS B 459 " ideal model delta harmonic sigma weight residual 180.00 146.54 33.46 0 5.00e+00 4.00e-02 4.48e+01 dihedral pdb=" CA GLY E 457 " pdb=" C GLY E 457 " pdb=" N PHE E 458 " pdb=" CA PHE E 458 " ideal model delta harmonic sigma weight residual -180.00 -150.08 -29.92 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA ILE E 149 " pdb=" C ILE E 149 " pdb=" N PRO E 150 " pdb=" CA PRO E 150 " ideal model delta harmonic sigma weight residual 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 11731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1726 0.069 - 0.139: 167 0.139 - 0.208: 0 0.208 - 0.277: 0 0.277 - 0.347: 4 Chirality restraints: 1897 Sorted by residual: chirality pdb=" CA PHE E 458 " pdb=" N PHE E 458 " pdb=" C PHE E 458 " pdb=" CB PHE E 458 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA PHE B 458 " pdb=" N PHE B 458 " pdb=" C PHE B 458 " pdb=" CB PHE B 458 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CA TYR B 486 " pdb=" N TYR B 486 " pdb=" C TYR B 486 " pdb=" CB TYR B 486 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 1894 not shown) Planarity restraints: 3643 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 458 " 0.043 2.00e-02 2.50e+03 2.48e-02 1.85e+01 pdb=" CG PHE E 458 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 PHE E 458 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE E 458 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE E 458 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 458 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE E 458 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE E 458 " -0.003 2.00e-02 2.50e+03 pdb=" HD2 PHE E 458 " -0.004 2.00e-02 2.50e+03 pdb=" HE1 PHE E 458 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE E 458 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE E 458 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 458 " -0.025 2.00e-02 2.50e+03 1.32e-02 5.19e+00 pdb=" CG PHE B 458 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE B 458 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 458 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 458 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 458 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE B 458 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE B 458 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE B 458 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE B 458 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE B 458 " -0.003 2.00e-02 2.50e+03 pdb=" HZ PHE B 458 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 486 " 0.026 2.00e-02 2.50e+03 1.29e-02 4.96e+00 pdb=" CG TYR B 486 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR B 486 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 486 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 486 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 486 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 486 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 486 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 TYR B 486 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 TYR B 486 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR B 486 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR B 486 " 0.002 2.00e-02 2.50e+03 ... (remaining 3640 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.40: 10557 2.40 - 2.95: 56552 2.95 - 3.50: 65201 3.50 - 4.05: 90954 4.05 - 4.60: 134291 Nonbonded interactions: 357555 Sorted by model distance: nonbonded pdb=" HB3 LYS B 403 " pdb=" HZ2 LYS B 403 " model vdw 1.844 2.270 nonbonded pdb=" HG SER B 199 " pdb=" H ALA B 202 " model vdw 1.845 2.100 nonbonded pdb=" HD2 PHE E 388 " pdb=" HE3 TRP E 450 " model vdw 1.861 2.100 nonbonded pdb=" O ILE B 253 " pdb="HD21 ASN B 257 " model vdw 1.883 2.450 nonbonded pdb=" H THR E 78 " pdb=" HG1 THR E 78 " model vdw 1.885 2.100 ... (remaining 357550 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 'A' and (resid 6 through 290 or (resid 298 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB \ 2 or name HB3 or name HD21 or name HD22)) or resid 299 through 424)) selection = (chain 'C' and (resid 6 through 186 or (resid 211 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name OD2 or name HA or name HB \ 2 or name HB3)) or resid 212 through 251 or resid 258 through 424)) } ncs_group { reference = (chain 'B' and resid 72 through 496) selection = (chain 'E' and (resid 72 through 353 or (resid 380 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name OD2 or name HA or name H \ B2 or name HB3)) or resid 381 through 496)) } 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: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 22.410 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 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:7.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12596 Z= 0.140 Angle : 0.544 8.392 17010 Z= 0.292 Chirality : 0.043 0.347 1897 Planarity : 0.004 0.054 2160 Dihedral : 15.200 89.376 4661 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.85 % Allowed : 12.64 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.22), residues: 1536 helix: 1.15 (0.23), residues: 571 sheet: 0.82 (0.28), residues: 335 loop : 0.55 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 77 TYR 0.036 0.002 TYR B 486 PHE 0.073 0.002 PHE E 458 TRP 0.016 0.001 TRP E 431 HIS 0.003 0.001 HIS E 391 Details of bonding type rmsd covalent geometry : bond 0.00318 (12596) covalent geometry : angle 0.54371 (17010) hydrogen bonds : bond 0.12503 ( 612) hydrogen bonds : angle 6.35421 ( 1677) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 324 is missing expected H atoms. Skipping. Residue TYR 328 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue TYR 328 is missing expected H atoms. Skipping. Evaluate side-chains 204 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 236 PHE cc_start: 0.6739 (t80) cc_final: 0.6406 (t80) REVERT: A 315 MET cc_start: 0.5029 (mtt) cc_final: 0.4372 (mmm) REVERT: A 343 GLU cc_start: 0.7126 (tp30) cc_final: 0.6655 (mm-30) REVERT: A 346 ASN cc_start: 0.7453 (m-40) cc_final: 0.6856 (t0) REVERT: A 357 ASN cc_start: 0.7604 (m-40) cc_final: 0.6942 (p0) REVERT: C 50 HIS cc_start: 0.8069 (t70) cc_final: 0.7456 (t70) REVERT: C 111 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7316 (pt0) REVERT: C 126 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8147 (mt0) REVERT: C 131 ASP cc_start: 0.7153 (p0) cc_final: 0.6827 (p0) REVERT: C 308 PHE cc_start: 0.7357 (t80) cc_final: 0.6849 (t80) REVERT: C 343 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6799 (mp0) REVERT: C 376 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7294 (mt-10) REVERT: C 416 LYS cc_start: 0.7678 (mttt) cc_final: 0.6842 (tmtt) REVERT: B 84 LYS cc_start: 0.7478 (tttt) cc_final: 0.7170 (ttpp) REVERT: B 125 GLU cc_start: 0.8205 (tt0) cc_final: 0.7861 (tm-30) REVERT: B 333 MET cc_start: 0.7946 (mmm) cc_final: 0.7693 (tpp) REVERT: B 400 GLU cc_start: 0.8117 (tp30) cc_final: 0.7673 (tm-30) REVERT: E 383 GLN cc_start: 0.8491 (mt0) cc_final: 0.8077 (mm110) REVERT: E 410 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7816 (tm-30) REVERT: E 472 LYS cc_start: 0.8439 (mttt) cc_final: 0.8026 (mmpt) outliers start: 25 outliers final: 16 residues processed: 190 average time/residue: 1.2576 time to fit residues: 258.8946 Evaluate side-chains 195 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 410 GLU Chi-restraints excluded: chain E residue 434 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.144868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.088637 restraints weight = 36938.358| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.78 r_work: 0.2862 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.0515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12596 Z= 0.202 Angle : 0.549 9.525 17010 Z= 0.298 Chirality : 0.045 0.439 1897 Planarity : 0.005 0.055 2160 Dihedral : 7.215 59.822 1734 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.51 % Allowed : 11.90 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.22), residues: 1536 helix: 1.32 (0.22), residues: 582 sheet: 0.86 (0.29), residues: 336 loop : 0.41 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 77 TYR 0.041 0.002 TYR B 486 PHE 0.077 0.002 PHE E 458 TRP 0.016 0.001 TRP B 431 HIS 0.005 0.001 HIS E 391 Details of bonding type rmsd covalent geometry : bond 0.00473 (12596) covalent geometry : angle 0.54880 (17010) hydrogen bonds : bond 0.04496 ( 612) hydrogen bonds : angle 5.42431 ( 1677) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 324 is missing expected H atoms. Skipping. Residue TYR 328 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue TYR 328 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 PHE cc_start: 0.6609 (t80) cc_final: 0.6326 (t80) REVERT: A 315 MET cc_start: 0.5004 (mtt) cc_final: 0.4334 (mmm) REVERT: A 343 GLU cc_start: 0.7130 (tp30) cc_final: 0.6595 (mm-30) REVERT: A 346 ASN cc_start: 0.7376 (m-40) cc_final: 0.6820 (t0) REVERT: A 357 ASN cc_start: 0.7493 (m-40) cc_final: 0.6658 (p0) REVERT: A 423 MET cc_start: 0.6478 (pmt) cc_final: 0.6268 (pmm) REVERT: C 50 HIS cc_start: 0.8094 (t70) cc_final: 0.7532 (t70) REVERT: C 111 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7297 (mp0) REVERT: C 131 ASP cc_start: 0.7262 (p0) cc_final: 0.6609 (p0) REVERT: C 343 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6712 (mp0) REVERT: C 376 GLU cc_start: 0.7402 (mm-30) cc_final: 0.6802 (mt-10) REVERT: C 416 LYS cc_start: 0.7579 (mttt) cc_final: 0.6769 (tmtt) REVERT: B 84 LYS cc_start: 0.7021 (tttt) cc_final: 0.6702 (ttpp) REVERT: B 125 GLU cc_start: 0.7991 (tt0) cc_final: 0.7514 (tm-30) REVERT: B 128 MET cc_start: 0.8620 (tpp) cc_final: 0.8381 (tpp) REVERT: B 287 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7208 (ptp-170) REVERT: B 321 GLU cc_start: 0.8064 (mp0) cc_final: 0.7407 (mp0) REVERT: B 333 MET cc_start: 0.8212 (mmm) cc_final: 0.7822 (tpp) REVERT: B 400 GLU cc_start: 0.8021 (tp30) cc_final: 0.7385 (tm-30) REVERT: E 287 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7996 (ptt180) REVERT: E 383 GLN cc_start: 0.8550 (mt0) cc_final: 0.7975 (mm110) REVERT: E 410 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: E 472 LYS cc_start: 0.8406 (mttt) cc_final: 0.7835 (mmpt) outliers start: 34 outliers final: 16 residues processed: 196 average time/residue: 1.3188 time to fit residues: 280.0963 Evaluate side-chains 192 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 287 ARG Chi-restraints excluded: chain E residue 410 GLU Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 475 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 117 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 145 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 283 ASN C 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.144974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.088814 restraints weight = 36904.413| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.77 r_work: 0.2864 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.0630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12596 Z= 0.190 Angle : 0.535 9.393 17010 Z= 0.290 Chirality : 0.045 0.424 1897 Planarity : 0.005 0.054 2160 Dihedral : 7.014 59.703 1724 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.51 % Allowed : 12.42 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.22), residues: 1536 helix: 1.47 (0.22), residues: 582 sheet: 0.85 (0.29), residues: 336 loop : 0.37 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 77 TYR 0.040 0.002 TYR B 486 PHE 0.074 0.002 PHE E 458 TRP 0.018 0.001 TRP B 431 HIS 0.004 0.001 HIS E 391 Details of bonding type rmsd covalent geometry : bond 0.00444 (12596) covalent geometry : angle 0.53505 (17010) hydrogen bonds : bond 0.04383 ( 612) hydrogen bonds : angle 5.28532 ( 1677) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 324 is missing expected H atoms. Skipping. Residue TYR 328 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue TYR 328 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 PHE cc_start: 0.6553 (t80) cc_final: 0.6339 (t80) REVERT: A 315 MET cc_start: 0.5094 (mtt) cc_final: 0.4382 (mmm) REVERT: A 343 GLU cc_start: 0.7087 (tp30) cc_final: 0.6565 (mm-30) REVERT: A 346 ASN cc_start: 0.7392 (m-40) cc_final: 0.6801 (t0) REVERT: A 348 VAL cc_start: 0.8017 (t) cc_final: 0.7649 (m) REVERT: A 357 ASN cc_start: 0.7463 (m-40) cc_final: 0.6622 (p0) REVERT: A 423 MET cc_start: 0.6565 (pmt) cc_final: 0.6346 (pmm) REVERT: C 50 HIS cc_start: 0.8115 (t70) cc_final: 0.7542 (t70) REVERT: C 111 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7268 (mp0) REVERT: C 131 ASP cc_start: 0.7201 (p0) cc_final: 0.6598 (p0) REVERT: C 376 GLU cc_start: 0.7416 (mm-30) cc_final: 0.6794 (mt-10) REVERT: C 416 LYS cc_start: 0.7596 (mttt) cc_final: 0.6787 (tmtt) REVERT: B 84 LYS cc_start: 0.7013 (tttt) cc_final: 0.6689 (ttpp) REVERT: B 125 GLU cc_start: 0.7995 (tt0) cc_final: 0.7495 (tm-30) REVERT: B 321 GLU cc_start: 0.8081 (mp0) cc_final: 0.7376 (mp0) REVERT: B 333 MET cc_start: 0.8192 (mmm) cc_final: 0.7866 (tpp) REVERT: B 400 GLU cc_start: 0.8040 (tp30) cc_final: 0.7360 (tm-30) REVERT: E 383 GLN cc_start: 0.8560 (mt0) cc_final: 0.8002 (mm110) REVERT: E 472 LYS cc_start: 0.8392 (mttt) cc_final: 0.7818 (mmpt) outliers start: 34 outliers final: 23 residues processed: 195 average time/residue: 1.2908 time to fit residues: 273.6733 Evaluate side-chains 197 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 410 GLU Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 458 PHE Chi-restraints excluded: chain E residue 475 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 125 optimal weight: 0.4980 chunk 74 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 283 ASN C 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.147255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.091672 restraints weight = 37076.092| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.77 r_work: 0.2907 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.0694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12596 Z= 0.113 Angle : 0.483 7.990 17010 Z= 0.259 Chirality : 0.042 0.328 1897 Planarity : 0.004 0.053 2160 Dihedral : 6.316 59.855 1717 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.22 % Allowed : 12.64 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.22), residues: 1536 helix: 1.70 (0.23), residues: 583 sheet: 0.74 (0.28), residues: 338 loop : 0.49 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 129 TYR 0.034 0.001 TYR B 486 PHE 0.065 0.001 PHE E 458 TRP 0.015 0.001 TRP B 431 HIS 0.002 0.001 HIS E 391 Details of bonding type rmsd covalent geometry : bond 0.00258 (12596) covalent geometry : angle 0.48310 (17010) hydrogen bonds : bond 0.03490 ( 612) hydrogen bonds : angle 5.03090 ( 1677) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 324 is missing expected H atoms. Skipping. Residue TYR 328 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue TYR 328 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.5024 (mtt) cc_final: 0.4320 (mmm) REVERT: A 343 GLU cc_start: 0.7130 (tp30) cc_final: 0.6608 (mm-30) REVERT: A 346 ASN cc_start: 0.7315 (m-40) cc_final: 0.6782 (t0) REVERT: A 348 VAL cc_start: 0.8012 (t) cc_final: 0.7653 (m) REVERT: A 357 ASN cc_start: 0.7382 (m-40) cc_final: 0.6603 (p0) REVERT: A 423 MET cc_start: 0.6576 (pmt) cc_final: 0.6370 (pmm) REVERT: C 50 HIS cc_start: 0.8083 (t70) cc_final: 0.7487 (t70) REVERT: C 111 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7241 (mp0) REVERT: C 131 ASP cc_start: 0.7116 (p0) cc_final: 0.6567 (p0) REVERT: C 343 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: C 376 GLU cc_start: 0.7397 (mm-30) cc_final: 0.6785 (mt-10) REVERT: C 386 GLN cc_start: 0.8809 (tp40) cc_final: 0.8574 (tp40) REVERT: C 416 LYS cc_start: 0.7613 (mttt) cc_final: 0.6790 (tmtt) REVERT: B 84 LYS cc_start: 0.7011 (tttt) cc_final: 0.6674 (ttpp) REVERT: B 125 GLU cc_start: 0.7963 (tt0) cc_final: 0.7458 (tm-30) REVERT: B 333 MET cc_start: 0.8154 (mmm) cc_final: 0.7851 (tpp) REVERT: B 400 GLU cc_start: 0.8002 (tp30) cc_final: 0.7364 (tm-30) REVERT: E 383 GLN cc_start: 0.8511 (mt0) cc_final: 0.7936 (mm110) REVERT: E 410 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: E 472 LYS cc_start: 0.8382 (mttt) cc_final: 0.7810 (mmpt) outliers start: 30 outliers final: 15 residues processed: 196 average time/residue: 1.2068 time to fit residues: 257.1621 Evaluate side-chains 194 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 287 ARG Chi-restraints excluded: chain E residue 410 GLU Chi-restraints excluded: chain E residue 458 PHE Chi-restraints excluded: chain E residue 475 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 76 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 283 ASN C 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.146311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.090821 restraints weight = 37122.539| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.77 r_work: 0.2882 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12596 Z= 0.146 Angle : 0.506 8.393 17010 Z= 0.272 Chirality : 0.043 0.378 1897 Planarity : 0.004 0.053 2160 Dihedral : 6.315 59.502 1713 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.29 % Allowed : 13.01 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.22), residues: 1536 helix: 1.74 (0.23), residues: 583 sheet: 0.73 (0.29), residues: 338 loop : 0.48 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 77 TYR 0.037 0.002 TYR B 486 PHE 0.067 0.002 PHE E 458 TRP 0.015 0.001 TRP B 431 HIS 0.003 0.001 HIS E 391 Details of bonding type rmsd covalent geometry : bond 0.00342 (12596) covalent geometry : angle 0.50611 (17010) hydrogen bonds : bond 0.03801 ( 612) hydrogen bonds : angle 5.05108 ( 1677) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 324 is missing expected H atoms. Skipping. Residue TYR 328 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue TYR 328 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6188 (tt) REVERT: A 236 PHE cc_start: 0.6620 (t80) cc_final: 0.6395 (t80) REVERT: A 315 MET cc_start: 0.5062 (mtt) cc_final: 0.4335 (mmm) REVERT: A 343 GLU cc_start: 0.7131 (tp30) cc_final: 0.6644 (mm-30) REVERT: A 346 ASN cc_start: 0.7332 (m-40) cc_final: 0.6892 (t0) REVERT: A 348 VAL cc_start: 0.8093 (t) cc_final: 0.7749 (m) REVERT: A 357 ASN cc_start: 0.7459 (m-40) cc_final: 0.6742 (p0) REVERT: A 423 MET cc_start: 0.6494 (pmt) cc_final: 0.6285 (pmm) REVERT: C 50 HIS cc_start: 0.8147 (t70) cc_final: 0.7569 (t70) REVERT: C 111 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7290 (mp0) REVERT: C 131 ASP cc_start: 0.7193 (p0) cc_final: 0.6663 (p0) REVERT: C 376 GLU cc_start: 0.7499 (mm-30) cc_final: 0.6967 (mt-10) REVERT: C 416 LYS cc_start: 0.7666 (mttt) cc_final: 0.6828 (tmtt) REVERT: B 84 LYS cc_start: 0.7166 (tttt) cc_final: 0.6856 (ttpp) REVERT: B 125 GLU cc_start: 0.8083 (tt0) cc_final: 0.7648 (tm-30) REVERT: B 321 GLU cc_start: 0.8204 (mp0) cc_final: 0.7585 (mp0) REVERT: B 333 MET cc_start: 0.8253 (mmm) cc_final: 0.7990 (tpp) REVERT: B 400 GLU cc_start: 0.8139 (tp30) cc_final: 0.7556 (tm-30) REVERT: E 383 GLN cc_start: 0.8520 (mt0) cc_final: 0.8040 (mm110) REVERT: E 410 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7771 (tm-30) REVERT: E 472 LYS cc_start: 0.8444 (mttt) cc_final: 0.7938 (mmpt) outliers start: 31 outliers final: 19 residues processed: 194 average time/residue: 1.2223 time to fit residues: 257.7826 Evaluate side-chains 195 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 410 GLU Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 458 PHE Chi-restraints excluded: chain E residue 475 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 146 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.145365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.089348 restraints weight = 37021.723| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.78 r_work: 0.2862 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12596 Z= 0.182 Angle : 0.533 9.180 17010 Z= 0.288 Chirality : 0.044 0.422 1897 Planarity : 0.004 0.052 2160 Dihedral : 6.508 59.186 1713 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.51 % Allowed : 13.01 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.22), residues: 1536 helix: 1.69 (0.23), residues: 582 sheet: 0.76 (0.29), residues: 338 loop : 0.44 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 77 TYR 0.040 0.002 TYR B 486 PHE 0.072 0.002 PHE E 458 TRP 0.015 0.001 TRP B 431 HIS 0.004 0.001 HIS E 391 Details of bonding type rmsd covalent geometry : bond 0.00428 (12596) covalent geometry : angle 0.53255 (17010) hydrogen bonds : bond 0.04113 ( 612) hydrogen bonds : angle 5.13765 ( 1677) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 324 is missing expected H atoms. Skipping. Residue TYR 328 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue TYR 328 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6092 (tt) REVERT: A 315 MET cc_start: 0.5083 (mtt) cc_final: 0.4348 (mmm) REVERT: A 343 GLU cc_start: 0.7094 (tp30) cc_final: 0.6597 (mm-30) REVERT: A 346 ASN cc_start: 0.7333 (m-40) cc_final: 0.6913 (t0) REVERT: A 348 VAL cc_start: 0.8076 (t) cc_final: 0.7718 (m) REVERT: A 357 ASN cc_start: 0.7472 (m-40) cc_final: 0.6687 (p0) REVERT: A 423 MET cc_start: 0.6515 (pmt) cc_final: 0.6275 (pmm) REVERT: C 50 HIS cc_start: 0.8144 (t70) cc_final: 0.7551 (t70) REVERT: C 82 ASP cc_start: 0.7894 (m-30) cc_final: 0.7617 (m-30) REVERT: C 111 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7277 (pt0) REVERT: C 131 ASP cc_start: 0.7179 (p0) cc_final: 0.6608 (p0) REVERT: C 376 GLU cc_start: 0.7437 (mm-30) cc_final: 0.6860 (mt-10) REVERT: C 416 LYS cc_start: 0.7637 (mttt) cc_final: 0.6808 (tmtt) REVERT: B 84 LYS cc_start: 0.7082 (tttt) cc_final: 0.6759 (ttpp) REVERT: B 125 GLU cc_start: 0.8044 (tt0) cc_final: 0.7571 (tm-30) REVERT: B 333 MET cc_start: 0.8204 (mmm) cc_final: 0.7929 (tpp) REVERT: B 400 GLU cc_start: 0.8097 (tp30) cc_final: 0.7435 (tm-30) REVERT: E 383 GLN cc_start: 0.8521 (mt0) cc_final: 0.7997 (mm110) REVERT: E 410 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7748 (tm-30) REVERT: E 472 LYS cc_start: 0.8436 (mttt) cc_final: 0.7879 (mmpt) outliers start: 34 outliers final: 18 residues processed: 193 average time/residue: 1.4002 time to fit residues: 292.6069 Evaluate side-chains 194 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 287 ARG Chi-restraints excluded: chain E residue 410 GLU Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 475 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 29 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 283 ASN ** A 303 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 = 0.3720 r_free = 0.3720 target = 0.145720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.090072 restraints weight = 37093.063| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.76 r_work: 0.2868 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12596 Z= 0.167 Angle : 0.524 8.962 17010 Z= 0.282 Chirality : 0.044 0.391 1897 Planarity : 0.004 0.052 2160 Dihedral : 6.298 59.056 1711 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.22 % Allowed : 13.30 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.22), residues: 1536 helix: 1.72 (0.23), residues: 582 sheet: 0.75 (0.29), residues: 338 loop : 0.45 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 129 TYR 0.038 0.002 TYR B 486 PHE 0.074 0.002 PHE E 458 TRP 0.016 0.001 TRP B 431 HIS 0.003 0.001 HIS E 391 Details of bonding type rmsd covalent geometry : bond 0.00391 (12596) covalent geometry : angle 0.52410 (17010) hydrogen bonds : bond 0.03957 ( 612) hydrogen bonds : angle 5.09377 ( 1677) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 324 is missing expected H atoms. Skipping. Residue TYR 328 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue TYR 328 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6206 (tt) REVERT: A 315 MET cc_start: 0.5086 (mtt) cc_final: 0.4373 (mmm) REVERT: A 343 GLU cc_start: 0.7095 (tp30) cc_final: 0.6566 (mm-30) REVERT: A 348 VAL cc_start: 0.8100 (t) cc_final: 0.7762 (m) REVERT: A 357 ASN cc_start: 0.7502 (m-40) cc_final: 0.6769 (p0) REVERT: A 391 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7286 (mp0) REVERT: A 423 MET cc_start: 0.6497 (pmt) cc_final: 0.6286 (pmm) REVERT: C 50 HIS cc_start: 0.8155 (t70) cc_final: 0.7577 (t70) REVERT: C 82 ASP cc_start: 0.7905 (m-30) cc_final: 0.7625 (m-30) REVERT: C 111 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7271 (mp0) REVERT: C 131 ASP cc_start: 0.7221 (p0) cc_final: 0.6669 (p0) REVERT: C 343 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: C 376 GLU cc_start: 0.7497 (mm-30) cc_final: 0.6908 (mt-10) REVERT: C 416 LYS cc_start: 0.7668 (mttt) cc_final: 0.6839 (tmtt) REVERT: B 84 LYS cc_start: 0.7171 (tttt) cc_final: 0.6852 (ttpp) REVERT: B 125 GLU cc_start: 0.8112 (tt0) cc_final: 0.7675 (tm-30) REVERT: B 321 GLU cc_start: 0.8246 (mp0) cc_final: 0.7650 (mp0) REVERT: B 333 MET cc_start: 0.8263 (mmm) cc_final: 0.8003 (tpp) REVERT: B 400 GLU cc_start: 0.8149 (tp30) cc_final: 0.7567 (tm-30) REVERT: E 383 GLN cc_start: 0.8519 (mt0) cc_final: 0.8044 (mm110) REVERT: E 410 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7772 (tm-30) outliers start: 30 outliers final: 18 residues processed: 188 average time/residue: 1.3991 time to fit residues: 284.9628 Evaluate side-chains 196 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 287 ARG Chi-restraints excluded: chain E residue 410 GLU Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 458 PHE Chi-restraints excluded: chain E residue 475 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 27 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 283 ASN ** A 303 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 = 0.3721 r_free = 0.3721 target = 0.145820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.090319 restraints weight = 37140.627| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.76 r_work: 0.2871 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12596 Z= 0.161 Angle : 0.523 8.805 17010 Z= 0.280 Chirality : 0.044 0.391 1897 Planarity : 0.004 0.052 2160 Dihedral : 6.268 59.381 1711 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.14 % Allowed : 13.53 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.22), residues: 1536 helix: 1.76 (0.23), residues: 582 sheet: 0.75 (0.29), residues: 338 loop : 0.47 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 129 TYR 0.038 0.002 TYR B 486 PHE 0.072 0.002 PHE E 458 TRP 0.016 0.001 TRP B 431 HIS 0.003 0.001 HIS E 391 Details of bonding type rmsd covalent geometry : bond 0.00377 (12596) covalent geometry : angle 0.52273 (17010) hydrogen bonds : bond 0.03903 ( 612) hydrogen bonds : angle 5.07003 ( 1677) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 324 is missing expected H atoms. Skipping. Residue TYR 328 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue TYR 328 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6219 (tt) REVERT: A 315 MET cc_start: 0.5082 (mtt) cc_final: 0.4369 (mmm) REVERT: A 343 GLU cc_start: 0.7118 (tp30) cc_final: 0.6651 (mm-30) REVERT: A 346 ASN cc_start: 0.7307 (m-40) cc_final: 0.6911 (t0) REVERT: A 348 VAL cc_start: 0.8101 (t) cc_final: 0.7751 (m) REVERT: A 357 ASN cc_start: 0.7504 (m-40) cc_final: 0.6758 (p0) REVERT: A 391 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7317 (mp0) REVERT: A 423 MET cc_start: 0.6536 (pmt) cc_final: 0.6325 (pmm) REVERT: C 50 HIS cc_start: 0.8160 (t70) cc_final: 0.7577 (t70) REVERT: C 82 ASP cc_start: 0.7924 (m-30) cc_final: 0.7641 (m-30) REVERT: C 111 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7272 (mp0) REVERT: C 131 ASP cc_start: 0.7209 (p0) cc_final: 0.6665 (p0) REVERT: C 343 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: C 376 GLU cc_start: 0.7514 (mm-30) cc_final: 0.6945 (mt-10) REVERT: C 386 GLN cc_start: 0.8898 (tp40) cc_final: 0.8689 (tp40) REVERT: C 416 LYS cc_start: 0.7685 (mttt) cc_final: 0.6858 (tmtt) REVERT: B 84 LYS cc_start: 0.7153 (tttt) cc_final: 0.6841 (ttpp) REVERT: B 125 GLU cc_start: 0.8109 (tt0) cc_final: 0.7670 (tm-30) REVERT: B 321 GLU cc_start: 0.8236 (mp0) cc_final: 0.7611 (mp0) REVERT: B 333 MET cc_start: 0.8277 (mmm) cc_final: 0.8030 (tpp) REVERT: B 400 GLU cc_start: 0.8139 (tp30) cc_final: 0.7560 (tm-30) REVERT: B 458 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.7305 (m-80) REVERT: E 383 GLN cc_start: 0.8515 (mt0) cc_final: 0.8038 (mm110) REVERT: E 410 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7741 (tm-30) outliers start: 29 outliers final: 19 residues processed: 191 average time/residue: 1.3749 time to fit residues: 284.9049 Evaluate side-chains 198 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 287 ARG Chi-restraints excluded: chain E residue 410 GLU Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 475 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 145 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 283 ASN ** A 303 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 = 0.3736 r_free = 0.3736 target = 0.147131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.091682 restraints weight = 37333.814| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.77 r_work: 0.2894 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12596 Z= 0.127 Angle : 0.503 8.428 17010 Z= 0.267 Chirality : 0.043 0.327 1897 Planarity : 0.004 0.052 2160 Dihedral : 6.073 58.786 1711 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.85 % Allowed : 13.82 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.22), residues: 1536 helix: 1.83 (0.23), residues: 583 sheet: 0.66 (0.29), residues: 341 loop : 0.55 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 289 TYR 0.034 0.001 TYR B 486 PHE 0.076 0.002 PHE E 458 TRP 0.016 0.001 TRP B 431 HIS 0.003 0.001 HIS E 298 Details of bonding type rmsd covalent geometry : bond 0.00295 (12596) covalent geometry : angle 0.50301 (17010) hydrogen bonds : bond 0.03547 ( 612) hydrogen bonds : angle 4.96469 ( 1677) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 324 is missing expected H atoms. Skipping. Residue TYR 328 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue TYR 328 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 6 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6207 (tt) REVERT: A 315 MET cc_start: 0.5087 (mtt) cc_final: 0.4362 (mmm) REVERT: A 343 GLU cc_start: 0.7120 (tp30) cc_final: 0.6661 (mm-30) REVERT: A 346 ASN cc_start: 0.7267 (m-40) cc_final: 0.6924 (t0) REVERT: A 348 VAL cc_start: 0.8093 (t) cc_final: 0.7744 (m) REVERT: A 357 ASN cc_start: 0.7456 (m-40) cc_final: 0.6730 (p0) REVERT: A 423 MET cc_start: 0.6560 (pmt) cc_final: 0.6360 (pmm) REVERT: C 50 HIS cc_start: 0.8134 (t70) cc_final: 0.7619 (t70) REVERT: C 82 ASP cc_start: 0.7921 (m-30) cc_final: 0.7636 (m-30) REVERT: C 111 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7273 (mp0) REVERT: C 131 ASP cc_start: 0.7080 (p0) cc_final: 0.6552 (p0) REVERT: C 343 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6749 (mp0) REVERT: C 376 GLU cc_start: 0.7506 (mm-30) cc_final: 0.6949 (mt-10) REVERT: C 386 GLN cc_start: 0.8888 (tp40) cc_final: 0.8647 (tp40) REVERT: C 416 LYS cc_start: 0.7688 (mttt) cc_final: 0.6859 (tmtt) REVERT: B 84 LYS cc_start: 0.7161 (tttt) cc_final: 0.6849 (ttpp) REVERT: B 125 GLU cc_start: 0.8084 (tt0) cc_final: 0.7646 (tm-30) REVERT: B 260 GLN cc_start: 0.8652 (mt0) cc_final: 0.8221 (mm110) REVERT: B 321 GLU cc_start: 0.8231 (mp0) cc_final: 0.7593 (mp0) REVERT: B 333 MET cc_start: 0.8269 (mmm) cc_final: 0.8022 (tpp) REVERT: B 400 GLU cc_start: 0.8135 (tp30) cc_final: 0.7569 (tm-30) REVERT: B 458 PHE cc_start: 0.7573 (OUTLIER) cc_final: 0.7078 (m-80) REVERT: E 383 GLN cc_start: 0.8506 (mt0) cc_final: 0.8022 (mm110) REVERT: E 410 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7760 (tm-30) outliers start: 25 outliers final: 14 residues processed: 186 average time/residue: 1.2889 time to fit residues: 260.4180 Evaluate side-chains 192 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 410 GLU Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 475 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 35 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.146944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.091356 restraints weight = 37001.033| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.78 r_work: 0.2888 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12596 Z= 0.133 Angle : 0.511 10.116 17010 Z= 0.271 Chirality : 0.043 0.345 1897 Planarity : 0.004 0.052 2160 Dihedral : 6.015 58.550 1711 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.63 % Allowed : 14.26 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.22), residues: 1536 helix: 1.86 (0.23), residues: 583 sheet: 0.66 (0.29), residues: 341 loop : 0.56 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 289 TYR 0.035 0.002 TYR B 486 PHE 0.073 0.002 PHE E 458 TRP 0.017 0.001 TRP C 156 HIS 0.003 0.001 HIS E 391 Details of bonding type rmsd covalent geometry : bond 0.00310 (12596) covalent geometry : angle 0.51104 (17010) hydrogen bonds : bond 0.03609 ( 612) hydrogen bonds : angle 4.95672 ( 1677) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 324 is missing expected H atoms. Skipping. Residue TYR 328 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue TYR 328 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: A 6 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6090 (tt) REVERT: A 315 MET cc_start: 0.5057 (mtt) cc_final: 0.4340 (mmm) REVERT: A 343 GLU cc_start: 0.7095 (tp30) cc_final: 0.6651 (mm-30) REVERT: A 346 ASN cc_start: 0.7223 (m-40) cc_final: 0.6927 (t0) REVERT: A 357 ASN cc_start: 0.7380 (m-40) cc_final: 0.6644 (p0) REVERT: A 423 MET cc_start: 0.6565 (pmt) cc_final: 0.6356 (pmm) REVERT: C 50 HIS cc_start: 0.8114 (t70) cc_final: 0.7585 (t70) REVERT: C 82 ASP cc_start: 0.7954 (m-30) cc_final: 0.7653 (m-30) REVERT: C 111 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7233 (mp0) REVERT: C 131 ASP cc_start: 0.6999 (p0) cc_final: 0.6466 (p0) REVERT: C 343 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7194 (mm-30) REVERT: C 376 GLU cc_start: 0.7467 (mm-30) cc_final: 0.6885 (mt-10) REVERT: C 386 GLN cc_start: 0.8822 (tp40) cc_final: 0.8574 (tp40) REVERT: C 416 LYS cc_start: 0.7644 (mttt) cc_final: 0.6830 (tmtt) REVERT: B 84 LYS cc_start: 0.7079 (tttt) cc_final: 0.6756 (ttpp) REVERT: B 125 GLU cc_start: 0.8013 (tt0) cc_final: 0.7531 (tm-30) REVERT: B 260 GLN cc_start: 0.8639 (mt0) cc_final: 0.8141 (mm110) REVERT: B 400 GLU cc_start: 0.8039 (tp30) cc_final: 0.7415 (tm-30) REVERT: E 383 GLN cc_start: 0.8497 (mt0) cc_final: 0.7962 (mm110) outliers start: 22 outliers final: 17 residues processed: 186 average time/residue: 1.2885 time to fit residues: 260.2850 Evaluate side-chains 191 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 342 MET Chi-restraints excluded: chain C residue 343 GLU Chi-restraints excluded: chain C residue 365 ASP Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 475 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 146 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.147380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.091822 restraints weight = 37248.723| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.79 r_work: 0.2896 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12596 Z= 0.125 Angle : 0.502 8.020 17010 Z= 0.266 Chirality : 0.042 0.322 1897 Planarity : 0.004 0.052 2160 Dihedral : 5.692 58.471 1708 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.70 % Allowed : 14.34 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.23), residues: 1536 helix: 1.90 (0.23), residues: 583 sheet: 0.66 (0.29), residues: 341 loop : 0.58 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 289 TYR 0.034 0.001 TYR B 486 PHE 0.073 0.002 PHE E 458 TRP 0.016 0.001 TRP B 431 HIS 0.002 0.001 HIS E 391 Details of bonding type rmsd covalent geometry : bond 0.00291 (12596) covalent geometry : angle 0.50244 (17010) hydrogen bonds : bond 0.03480 ( 612) hydrogen bonds : angle 4.91034 ( 1677) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10865.39 seconds wall clock time: 184 minutes 0.91 seconds (11040.91 seconds total)