Starting phenix.real_space_refine on Fri Oct 23 22:13:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9spe_55078/10_2026/9spe_55078.cif Found real_map, /net/cci-nas-00/data/ceres_data/9spe_55078/10_2026/9spe_55078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9spe_55078/10_2026/9spe_55078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9spe_55078/10_2026/9spe_55078.map" model { file = "/net/cci-nas-00/data/ceres_data/9spe_55078/10_2026/9spe_55078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9spe_55078/10_2026/9spe_55078.cif" } resolution = 3.25 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 72 5.16 5 C 7103 2.51 5 N 1927 2.21 5 O 2118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11226 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 531 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 4, 'TRANS': 59} Chain breaks: 1 Chain: "B" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1948 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 8, 'TRANS': 239} Chain breaks: 2 Chain: "C" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1569 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 2 Chain: "D" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 248 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "P" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3310 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 409} Chain breaks: 3 Chain: "R" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3521 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 441} Chain breaks: 1 Chain: "P" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'FDA': 1, 'NAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8510 SG CYS R 122 40.441 77.343 76.877 1.00 37.32 S ATOM 8510 SG CYS R 122 40.441 77.343 76.877 1.00 37.32 S Time building chain proxies: 2.45, per 1000 atoms: 0.22 Number of scatterers: 11226 At special positions: 0 Unit cell: (83.2, 122.85, 152.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 72 16.00 P 4 15.00 Mg 2 11.99 O 2118 8.00 N 1927 7.00 C 7103 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 517.4 milliseconds 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2624 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 10 sheets defined 51.2% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 12 through 17 removed outlier: 3.788A pdb=" N LEU A 16 " --> pdb=" O ASP A 12 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 17 " --> pdb=" O SER A 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 12 through 17' Processing helix chain 'A' and resid 23 through 34 Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 68 through 78 Processing helix chain 'B' and resid 12 through 23 Processing helix chain 'B' and resid 27 through 30 removed outlier: 3.688A pdb=" N LEU B 30 " --> pdb=" O GLY B 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 27 through 30' Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 45 through 63 Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 96 through 100 removed outlier: 3.701A pdb=" N SER B 100 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 removed outlier: 4.424A pdb=" N LEU B 107 " --> pdb=" O ILE B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 130 Processing helix chain 'B' and resid 145 through 158 Processing helix chain 'B' and resid 166 through 185 removed outlier: 3.719A pdb=" N LYS B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 190 removed outlier: 4.265A pdb=" N VAL B 190 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 237 Processing helix chain 'B' and resid 238 through 239 No H-bonds generated for 'chain 'B' and resid 238 through 239' Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'B' and resid 245 through 258 Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 267 through 274 Processing helix chain 'C' and resid 3 through 9 Processing helix chain 'C' and resid 21 through 36 Processing helix chain 'C' and resid 45 through 50 Processing helix chain 'C' and resid 55 through 67 Processing helix chain 'C' and resid 75 through 93 Processing helix chain 'C' and resid 127 through 141 Processing helix chain 'C' and resid 148 through 164 Processing helix chain 'C' and resid 165 through 171 Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 194 through 231 Processing helix chain 'D' and resid 707 through 731 removed outlier: 4.147A pdb=" N THR D 711 " --> pdb=" O ILE D 707 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL D 712 " --> pdb=" O LEU D 708 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLN D 713 " --> pdb=" O ALA D 709 " (cutoff:3.500A) Processing helix chain 'P' and resid 19 through 33 Processing helix chain 'P' and resid 133 through 147 removed outlier: 3.857A pdb=" N LYS P 146 " --> pdb=" O LYS P 142 " (cutoff:3.500A) Processing helix chain 'P' and resid 156 through 166 removed outlier: 3.977A pdb=" N TYR P 164 " --> pdb=" O LEU P 160 " (cutoff:3.500A) Processing helix chain 'P' and resid 186 through 198 removed outlier: 3.632A pdb=" N ILE P 198 " --> pdb=" O THR P 194 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 243 removed outlier: 3.544A pdb=" N LEU P 243 " --> pdb=" O HIS P 240 " (cutoff:3.500A) Processing helix chain 'P' and resid 269 through 276 Processing helix chain 'P' and resid 323 through 328 removed outlier: 3.936A pdb=" N HIS P 328 " --> pdb=" O GLU P 324 " (cutoff:3.500A) Processing helix chain 'P' and resid 375 through 396 Processing helix chain 'P' and resid 402 through 406 removed outlier: 3.603A pdb=" N PHE P 405 " --> pdb=" O ASP P 402 " (cutoff:3.500A) Processing helix chain 'P' and resid 467 through 478 Processing helix chain 'P' and resid 484 through 490 Processing helix chain 'P' and resid 494 through 499 Processing helix chain 'R' and resid 5 through 10 Processing helix chain 'R' and resid 39 through 56 removed outlier: 3.769A pdb=" N LYS R 44 " --> pdb=" O ASP R 40 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU R 45 " --> pdb=" O ALA R 41 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU R 50 " --> pdb=" O MET R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 74 Processing helix chain 'R' and resid 112 through 117 Processing helix chain 'R' and resid 134 through 138 removed outlier: 4.418A pdb=" N GLN R 137 " --> pdb=" O SER R 134 " (cutoff:3.500A) Proline residue: R 138 - end of helix No H-bonds generated for 'chain 'R' and resid 134 through 138' Processing helix chain 'R' and resid 139 through 151 Processing helix chain 'R' and resid 164 through 175 Processing helix chain 'R' and resid 175 through 182 removed outlier: 3.848A pdb=" N SER R 179 " --> pdb=" O GLY R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 192 Processing helix chain 'R' and resid 193 through 198 Processing helix chain 'R' and resid 208 through 216 Processing helix chain 'R' and resid 239 through 247 Processing helix chain 'R' and resid 264 through 285 removed outlier: 3.838A pdb=" N LYS R 279 " --> pdb=" O VAL R 275 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS R 282 " --> pdb=" O GLU R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 337 Processing helix chain 'R' and resid 415 through 422 Processing helix chain 'R' and resid 477 through 488 Processing sheet with id=AA1, first strand: chain 'P' and resid 80 through 82 removed outlier: 6.154A pdb=" N LEU P 110 " --> pdb=" O TYR P 354 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 87 through 91 Processing sheet with id=AA3, first strand: chain 'P' and resid 116 through 117 Processing sheet with id=AA4, first strand: chain 'P' and resid 128 through 129 removed outlier: 6.836A pdb=" N MET P 151 " --> pdb=" O VAL P 314 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE P 150 " --> pdb=" O ILE P 172 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ALA P 174 " --> pdb=" O ILE P 150 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE P 152 " --> pdb=" O ALA P 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 263 through 268 removed outlier: 3.945A pdb=" N LYS P 265 " --> pdb=" O GLU P 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 340 through 342 removed outlier: 5.512A pdb=" N LEU P 340 " --> pdb=" O THR P 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'P' and resid 409 through 414 removed outlier: 4.095A pdb=" N LYS P 418 " --> pdb=" O GLY P 463 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL P 450 " --> pdb=" O MET P 457 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA P 459 " --> pdb=" O LYS P 448 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS P 448 " --> pdb=" O ALA P 459 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU P 461 " --> pdb=" O TYR P 446 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TYR P 446 " --> pdb=" O LEU P 461 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 12 through 16 removed outlier: 5.689A pdb=" N LYS R 14 " --> pdb=" O ARG R 21 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ARG R 21 " --> pdb=" O LYS R 14 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE R 83 " --> pdb=" O MET R 99 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLY R 97 " --> pdb=" O LEU R 85 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN R 98 " --> pdb=" O LYS R 375 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS R 375 " --> pdb=" O ASN R 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 346 through 352 removed outlier: 5.763A pdb=" N VAL R 347 " --> pdb=" O ARG R 128 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ARG R 128 " --> pdb=" O VAL R 347 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR R 349 " --> pdb=" O LEU R 126 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL R 254 " --> pdb=" O THR R 129 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLN R 253 " --> pdb=" O VAL R 234 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL R 234 " --> pdb=" O GLN R 253 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE R 231 " --> pdb=" O ILE R 500 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LYS R 496 " --> pdb=" O ASP R 235 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE R 237 " --> pdb=" O ALA R 494 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ALA R 494 " --> pdb=" O ILE R 237 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LYS R 493 " --> pdb=" O THR R 413 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N THR R 413 " --> pdb=" O LYS R 493 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 378 through 379 577 hydrogen bonds defined for protein. 1644 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.76 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2923 1.33 - 1.45: 1950 1.45 - 1.57: 6435 1.57 - 1.69: 8 1.69 - 1.81: 115 Bond restraints: 11431 Sorted by residual: bond pdb=" C VAL R 27 " pdb=" N PRO R 28 " ideal model delta sigma weight residual 1.335 1.355 -0.020 1.38e-02 5.25e+03 2.00e+00 bond pdb=" CB PHE P 192 " pdb=" CG PHE P 192 " ideal model delta sigma weight residual 1.502 1.531 -0.029 2.30e-02 1.89e+03 1.60e+00 bond pdb=" C VAL P 369 " pdb=" O VAL P 369 " ideal model delta sigma weight residual 1.236 1.222 0.015 1.19e-02 7.06e+03 1.50e+00 bond pdb=" CB PHE C 28 " pdb=" CG PHE C 28 " ideal model delta sigma weight residual 1.502 1.529 -0.027 2.30e-02 1.89e+03 1.34e+00 bond pdb=" CB GLN R 201 " pdb=" CG GLN R 201 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.14e+00 ... (remaining 11426 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 15274 2.38 - 4.77: 142 4.77 - 7.15: 18 7.15 - 9.54: 0 9.54 - 11.92: 2 Bond angle restraints: 15436 Sorted by residual: angle pdb=" N ILE R 355 " pdb=" CA ILE R 355 " pdb=" C ILE R 355 " ideal model delta sigma weight residual 107.88 113.31 -5.43 1.38e+00 5.25e-01 1.55e+01 angle pdb=" CA LEU P 489 " pdb=" CB LEU P 489 " pdb=" CG LEU P 489 " ideal model delta sigma weight residual 116.30 128.22 -11.92 3.50e+00 8.16e-02 1.16e+01 angle pdb=" C ILE C 187 " pdb=" N LEU C 188 " pdb=" CA LEU C 188 " ideal model delta sigma weight residual 121.54 127.61 -6.07 1.91e+00 2.74e-01 1.01e+01 angle pdb=" CA LEU R 42 " pdb=" CB LEU R 42 " pdb=" CG LEU R 42 " ideal model delta sigma weight residual 116.30 126.31 -10.01 3.50e+00 8.16e-02 8.19e+00 angle pdb=" CA GLU P 486 " pdb=" CB GLU P 486 " pdb=" CG GLU P 486 " ideal model delta sigma weight residual 114.10 119.67 -5.57 2.00e+00 2.50e-01 7.77e+00 ... (remaining 15431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.50: 6226 22.50 - 45.01: 623 45.01 - 67.51: 94 67.51 - 90.02: 18 90.02 - 112.52: 1 Dihedral angle restraints: 6962 sinusoidal: 2897 harmonic: 4065 Sorted by residual: dihedral pdb=" CA VAL R 38 " pdb=" C VAL R 38 " pdb=" N ASN R 39 " pdb=" CA ASN R 39 " ideal model delta harmonic sigma weight residual 180.00 160.62 19.38 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" O5' FDA P 602 " pdb=" O3P FDA P 602 " pdb=" P FDA P 602 " pdb=" PA FDA P 602 " ideal model delta sinusoidal sigma weight residual 137.49 24.97 112.52 1 3.00e+01 1.11e-03 1.48e+01 dihedral pdb=" CA ASN R 121 " pdb=" C ASN R 121 " pdb=" N CYS R 122 " pdb=" CA CYS R 122 " ideal model delta harmonic sigma weight residual 180.00 161.67 18.33 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 6959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1086 0.032 - 0.064: 407 0.064 - 0.095: 145 0.095 - 0.127: 71 0.127 - 0.159: 15 Chirality restraints: 1724 Sorted by residual: chirality pdb=" CA ILE R 401 " pdb=" N ILE R 401 " pdb=" C ILE R 401 " pdb=" CB ILE R 401 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA VAL D 705 " pdb=" N VAL D 705 " pdb=" C VAL D 705 " pdb=" CB VAL D 705 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA ILE R 161 " pdb=" N ILE R 161 " pdb=" C ILE R 161 " pdb=" CB ILE R 161 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 1721 not shown) Planarity restraints: 1974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 252 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.06e+00 pdb=" C ILE B 252 " 0.043 2.00e-02 2.50e+03 pdb=" O ILE B 252 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR B 253 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG R 498 " 0.039 5.00e-02 4.00e+02 5.91e-02 5.58e+00 pdb=" N PRO R 499 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO R 499 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 499 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP P 384 " 0.014 2.00e-02 2.50e+03 1.32e-02 4.39e+00 pdb=" CG TRP P 384 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP P 384 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP P 384 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP P 384 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP P 384 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP P 384 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 384 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 384 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP P 384 " 0.001 2.00e-02 2.50e+03 ... (remaining 1971 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 6 2.43 - 3.05: 7030 3.05 - 3.67: 17175 3.67 - 4.28: 25174 4.28 - 4.90: 42384 Nonbonded interactions: 91769 Sorted by model distance: nonbonded pdb=" OD2 ASP R 119 " pdb="MG MG R 602 " model vdw 1.813 2.170 nonbonded pdb=" NE2 HIS R 227 " pdb="MG MG R 602 " model vdw 1.978 2.250 nonbonded pdb=" NE2 HIS R 353 " pdb="MG MG R 601 " model vdw 2.034 2.250 nonbonded pdb=" NE2 HIS R 259 " pdb="MG MG R 601 " model vdw 2.037 2.250 nonbonded pdb=" SG CYS R 122 " pdb="MG MG R 602 " model vdw 2.258 2.530 ... (remaining 91764 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.700 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 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 0.041 11431 Z= 0.150 Angle : 0.616 11.921 15436 Z= 0.333 Chirality : 0.043 0.159 1724 Planarity : 0.004 0.059 1974 Dihedral : 17.287 112.523 4338 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.66 % Allowed : 21.38 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.23), residues: 1387 helix: 1.81 (0.21), residues: 644 sheet: -1.60 (0.43), residues: 138 loop : -0.79 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 228 TYR 0.014 0.001 TYR R 306 PHE 0.022 0.002 PHE P 140 TRP 0.036 0.001 TRP P 384 HIS 0.006 0.001 HIS C 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (11431) covalent geometry : angle 0.61602 / 0.33 (15436) hydrogen bonds : bond 0.11620 / 7.88 ( 577) hydrogen bonds : angle 5.25617 / 3.60 ( 1644) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.6216 (ttp) cc_final: 0.5068 (ptm) REVERT: B 49 SER cc_start: 0.5604 (m) cc_final: 0.5212 (p) REVERT: B 149 GLU cc_start: 0.7620 (mm-30) cc_final: 0.6993 (mm-30) REVERT: B 197 MET cc_start: 0.7031 (ptp) cc_final: 0.6816 (pmm) REVERT: B 241 ARG cc_start: 0.8215 (ttm170) cc_final: 0.7614 (ttt-90) REVERT: C 18 ASN cc_start: 0.6783 (t0) cc_final: 0.6084 (m-40) REVERT: C 78 GLU cc_start: 0.7595 (mp0) cc_final: 0.7238 (pm20) REVERT: C 135 MET cc_start: 0.5831 (tpt) cc_final: 0.5423 (tmm) REVERT: C 152 MET cc_start: 0.6479 (mtp) cc_final: 0.5924 (mtp) REVERT: D 713 GLN cc_start: 0.7429 (mp10) cc_final: 0.6940 (pt0) REVERT: R 67 LYS cc_start: 0.7145 (mmtt) cc_final: 0.6570 (mmtt) REVERT: R 118 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.6791 (m-80) outliers start: 32 outliers final: 30 residues processed: 194 average time/residue: 0.0994 time to fit residues: 28.3850 Evaluate side-chains 198 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 712 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 734 ASN Chi-restraints excluded: chain P residue 97 ILE Chi-restraints excluded: chain P residue 166 ILE Chi-restraints excluded: chain P residue 313 ILE Chi-restraints excluded: chain P residue 319 VAL Chi-restraints excluded: chain P residue 495 ILE Chi-restraints excluded: chain R residue 89 HIS Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 118 PHE Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 379 ARG Chi-restraints excluded: chain R residue 413 THR Chi-restraints excluded: chain R residue 478 VAL Chi-restraints excluded: chain R residue 482 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 HIS ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 142 GLN ** R 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 393 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 = 0.4749 r_free = 0.4749 target = 0.229248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.184856 restraints weight = 13314.213| |-----------------------------------------------------------------------------| r_work (start): 0.4382 rms_B_bonded: 2.98 r_work: 0.4233 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.0701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11431 Z= 0.156 Angle : 0.553 8.891 15436 Z= 0.286 Chirality : 0.042 0.163 1724 Planarity : 0.004 0.048 1974 Dihedral : 8.506 113.710 1662 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.24 % Allowed : 20.55 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.23), residues: 1387 helix: 1.90 (0.20), residues: 644 sheet: -1.58 (0.42), residues: 138 loop : -0.75 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 221 TYR 0.017 0.002 TYR R 306 PHE 0.017 0.002 PHE P 140 TRP 0.018 0.001 TRP P 384 HIS 0.006 0.001 HIS C 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (11431) covalent geometry : angle 0.55306 / 0.29 (15436) hydrogen bonds : bond 0.03681 / 2.43 ( 577) hydrogen bonds : angle 4.61385 / 3.18 ( 1644) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 177 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.5840 (ttp) cc_final: 0.4665 (ptp) REVERT: B 30 LEU cc_start: 0.5026 (mt) cc_final: 0.4621 (tt) REVERT: B 149 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6707 (mm-30) REVERT: B 197 MET cc_start: 0.7100 (ptp) cc_final: 0.6614 (pmm) REVERT: B 222 ARG cc_start: 0.5610 (mtp85) cc_final: 0.5386 (mtp85) REVERT: B 241 ARG cc_start: 0.7969 (ttm170) cc_final: 0.7585 (mtp180) REVERT: C 18 ASN cc_start: 0.6941 (t0) cc_final: 0.6244 (m-40) REVERT: C 135 MET cc_start: 0.5670 (tpt) cc_final: 0.5156 (tmm) REVERT: C 152 MET cc_start: 0.6471 (mtp) cc_final: 0.5983 (mtp) REVERT: C 207 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7768 (mp) REVERT: D 713 GLN cc_start: 0.7584 (mp10) cc_final: 0.6922 (pt0) REVERT: P 138 GLN cc_start: 0.5810 (mt0) cc_final: 0.5125 (tt0) REVERT: P 464 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7521 (tm-30) REVERT: R 66 MET cc_start: 0.7247 (mtp) cc_final: 0.6968 (mtt) REVERT: R 118 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.7122 (m-80) REVERT: R 379 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7507 (ttm170) outliers start: 51 outliers final: 32 residues processed: 215 average time/residue: 0.0912 time to fit residues: 28.8192 Evaluate side-chains 207 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 712 VAL Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain P residue 97 ILE Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain P residue 313 ILE Chi-restraints excluded: chain P residue 319 VAL Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 361 THR Chi-restraints excluded: chain P residue 440 CYS Chi-restraints excluded: chain P residue 464 GLU Chi-restraints excluded: chain P residue 495 ILE Chi-restraints excluded: chain R residue 89 HIS Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 118 PHE Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 379 ARG Chi-restraints excluded: chain R residue 388 ILE Chi-restraints excluded: chain R residue 478 VAL Chi-restraints excluded: chain R residue 482 VAL Chi-restraints excluded: chain R residue 485 CYS Chi-restraints excluded: chain R residue 495 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [1, 55, 53, 102, 101, 33, 125, 68, 138, 11, 106] chunk 1 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 138 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.231538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.187000 restraints weight = 13281.516| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 2.90 r_work: 0.4257 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11431 Z= 0.123 Angle : 0.516 7.248 15436 Z= 0.266 Chirality : 0.041 0.153 1724 Planarity : 0.003 0.045 1974 Dihedral : 8.095 113.307 1647 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.83 % Allowed : 21.63 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.23), residues: 1387 helix: 2.11 (0.20), residues: 644 sheet: -1.54 (0.42), residues: 138 loop : -0.73 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 228 TYR 0.015 0.001 TYR R 306 PHE 0.013 0.001 PHE P 140 TRP 0.021 0.001 TRP P 384 HIS 0.004 0.001 HIS C 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (11431) covalent geometry : angle 0.51631 / 0.27 (15436) hydrogen bonds : bond 0.03330 / 2.19 ( 577) hydrogen bonds : angle 4.44219 / 3.06 ( 1644) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 187 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.5802 (ttp) cc_final: 0.4628 (ptp) REVERT: B 30 LEU cc_start: 0.5157 (mt) cc_final: 0.4726 (tt) REVERT: B 90 GLU cc_start: 0.6059 (tt0) cc_final: 0.4396 (tp30) REVERT: B 149 GLU cc_start: 0.7363 (mm-30) cc_final: 0.6714 (mm-30) REVERT: B 197 MET cc_start: 0.7149 (ptp) cc_final: 0.6612 (pmm) REVERT: B 241 ARG cc_start: 0.7982 (ttm170) cc_final: 0.7613 (mtp180) REVERT: C 1 MET cc_start: 0.5440 (ttm) cc_final: 0.5223 (tpp) REVERT: C 4 ARG cc_start: 0.5273 (OUTLIER) cc_final: 0.3780 (ttm110) REVERT: C 18 ASN cc_start: 0.6938 (t0) cc_final: 0.6239 (m-40) REVERT: C 135 MET cc_start: 0.5645 (tpt) cc_final: 0.5130 (tmm) REVERT: C 152 MET cc_start: 0.6462 (mtp) cc_final: 0.5980 (mtp) REVERT: C 163 ARG cc_start: 0.8185 (mmm160) cc_final: 0.7758 (mmm160) REVERT: D 713 GLN cc_start: 0.7494 (mp10) cc_final: 0.6907 (pt0) REVERT: P 138 GLN cc_start: 0.5871 (mt0) cc_final: 0.5144 (tt0) REVERT: P 464 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7497 (tm-30) REVERT: R 23 LYS cc_start: 0.8057 (tmtt) cc_final: 0.7384 (tptt) REVERT: R 66 MET cc_start: 0.7260 (mtp) cc_final: 0.6990 (mtt) REVERT: R 118 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.7076 (m-80) REVERT: R 379 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7451 (ttm170) outliers start: 46 outliers final: 32 residues processed: 221 average time/residue: 0.0999 time to fit residues: 32.3587 Evaluate side-chains 212 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain C residue 4 ARG Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 712 VAL Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain P residue 97 ILE Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain P residue 313 ILE Chi-restraints excluded: chain P residue 319 VAL Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 440 CYS Chi-restraints excluded: chain P residue 464 GLU Chi-restraints excluded: chain P residue 495 ILE Chi-restraints excluded: chain R residue 89 HIS Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 118 PHE Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 363 VAL Chi-restraints excluded: chain R residue 379 ARG Chi-restraints excluded: chain R residue 413 THR Chi-restraints excluded: chain R residue 478 VAL Chi-restraints excluded: chain R residue 482 VAL Chi-restraints excluded: chain R residue 495 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [95, 13, 75, 20, 49, 137, 2, 57, 58, 90, 78] chunk 95 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 155 ASN ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 428 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.222214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.177246 restraints weight = 13711.169| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 2.71 r_work: 0.4166 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 11431 Z= 0.247 Angle : 0.655 9.074 15436 Z= 0.338 Chirality : 0.045 0.184 1724 Planarity : 0.004 0.052 1974 Dihedral : 8.782 114.823 1646 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 6.57 % Allowed : 19.97 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.23), residues: 1387 helix: 1.54 (0.20), residues: 648 sheet: -1.81 (0.41), residues: 138 loop : -0.98 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 221 TYR 0.024 0.002 TYR R 306 PHE 0.022 0.002 PHE R 102 TRP 0.021 0.002 TRP P 384 HIS 0.008 0.002 HIS R 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.25 (11431) covalent geometry : angle 0.65503 / 0.34 (15436) hydrogen bonds : bond 0.04045 / 2.67 ( 577) hydrogen bonds : angle 4.83884 / 3.35 ( 1644) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 181 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 LEU cc_start: 0.5222 (mt) cc_final: 0.4799 (tt) REVERT: B 49 SER cc_start: 0.5308 (m) cc_final: 0.4954 (p) REVERT: B 149 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6658 (mm-30) REVERT: B 197 MET cc_start: 0.7063 (ptp) cc_final: 0.6419 (pmm) REVERT: B 206 GLN cc_start: 0.7883 (tp40) cc_final: 0.7031 (tt0) REVERT: B 222 ARG cc_start: 0.5642 (mtp85) cc_final: 0.5406 (mtt90) REVERT: B 241 ARG cc_start: 0.7929 (ttm170) cc_final: 0.7416 (mtp180) REVERT: B 252 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7568 (mm) REVERT: C 1 MET cc_start: 0.5401 (ttm) cc_final: 0.4814 (ttm) REVERT: C 135 MET cc_start: 0.5625 (tpt) cc_final: 0.5131 (tmm) REVERT: C 152 MET cc_start: 0.6625 (mtp) cc_final: 0.6306 (mtp) REVERT: C 207 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7785 (mp) REVERT: D 713 GLN cc_start: 0.7583 (mp10) cc_final: 0.6964 (pt0) REVERT: P 138 GLN cc_start: 0.6099 (mt0) cc_final: 0.5338 (tt0) REVERT: P 177 ASP cc_start: 0.6530 (m-30) cc_final: 0.6127 (m-30) REVERT: P 295 MET cc_start: 0.5452 (tpp) cc_final: 0.5079 (tmm) REVERT: P 486 GLU cc_start: 0.7232 (tp30) cc_final: 0.7002 (tp30) REVERT: R 23 LYS cc_start: 0.8162 (tmtt) cc_final: 0.7492 (tptt) REVERT: R 51 ARG cc_start: 0.5664 (ttp-170) cc_final: 0.4997 (tpp-160) REVERT: R 110 VAL cc_start: 0.5477 (OUTLIER) cc_final: 0.5261 (m) REVERT: R 118 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.7543 (m-80) REVERT: R 379 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7510 (ttm170) outliers start: 79 outliers final: 51 residues processed: 241 average time/residue: 0.0972 time to fit residues: 33.8570 Evaluate side-chains 226 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 170 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 2 PHE Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain D residue 712 VAL Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 734 ASN Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain P residue 97 ILE Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain P residue 175 ILE Chi-restraints excluded: chain P residue 300 VAL Chi-restraints excluded: chain P residue 313 ILE Chi-restraints excluded: chain P residue 319 VAL Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 361 THR Chi-restraints excluded: chain P residue 440 CYS Chi-restraints excluded: chain P residue 495 ILE Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 89 HIS Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 118 PHE Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 363 VAL Chi-restraints excluded: chain R residue 379 ARG Chi-restraints excluded: chain R residue 400 LEU Chi-restraints excluded: chain R residue 413 THR Chi-restraints excluded: chain R residue 428 HIS Chi-restraints excluded: chain R residue 478 VAL Chi-restraints excluded: chain R residue 479 THR Chi-restraints excluded: chain R residue 485 CYS Chi-restraints excluded: chain R residue 495 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [88, 119, 86, 42, 98, 40, 115, 21, 11, 118, 63] chunk 88 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 155 ASN ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 428 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.228144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.183260 restraints weight = 13423.800| |-----------------------------------------------------------------------------| r_work (start): 0.4366 rms_B_bonded: 3.14 r_work: 0.4210 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11431 Z= 0.131 Angle : 0.552 9.432 15436 Z= 0.282 Chirality : 0.042 0.156 1724 Planarity : 0.004 0.045 1974 Dihedral : 8.286 114.829 1643 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.07 % Allowed : 21.05 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.23), residues: 1387 helix: 1.92 (0.20), residues: 644 sheet: -1.91 (0.39), residues: 154 loop : -0.84 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 444 TYR 0.016 0.001 TYR R 306 PHE 0.012 0.001 PHE R 36 TRP 0.024 0.001 TRP P 384 HIS 0.008 0.001 HIS R 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (11431) covalent geometry : angle 0.55236 / 0.28 (15436) hydrogen bonds : bond 0.03345 / 2.21 ( 577) hydrogen bonds : angle 4.50788 / 3.12 ( 1644) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 184 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.5639 (ttm) cc_final: 0.4554 (ptp) REVERT: B 30 LEU cc_start: 0.5218 (mt) cc_final: 0.4832 (tt) REVERT: B 49 SER cc_start: 0.5184 (m) cc_final: 0.4863 (p) REVERT: B 90 GLU cc_start: 0.6118 (tt0) cc_final: 0.4642 (tp30) REVERT: B 149 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6643 (mm-30) REVERT: B 197 MET cc_start: 0.6991 (ptp) cc_final: 0.6413 (pmm) REVERT: B 206 GLN cc_start: 0.7840 (tp40) cc_final: 0.6988 (tt0) REVERT: B 222 ARG cc_start: 0.5576 (mtp85) cc_final: 0.5203 (mtt90) REVERT: B 241 ARG cc_start: 0.7875 (ttm170) cc_final: 0.7474 (mtp180) REVERT: B 252 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7535 (mm) REVERT: C 135 MET cc_start: 0.5604 (tpt) cc_final: 0.5125 (tmm) REVERT: C 152 MET cc_start: 0.6616 (mtp) cc_final: 0.5996 (mtp) REVERT: D 713 GLN cc_start: 0.7460 (mp10) cc_final: 0.6940 (pt0) REVERT: P 295 MET cc_start: 0.5418 (tpp) cc_final: 0.5034 (tmm) REVERT: R 23 LYS cc_start: 0.8072 (tmtt) cc_final: 0.7455 (tptt) REVERT: R 66 MET cc_start: 0.7375 (mtp) cc_final: 0.7120 (mtt) REVERT: R 118 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.7124 (m-80) REVERT: R 246 MET cc_start: 0.6711 (mtt) cc_final: 0.6500 (mtt) REVERT: R 379 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7493 (ttm170) outliers start: 61 outliers final: 46 residues processed: 226 average time/residue: 0.1010 time to fit residues: 33.1265 Evaluate side-chains 223 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 174 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain C residue 2 PHE Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 712 VAL Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 734 ASN Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain P residue 97 ILE Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain P residue 313 ILE Chi-restraints excluded: chain P residue 319 VAL Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 422 LEU Chi-restraints excluded: chain P residue 440 CYS Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 89 HIS Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 118 PHE Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 363 VAL Chi-restraints excluded: chain R residue 374 ARG Chi-restraints excluded: chain R residue 379 ARG Chi-restraints excluded: chain R residue 395 THR Chi-restraints excluded: chain R residue 400 LEU Chi-restraints excluded: chain R residue 478 VAL Chi-restraints excluded: chain R residue 482 VAL Chi-restraints excluded: chain R residue 485 CYS Chi-restraints excluded: chain R residue 495 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [86, 138, 28, 57, 82, 23, 34, 39, 8, 72, 49] chunk 86 optimal weight: 0.8980 chunk 138 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 95 HIS P 155 ASN ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 361 HIS ** R 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.221331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.179250 restraints weight = 13512.006| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 2.42 r_work: 0.4116 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3976 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 11431 Z= 0.240 Angle : 0.666 8.893 15436 Z= 0.340 Chirality : 0.045 0.161 1724 Planarity : 0.004 0.056 1974 Dihedral : 8.633 114.273 1641 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.99 % Allowed : 21.88 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.23), residues: 1387 helix: 1.48 (0.20), residues: 649 sheet: -1.63 (0.44), residues: 123 loop : -1.07 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 221 TYR 0.024 0.002 TYR R 306 PHE 0.021 0.002 PHE R 102 TRP 0.024 0.002 TRP P 384 HIS 0.007 0.001 HIS C 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.24 (11431) covalent geometry : angle 0.66597 / 0.34 (15436) hydrogen bonds : bond 0.03941 / 2.60 ( 577) hydrogen bonds : angle 4.83079 / 3.35 ( 1644) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 176 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.5556 (ttm) cc_final: 0.4641 (ptm) REVERT: B 30 LEU cc_start: 0.5026 (mt) cc_final: 0.4656 (tt) REVERT: B 49 SER cc_start: 0.5146 (m) cc_final: 0.4792 (p) REVERT: B 149 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6670 (mm-30) REVERT: B 197 MET cc_start: 0.7069 (ptp) cc_final: 0.6399 (pmm) REVERT: B 222 ARG cc_start: 0.5905 (mtp85) cc_final: 0.5569 (mtt90) REVERT: B 241 ARG cc_start: 0.7833 (ttm170) cc_final: 0.7486 (mtp180) REVERT: B 252 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7721 (mm) REVERT: C 135 MET cc_start: 0.5582 (tpt) cc_final: 0.5061 (tmm) REVERT: C 152 MET cc_start: 0.6723 (mtp) cc_final: 0.6424 (mtp) REVERT: D 713 GLN cc_start: 0.7579 (mp10) cc_final: 0.6986 (pt0) REVERT: P 177 ASP cc_start: 0.6602 (m-30) cc_final: 0.6253 (m-30) REVERT: P 260 MET cc_start: 0.7803 (tpp) cc_final: 0.7574 (tpt) REVERT: P 295 MET cc_start: 0.5416 (tpp) cc_final: 0.5136 (tmm) REVERT: P 425 TYR cc_start: 0.7450 (p90) cc_final: 0.7204 (p90) REVERT: R 23 LYS cc_start: 0.8220 (tmtt) cc_final: 0.7599 (tptt) REVERT: R 118 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.7499 (m-10) REVERT: R 379 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7541 (ttm170) outliers start: 72 outliers final: 53 residues processed: 229 average time/residue: 0.0978 time to fit residues: 32.4206 Evaluate side-chains 227 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 171 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 2 PHE Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 712 VAL Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain P residue 97 ILE Chi-restraints excluded: chain P residue 99 THR Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain P residue 175 ILE Chi-restraints excluded: chain P residue 300 VAL Chi-restraints excluded: chain P residue 313 ILE Chi-restraints excluded: chain P residue 319 VAL Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 422 LEU Chi-restraints excluded: chain P residue 440 CYS Chi-restraints excluded: chain P residue 495 ILE Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 89 HIS Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 118 PHE Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 363 VAL Chi-restraints excluded: chain R residue 374 ARG Chi-restraints excluded: chain R residue 379 ARG Chi-restraints excluded: chain R residue 395 THR Chi-restraints excluded: chain R residue 400 LEU Chi-restraints excluded: chain R residue 413 THR Chi-restraints excluded: chain R residue 428 HIS Chi-restraints excluded: chain R residue 478 VAL Chi-restraints excluded: chain R residue 485 CYS Chi-restraints excluded: chain R residue 495 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [52, 41, 94, 28, 61, 51, 120, 32, 115, 99, 14] chunk 52 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 155 ASN ** R 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.228149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.184015 restraints weight = 13407.808| |-----------------------------------------------------------------------------| r_work (start): 0.4374 rms_B_bonded: 2.93 r_work: 0.4217 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11431 Z= 0.127 Angle : 0.556 8.066 15436 Z= 0.283 Chirality : 0.042 0.168 1724 Planarity : 0.004 0.046 1974 Dihedral : 8.134 114.369 1641 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.49 % Allowed : 22.05 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.23), residues: 1387 helix: 1.95 (0.20), residues: 643 sheet: -1.50 (0.45), residues: 125 loop : -0.89 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 374 TYR 0.015 0.001 TYR R 306 PHE 0.012 0.002 PHE C 28 TRP 0.024 0.001 TRP P 384 HIS 0.005 0.001 HIS R 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (11431) covalent geometry : angle 0.55585 / 0.28 (15436) hydrogen bonds : bond 0.03272 / 2.17 ( 577) hydrogen bonds : angle 4.46939 / 3.09 ( 1644) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 178 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.5566 (OUTLIER) cc_final: 0.4625 (ptm) REVERT: B 30 LEU cc_start: 0.5181 (mt) cc_final: 0.4777 (tt) REVERT: B 49 SER cc_start: 0.5179 (m) cc_final: 0.4816 (p) REVERT: B 90 GLU cc_start: 0.5901 (tt0) cc_final: 0.4310 (tp30) REVERT: B 149 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6683 (mm-30) REVERT: B 197 MET cc_start: 0.7007 (ptp) cc_final: 0.6379 (pmm) REVERT: B 222 ARG cc_start: 0.5615 (mtp85) cc_final: 0.5190 (mtt90) REVERT: B 241 ARG cc_start: 0.7848 (ttm170) cc_final: 0.7590 (mtp180) REVERT: C 1 MET cc_start: 0.5369 (ttm) cc_final: 0.4966 (tpp) REVERT: C 24 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.6291 (mp0) REVERT: C 135 MET cc_start: 0.5455 (tpt) cc_final: 0.5036 (tmm) REVERT: C 152 MET cc_start: 0.6657 (mtp) cc_final: 0.6031 (mtp) REVERT: D 713 GLN cc_start: 0.7389 (mp10) cc_final: 0.6921 (pt0) REVERT: P 260 MET cc_start: 0.7666 (tpp) cc_final: 0.7461 (tpt) REVERT: P 261 CYS cc_start: 0.5743 (m) cc_final: 0.5304 (m) REVERT: P 269 GLN cc_start: 0.2894 (OUTLIER) cc_final: 0.2524 (tp-100) REVERT: P 295 MET cc_start: 0.5465 (tpp) cc_final: 0.5215 (tmm) REVERT: P 425 TYR cc_start: 0.7204 (p90) cc_final: 0.6941 (p90) REVERT: P 486 GLU cc_start: 0.7016 (tp30) cc_final: 0.5895 (pt0) REVERT: R 23 LYS cc_start: 0.8082 (tmtt) cc_final: 0.7483 (tptt) REVERT: R 66 MET cc_start: 0.7371 (mtp) cc_final: 0.7139 (mtt) REVERT: R 118 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.7219 (m-10) REVERT: R 379 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7614 (ttt180) outliers start: 66 outliers final: 48 residues processed: 226 average time/residue: 0.0964 time to fit residues: 31.8820 Evaluate side-chains 229 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 176 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain C residue 2 PHE Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 712 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain P residue 97 ILE Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain P residue 243 LEU Chi-restraints excluded: chain P residue 269 GLN Chi-restraints excluded: chain P residue 313 ILE Chi-restraints excluded: chain P residue 319 VAL Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 361 THR Chi-restraints excluded: chain P residue 422 LEU Chi-restraints excluded: chain P residue 440 CYS Chi-restraints excluded: chain P residue 445 GLU Chi-restraints excluded: chain P residue 495 ILE Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 89 HIS Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 118 PHE Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 363 VAL Chi-restraints excluded: chain R residue 374 ARG Chi-restraints excluded: chain R residue 379 ARG Chi-restraints excluded: chain R residue 395 THR Chi-restraints excluded: chain R residue 400 LEU Chi-restraints excluded: chain R residue 413 THR Chi-restraints excluded: chain R residue 428 HIS Chi-restraints excluded: chain R residue 478 VAL Chi-restraints excluded: chain R residue 495 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [27, 71, 19, 94, 2, 80, 111, 24, 108, 89, 1] chunk 27 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 108 optimal weight: 0.3980 chunk 89 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 HIS ** R 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.227202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.182301 restraints weight = 13484.315| |-----------------------------------------------------------------------------| r_work (start): 0.4352 rms_B_bonded: 2.78 r_work: 0.4211 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11431 Z= 0.151 Angle : 0.584 8.932 15436 Z= 0.297 Chirality : 0.043 0.145 1724 Planarity : 0.004 0.076 1974 Dihedral : 8.120 112.969 1641 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.07 % Allowed : 22.55 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.23), residues: 1387 helix: 1.91 (0.20), residues: 649 sheet: -1.53 (0.45), residues: 125 loop : -0.89 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 374 TYR 0.020 0.001 TYR R 306 PHE 0.013 0.002 PHE C 28 TRP 0.030 0.001 TRP P 384 HIS 0.005 0.001 HIS R 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (11431) covalent geometry : angle 0.58403 / 0.30 (15436) hydrogen bonds : bond 0.03320 / 2.20 ( 577) hydrogen bonds : angle 4.50300 / 3.11 ( 1644) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 179 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.5610 (ttm) cc_final: 0.4657 (ptm) REVERT: B 30 LEU cc_start: 0.5038 (mt) cc_final: 0.4660 (tt) REVERT: B 49 SER cc_start: 0.5205 (m) cc_final: 0.4831 (p) REVERT: B 90 GLU cc_start: 0.5992 (tt0) cc_final: 0.4395 (tp30) REVERT: B 149 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6658 (mm-30) REVERT: B 197 MET cc_start: 0.7033 (ptp) cc_final: 0.6414 (pmm) REVERT: B 222 ARG cc_start: 0.5631 (mtp85) cc_final: 0.5269 (mtt90) REVERT: B 241 ARG cc_start: 0.7857 (ttm170) cc_final: 0.7539 (mtp180) REVERT: C 4 ARG cc_start: 0.5304 (OUTLIER) cc_final: 0.3938 (ttm110) REVERT: C 135 MET cc_start: 0.5413 (tpt) cc_final: 0.5000 (tmm) REVERT: C 152 MET cc_start: 0.6684 (mtp) cc_final: 0.6121 (mtt) REVERT: D 713 GLN cc_start: 0.7359 (mp10) cc_final: 0.6845 (pt0) REVERT: P 260 MET cc_start: 0.7672 (tpp) cc_final: 0.7465 (tpt) REVERT: P 261 CYS cc_start: 0.5807 (m) cc_final: 0.5391 (m) REVERT: P 269 GLN cc_start: 0.2911 (OUTLIER) cc_final: 0.2569 (tp-100) REVERT: P 425 TYR cc_start: 0.7270 (p90) cc_final: 0.7022 (p90) REVERT: P 486 GLU cc_start: 0.7036 (tp30) cc_final: 0.5923 (pt0) REVERT: R 23 LYS cc_start: 0.8089 (tmtt) cc_final: 0.7493 (tptt) REVERT: R 66 MET cc_start: 0.7373 (mtp) cc_final: 0.7147 (mtt) REVERT: R 118 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.7315 (m-10) REVERT: R 379 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7405 (ttm170) outliers start: 61 outliers final: 49 residues processed: 225 average time/residue: 0.0989 time to fit residues: 32.2225 Evaluate side-chains 225 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 172 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 2 PHE Chi-restraints excluded: chain C residue 4 ARG Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 712 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain P residue 97 ILE Chi-restraints excluded: chain P residue 99 THR Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain P residue 243 LEU Chi-restraints excluded: chain P residue 269 GLN Chi-restraints excluded: chain P residue 313 ILE Chi-restraints excluded: chain P residue 319 VAL Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 361 THR Chi-restraints excluded: chain P residue 422 LEU Chi-restraints excluded: chain P residue 440 CYS Chi-restraints excluded: chain P residue 445 GLU Chi-restraints excluded: chain P residue 464 GLU Chi-restraints excluded: chain P residue 495 ILE Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 89 HIS Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 118 PHE Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 363 VAL Chi-restraints excluded: chain R residue 379 ARG Chi-restraints excluded: chain R residue 395 THR Chi-restraints excluded: chain R residue 400 LEU Chi-restraints excluded: chain R residue 413 THR Chi-restraints excluded: chain R residue 428 HIS Chi-restraints excluded: chain R residue 478 VAL Chi-restraints excluded: chain R residue 495 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [28, 101, 100, 125, 113, 71, 5, 40, 130, 38, 88] chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 347 HIS R 80 HIS ** R 232 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 = 0.4733 r_free = 0.4733 target = 0.228813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.184669 restraints weight = 13335.036| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 2.77 r_work: 0.4236 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11431 Z= 0.135 Angle : 0.573 9.633 15436 Z= 0.289 Chirality : 0.042 0.145 1724 Planarity : 0.004 0.070 1974 Dihedral : 7.991 112.294 1641 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.83 % Allowed : 22.80 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.23), residues: 1387 helix: 2.00 (0.20), residues: 650 sheet: -1.53 (0.45), residues: 125 loop : -0.88 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 263 TYR 0.017 0.001 TYR R 306 PHE 0.011 0.001 PHE R 36 TRP 0.032 0.001 TRP P 384 HIS 0.005 0.001 HIS R 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (11431) covalent geometry : angle 0.57285 / 0.29 (15436) hydrogen bonds : bond 0.03192 / 2.12 ( 577) hydrogen bonds : angle 4.42399 / 3.05 ( 1644) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 183 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.5589 (OUTLIER) cc_final: 0.4662 (ptm) REVERT: B 30 LEU cc_start: 0.5075 (mt) cc_final: 0.4685 (tt) REVERT: B 49 SER cc_start: 0.5140 (m) cc_final: 0.4777 (p) REVERT: B 90 GLU cc_start: 0.5979 (tt0) cc_final: 0.4438 (tp30) REVERT: B 149 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6642 (mm-30) REVERT: B 197 MET cc_start: 0.7003 (ptp) cc_final: 0.6401 (pmm) REVERT: B 222 ARG cc_start: 0.5605 (mtp85) cc_final: 0.5187 (mtt90) REVERT: B 241 ARG cc_start: 0.7863 (ttm170) cc_final: 0.7541 (mtp180) REVERT: C 1 MET cc_start: 0.5330 (ttm) cc_final: 0.4922 (tpp) REVERT: C 135 MET cc_start: 0.5396 (tpt) cc_final: 0.5057 (tmm) REVERT: C 152 MET cc_start: 0.6679 (mtp) cc_final: 0.6057 (mtp) REVERT: D 713 GLN cc_start: 0.7266 (mp10) cc_final: 0.6967 (mp10) REVERT: P 260 MET cc_start: 0.7638 (tpp) cc_final: 0.7432 (tpt) REVERT: P 261 CYS cc_start: 0.5728 (m) cc_final: 0.5308 (m) REVERT: P 425 TYR cc_start: 0.7232 (p90) cc_final: 0.6949 (p90) REVERT: P 486 GLU cc_start: 0.7002 (tp30) cc_final: 0.5872 (pt0) REVERT: R 23 LYS cc_start: 0.8052 (tmtt) cc_final: 0.7463 (tptt) REVERT: R 66 MET cc_start: 0.7384 (mtp) cc_final: 0.7141 (mtt) REVERT: R 118 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.7263 (m-10) outliers start: 58 outliers final: 49 residues processed: 225 average time/residue: 0.0966 time to fit residues: 31.7826 Evaluate side-chains 230 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 179 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 2 PHE Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 712 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain P residue 97 ILE Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain P residue 175 ILE Chi-restraints excluded: chain P residue 243 LEU Chi-restraints excluded: chain P residue 313 ILE Chi-restraints excluded: chain P residue 319 VAL Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 361 THR Chi-restraints excluded: chain P residue 422 LEU Chi-restraints excluded: chain P residue 440 CYS Chi-restraints excluded: chain P residue 445 GLU Chi-restraints excluded: chain P residue 464 GLU Chi-restraints excluded: chain P residue 495 ILE Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 89 HIS Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain R residue 118 PHE Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 363 VAL Chi-restraints excluded: chain R residue 379 ARG Chi-restraints excluded: chain R residue 395 THR Chi-restraints excluded: chain R residue 400 LEU Chi-restraints excluded: chain R residue 413 THR Chi-restraints excluded: chain R residue 428 HIS Chi-restraints excluded: chain R residue 478 VAL Chi-restraints excluded: chain R residue 495 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [118, 65, 19, 94, 28, 68, 36, 32, 16, 79, 40] chunk 118 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 155 ASN ** R 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.226092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.181393 restraints weight = 13496.681| |-----------------------------------------------------------------------------| r_work (start): 0.4344 rms_B_bonded: 2.75 r_work: 0.4201 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11431 Z= 0.172 Angle : 0.611 9.765 15436 Z= 0.310 Chirality : 0.043 0.157 1724 Planarity : 0.004 0.075 1974 Dihedral : 8.161 110.835 1639 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.58 % Allowed : 22.96 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.23), residues: 1387 helix: 1.88 (0.20), residues: 648 sheet: -1.59 (0.45), residues: 125 loop : -0.97 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 221 TYR 0.021 0.001 TYR R 306 PHE 0.013 0.002 PHE R 102 TRP 0.027 0.001 TRP P 384 HIS 0.009 0.001 HIS R 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (11431) covalent geometry : angle 0.61050 / 0.31 (15436) hydrogen bonds : bond 0.03431 / 2.27 ( 577) hydrogen bonds : angle 4.55432 / 3.15 ( 1644) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 175 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.5547 (ttm) cc_final: 0.4604 (ptm) REVERT: B 30 LEU cc_start: 0.5014 (mt) cc_final: 0.4650 (tt) REVERT: B 49 SER cc_start: 0.5145 (m) cc_final: 0.4762 (p) REVERT: B 90 GLU cc_start: 0.5992 (tt0) cc_final: 0.4432 (tp30) REVERT: B 149 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6689 (mm-30) REVERT: B 222 ARG cc_start: 0.5615 (mtp85) cc_final: 0.5280 (mtt90) REVERT: B 241 ARG cc_start: 0.7832 (ttm170) cc_final: 0.7502 (mtp180) REVERT: C 1 MET cc_start: 0.5435 (ttm) cc_final: 0.5020 (tpp) REVERT: C 135 MET cc_start: 0.5399 (tpt) cc_final: 0.5050 (tmm) REVERT: C 152 MET cc_start: 0.6699 (mtp) cc_final: 0.6139 (mtt) REVERT: D 713 GLN cc_start: 0.7308 (mp10) cc_final: 0.6984 (mp10) REVERT: P 261 CYS cc_start: 0.5781 (m) cc_final: 0.5392 (m) REVERT: P 425 TYR cc_start: 0.7286 (p90) cc_final: 0.7034 (p90) REVERT: P 486 GLU cc_start: 0.7015 (tp30) cc_final: 0.5872 (pt0) REVERT: R 23 LYS cc_start: 0.8060 (tmtt) cc_final: 0.7480 (tptt) REVERT: R 66 MET cc_start: 0.7399 (mtp) cc_final: 0.7148 (mtt) REVERT: R 118 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.7412 (m-10) outliers start: 55 outliers final: 52 residues processed: 217 average time/residue: 0.0959 time to fit residues: 30.5036 Evaluate side-chains 225 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 172 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain C residue 2 PHE Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 712 VAL Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain P residue 38 ILE Chi-restraints excluded: chain P residue 97 ILE Chi-restraints excluded: chain P residue 99 THR Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain P residue 175 ILE Chi-restraints excluded: chain P residue 243 LEU Chi-restraints excluded: chain P residue 313 ILE Chi-restraints excluded: chain P residue 319 VAL Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain P residue 361 THR Chi-restraints excluded: chain P residue 422 LEU Chi-restraints excluded: chain P residue 440 CYS Chi-restraints excluded: chain P residue 445 GLU Chi-restraints excluded: chain P residue 464 GLU Chi-restraints excluded: chain P residue 495 ILE Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 89 HIS Chi-restraints excluded: chain R residue 90 SER Chi-restraints excluded: chain R residue 111 VAL Chi-restraints excluded: chain R residue 118 PHE Chi-restraints excluded: chain R residue 143 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 277 MET Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 363 VAL Chi-restraints excluded: chain R residue 379 ARG Chi-restraints excluded: chain R residue 395 THR Chi-restraints excluded: chain R residue 400 LEU Chi-restraints excluded: chain R residue 413 THR Chi-restraints excluded: chain R residue 428 HIS Chi-restraints excluded: chain R residue 478 VAL Chi-restraints excluded: chain R residue 495 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: [18, 107, 6, 130, 31, 115, 112, 83, 89, 109, 77] chunk 18 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 130 optimal weight: 0.0570 chunk 31 optimal weight: 0.0570 chunk 115 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 overall best weight: 1.1618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 155 ASN ** R 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.229318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.185043 restraints weight = 13499.748| |-----------------------------------------------------------------------------| r_work (start): 0.4381 rms_B_bonded: 2.77 r_work: 0.4241 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11431 Z= 0.133 Angle : 0.579 10.205 15436 Z= 0.293 Chirality : 0.042 0.147 1724 Planarity : 0.004 0.065 1974 Dihedral : 7.958 111.213 1639 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.66 % Allowed : 22.80 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.23), residues: 1387 helix: 2.00 (0.20), residues: 650 sheet: -1.31 (0.48), residues: 113 loop : -0.97 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 263 TYR 0.016 0.001 TYR R 306 PHE 0.012 0.001 PHE R 36 TRP 0.032 0.002 TRP P 384 HIS 0.007 0.001 HIS R 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (11431) covalent geometry : angle 0.57880 / 0.29 (15436) hydrogen bonds : bond 0.03195 / 2.11 ( 577) hydrogen bonds : angle 4.43788 / 3.06 ( 1644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2858.27 seconds wall clock time: 49 minutes 46.18 seconds (2986.18 seconds total)