Starting phenix.real_space_refine on Fri Jul 3 12:19:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8omr_16976/07_2026/8omr_16976.cif Found real_map, /net/cci-nas-00/data/ceres_data/8omr_16976/07_2026/8omr_16976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8omr_16976/07_2026/8omr_16976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8omr_16976/07_2026/8omr_16976.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8omr_16976/07_2026/8omr_16976.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8omr_16976/07_2026/8omr_16976.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8omr_16976/07_2026/8omr_16976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8omr_16976/07_2026/8omr_16976.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7626 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 75 5.49 5 S 48 5.16 5 C 4520 2.51 5 N 1341 2.21 5 O 1640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7626 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3010 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 390, 3000 Classifications: {'peptide': 390} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 368} Conformer: "B" Number of residues, atoms: 390, 3000 Classifications: {'peptide': 390} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 368} bond proxies already assigned to first conformer: 3053 Chain: "B" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3014 Classifications: {'peptide': 382} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 365} Chain breaks: 1 Chain: "C" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1589 Classifications: {'RNA': 75} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 7, 'rna3p_pur': 33, 'rna3p_pyr': 31} Link IDs: {'rna2p': 11, 'rna3p': 63} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' G%rna3p_pur:plan': 1, ' G%rna3p_pur:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' ZN': 1, '9DG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2336 SG CYS A 317 50.960 46.783 79.155 1.00 71.53 S ATOM 2349 SG CYS A 319 48.135 45.426 76.966 1.00 57.96 S ATOM 2369 SG CYS A 322 51.015 47.274 75.471 1.00 66.05 S ATOM 5496 SG CYS B 351 26.013 26.939 71.448 1.00 61.72 S ATOM 5508 SG CYS B 353 27.602 29.987 72.683 1.00 70.08 S ATOM 5532 SG CYS B 356 24.182 29.011 73.915 1.00 67.56 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A 335 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 335 " occ=0.50 Time building chain proxies: 1.88, per 1000 atoms: 0.25 Number of scatterers: 7626 At special positions: 0 Unit cell: (72.54, 99.06, 124.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 48 16.00 P 75 15.00 O 1640 8.00 N 1341 7.00 C 4520 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: 0.78 Conformation dependent library (CDL) restraints added in 387.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 348 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 319 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 322 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 317 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 382 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 351 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 356 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 353 " Number of angles added : 6 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1428 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 47.9% alpha, 11.8% beta 23 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 58 through 66 removed outlier: 3.581A pdb=" N GLY A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 80 Processing helix chain 'A' and resid 82 through 89 removed outlier: 3.571A pdb=" N ILE A 86 " --> pdb=" O GLY A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 97 Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 169 through 189 Processing helix chain 'A' and resid 206 through 218 Processing helix chain 'A' and resid 235 through 250 removed outlier: 3.649A pdb=" N ARG A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 281 through 288 removed outlier: 3.554A pdb=" N ARG A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.911A pdb=" N PHE A 306 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 325 removed outlier: 4.065A pdb=" N LYS A 324 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS A 325 " --> pdb=" O THR A 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 320 through 325' Processing helix chain 'A' and resid 326 through 335 removed outlier: 3.625A pdb=" N LEU A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N AHIS A 335 " --> pdb=" O HIS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 341 through 366 removed outlier: 4.244A pdb=" N LEU A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL A 347 " --> pdb=" O HIS A 343 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 356 " --> pdb=" O TYR A 352 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET A 357 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 382 removed outlier: 3.555A pdb=" N VAL A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG A 374 " --> pdb=" O PRO A 370 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP A 375 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.216A pdb=" N CYS A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 399 removed outlier: 3.639A pdb=" N ASP A 393 " --> pdb=" O THR A 389 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 394 " --> pdb=" O TRP A 390 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 125 through 137 removed outlier: 3.521A pdb=" N PHE B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 removed outlier: 4.071A pdb=" N SER B 150 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS B 151 " --> pdb=" O GLU B 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 147 through 151' Processing helix chain 'B' and resid 156 through 181 removed outlier: 3.820A pdb=" N VAL B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.718A pdb=" N LYS B 186 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 210 removed outlier: 4.159A pdb=" N ALA B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 240 removed outlier: 3.830A pdb=" N SER B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 264 removed outlier: 3.987A pdb=" N LEU B 261 " --> pdb=" O PRO B 257 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU B 262 " --> pdb=" O ASP B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 274 through 282 Processing helix chain 'B' and resid 353 through 359 Processing helix chain 'B' and resid 360 through 370 Processing helix chain 'B' and resid 373 through 401 removed outlier: 3.844A pdb=" N VAL B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU B 385 " --> pdb=" O MET B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 412 removed outlier: 3.874A pdb=" N LEU B 406 " --> pdb=" O LYS B 402 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 22 removed outlier: 6.732A pdb=" N MET A 17 " --> pdb=" O TRP A 34 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N TRP A 34 " --> pdb=" O MET A 17 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU A 19 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLU A 32 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 46 removed outlier: 3.546A pdb=" N PHE A 278 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET A 46 " --> pdb=" O PHE A 278 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 72 removed outlier: 3.562A pdb=" N ILE A 154 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET A 156 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY A 224 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 199 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 121 Processing sheet with id=AA5, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 9 removed outlier: 5.665A pdb=" N LEU B 5 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LYS B 16 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS B 7 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL B 9 " --> pdb=" O CYS B 12 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY B 15 " --> pdb=" O ILE B 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.825A pdb=" N GLY B 32 " --> pdb=" O PHE B 271 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 36 removed outlier: 6.917A pdb=" N LEU B 35 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N THR B 63 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR B 93 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS B 94 " --> pdb=" O TRP B 140 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN B 142 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N PHE B 141 " --> pdb=" O ILE B 190 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N VAL B 192 " --> pdb=" O PHE B 141 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 113 through 117 Processing sheet with id=AB1, first strand: chain 'B' and resid 284 through 286 244 hydrogen bonds defined for protein. 699 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 61 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 1.00 Time building geometry restraints manager: 0.93 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: 1581 1.33 - 1.45: 2123 1.45 - 1.57: 4014 1.57 - 1.69: 149 1.69 - 1.81: 71 Bond restraints: 7938 Sorted by residual: bond pdb=" CG ASP A 279 " pdb=" OD2 ASP A 279 " ideal model delta sigma weight residual 1.249 1.359 -0.110 1.90e-02 2.77e+03 3.34e+01 bond pdb=" O5' C C 48 " pdb=" C5' C C 48 " ideal model delta sigma weight residual 1.420 1.454 -0.034 1.50e-02 4.44e+03 5.29e+00 bond pdb=" O5' A C 1 " pdb=" C5' A C 1 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.83e+00 bond pdb=" O5' U C 58 " pdb=" C5' U C 58 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.68e+00 bond pdb=" O5' G C 15 " pdb=" C5' G C 15 " ideal model delta sigma weight residual 1.420 1.449 -0.029 1.50e-02 4.44e+03 3.63e+00 ... (remaining 7933 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 10715 2.42 - 4.83: 345 4.83 - 7.25: 41 7.25 - 9.66: 4 9.66 - 12.08: 1 Bond angle restraints: 11106 Sorted by residual: angle pdb=" O3' A C 57 " pdb=" P U C 58 " pdb=" O5' U C 58 " ideal model delta sigma weight residual 104.00 95.43 8.57 1.50e+00 4.44e-01 3.26e+01 angle pdb=" O3' U C 58 " pdb=" P U C 59 " pdb=" O5' U C 59 " ideal model delta sigma weight residual 104.00 96.91 7.09 1.50e+00 4.44e-01 2.23e+01 angle pdb=" C4' G C 56 " pdb=" C3' G C 56 " pdb=" O3' G C 56 " ideal model delta sigma weight residual 113.00 106.87 6.13 1.50e+00 4.44e-01 1.67e+01 angle pdb=" O3' A C 57 " pdb=" P U C 58 " pdb=" OP1 U C 58 " ideal model delta sigma weight residual 108.00 120.08 -12.08 3.00e+00 1.11e-01 1.62e+01 angle pdb=" C2' A C 12 " pdb=" C1' A C 12 " pdb=" N9 A C 12 " ideal model delta sigma weight residual 112.00 117.40 -5.40 1.50e+00 4.44e-01 1.30e+01 ... (remaining 11101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.64: 4583 29.64 - 59.28: 181 59.28 - 88.93: 79 88.93 - 118.57: 0 118.57 - 148.21: 1 Dihedral angle restraints: 4844 sinusoidal: 2627 harmonic: 2217 Sorted by residual: dihedral pdb=" C4' G C 34 " pdb=" C3' G C 34 " pdb=" C2' G C 34 " pdb=" C1' G C 34 " ideal model delta sinusoidal sigma weight residual 36.00 -21.05 57.05 1 8.00e+00 1.56e-02 6.84e+01 dihedral pdb=" O4' G C 34 " pdb=" C2' G C 34 " pdb=" C1' G C 34 " pdb=" C3' G C 34 " ideal model delta sinusoidal sigma weight residual 25.00 -30.91 55.91 1 8.00e+00 1.56e-02 6.59e+01 dihedral pdb=" C5' G C 34 " pdb=" C4' G C 34 " pdb=" C3' G C 34 " pdb=" O3' G C 34 " ideal model delta sinusoidal sigma weight residual 82.00 123.89 -41.89 1 8.00e+00 1.56e-02 3.83e+01 ... (remaining 4841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 1215 0.114 - 0.227: 85 0.227 - 0.341: 4 0.341 - 0.454: 3 0.454 - 0.568: 6 Chirality restraints: 1313 Sorted by residual: chirality pdb=" P A C 1 " pdb=" OP1 A C 1 " pdb=" OP2 A C 1 " pdb=" O5' A C 1 " both_signs ideal model delta sigma weight residual True 2.41 2.98 -0.57 2.00e-01 2.50e+01 8.06e+00 chirality pdb=" P C C 47 " pdb=" OP1 C C 47 " pdb=" OP2 C C 47 " pdb=" O5' C C 47 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.84e+00 chirality pdb=" P U C 16 " pdb=" OP1 U C 16 " pdb=" OP2 U C 16 " pdb=" O5' U C 16 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.64e+00 ... (remaining 1310 not shown) Planarity restraints: 1148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A C 21 " -0.037 2.00e-02 2.50e+03 2.20e-02 1.33e+01 pdb=" N9 A C 21 " 0.061 2.00e-02 2.50e+03 pdb=" C8 A C 21 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A C 21 " -0.005 2.00e-02 2.50e+03 pdb=" C5 A C 21 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A C 21 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A C 21 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A C 21 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A C 21 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A C 21 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A C 21 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C 12 " 0.037 2.00e-02 2.50e+03 1.98e-02 1.07e+01 pdb=" N9 A C 12 " -0.052 2.00e-02 2.50e+03 pdb=" C8 A C 12 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A C 12 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A C 12 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A C 12 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A C 12 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A C 12 " -0.000 2.00e-02 2.50e+03 pdb=" C2 A C 12 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A C 12 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A C 12 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 42 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.42e+00 pdb=" C THR A 42 " -0.053 2.00e-02 2.50e+03 pdb=" O THR A 42 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO A 43 " 0.018 2.00e-02 2.50e+03 ... (remaining 1145 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 1 2.19 - 2.87: 2730 2.87 - 3.54: 10057 3.54 - 4.22: 17336 4.22 - 4.90: 28650 Nonbonded interactions: 58774 Sorted by model distance: nonbonded pdb=" OD2 ASP A 279 " pdb=" C1' G C 34 " model vdw 1.512 3.470 nonbonded pdb=" OD2 ASP A 279 " pdb=" O4' G C 34 " model vdw 2.196 3.040 nonbonded pdb=" OG SER B 181 " pdb=" N GLU B 182 " model vdw 2.199 3.120 nonbonded pdb=" O MET A 175 " pdb=" OG SER A 178 " model vdw 2.218 3.040 nonbonded pdb=" OD1 ASN B 110 " pdb=" NE ARG B 166 " model vdw 2.232 3.120 ... (remaining 58769 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.870 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 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 : 0.010 0.110 7946 Z= 0.428 Angle : 1.009 12.077 11112 Z= 0.570 Chirality : 0.073 0.568 1313 Planarity : 0.008 0.075 1148 Dihedral : 16.975 148.211 3416 Min Nonbonded Distance : 1.512 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 6.62 % Allowed : 7.67 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.28), residues: 769 helix: -0.33 (0.28), residues: 325 sheet: -1.15 (0.61), residues: 70 loop : -2.04 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.003 ARG A 285 TYR 0.018 0.004 TYR B 354 PHE 0.028 0.003 PHE B 331 TRP 0.013 0.002 TRP A 240 HIS 0.008 0.002 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00951 / 0.43 ( 7938) covalent geometry : angle 1.00378 / 0.57 (11106) hydrogen bonds : bond 0.16748 / 11.48 ( 305) hydrogen bonds : angle 6.65423 / 4.84 ( 801) metal coordination : bond 0.02265 / 0.90 ( 8) metal coordination : angle 4.59186 / 2.74 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 51 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 71 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6854 (mp) REVERT: A 197 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8583 (tt) REVERT: A 368 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7145 (ptm160) REVERT: B 1 MET cc_start: 0.4226 (mtm) cc_final: 0.3501 (mtp) REVERT: B 97 HIS cc_start: 0.8290 (OUTLIER) cc_final: 0.7507 (p90) REVERT: B 123 GLU cc_start: 0.8388 (pm20) cc_final: 0.7945 (pt0) REVERT: B 228 THR cc_start: 0.7697 (OUTLIER) cc_final: 0.7371 (p) REVERT: B 249 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.6373 (mtt-85) REVERT: B 393 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.7009 (t80) REVERT: B 405 GLN cc_start: 0.7883 (tp40) cc_final: 0.7663 (tm-30) outliers start: 44 outliers final: 32 residues processed: 90 average time/residue: 0.0768 time to fit residues: 9.4346 Evaluate side-chains 79 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 40 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 99 PRO Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 393 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 GLN B 10 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.113287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.083718 restraints weight = 35184.749| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.54 r_work: 0.3047 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7946 Z= 0.118 Angle : 0.571 7.189 11112 Z= 0.292 Chirality : 0.038 0.198 1313 Planarity : 0.004 0.042 1148 Dihedral : 18.375 129.765 2031 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.16 % Allowed : 10.53 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -0.76 (0.30), residues: 769 helix: 0.66 (0.30), residues: 331 sheet: -0.70 (0.54), residues: 100 loop : -1.61 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 126 TYR 0.012 0.001 TYR B 354 PHE 0.013 0.001 PHE A 127 TRP 0.015 0.001 TRP A 240 HIS 0.004 0.001 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 ( 7938) covalent geometry : angle 0.56949 / 0.29 (11106) hydrogen bonds : bond 0.05195 / 3.42 ( 305) hydrogen bonds : angle 4.75221 / 3.51 ( 801) metal coordination : bond 0.00740 / 0.33 ( 8) metal coordination : angle 2.00939 / 1.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 49 time to evaluate : 0.168 Fit side-chains REVERT: B 1 MET cc_start: 0.5458 (mtm) cc_final: 0.4479 (mtp) REVERT: B 97 HIS cc_start: 0.8205 (OUTLIER) cc_final: 0.7386 (p90) REVERT: B 173 ASN cc_start: 0.8709 (m-40) cc_final: 0.8454 (m-40) REVERT: B 249 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.5568 (mmt-90) REVERT: B 393 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.7330 (t80) outliers start: 21 outliers final: 11 residues processed: 67 average time/residue: 0.0666 time to fit residues: 6.2490 Evaluate side-chains 53 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 393 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 13 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.111570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.082722 restraints weight = 35057.307| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.53 r_work: 0.2998 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7946 Z= 0.120 Angle : 0.538 6.380 11112 Z= 0.274 Chirality : 0.037 0.200 1313 Planarity : 0.004 0.032 1148 Dihedral : 18.218 104.305 1994 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.86 % Allowed : 11.43 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -0.55 (0.31), residues: 769 helix: 0.85 (0.31), residues: 335 sheet: -0.63 (0.53), residues: 102 loop : -1.55 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 126 TYR 0.010 0.001 TYR B 354 PHE 0.012 0.001 PHE A 127 TRP 0.011 0.001 TRP A 240 HIS 0.003 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 7938) covalent geometry : angle 0.53600 / 0.27 (11106) hydrogen bonds : bond 0.05207 / 3.51 ( 305) hydrogen bonds : angle 4.47526 / 3.32 ( 801) metal coordination : bond 0.00843 / 0.33 ( 8) metal coordination : angle 1.99242 / 1.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.252 Fit side-chains REVERT: B 1 MET cc_start: 0.5426 (mtm) cc_final: 0.4509 (mtp) REVERT: B 97 HIS cc_start: 0.8066 (OUTLIER) cc_final: 0.7318 (p90) REVERT: B 230 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8210 (mm-30) REVERT: B 249 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.5583 (mmt-90) REVERT: B 341 GLN cc_start: 0.7728 (pt0) cc_final: 0.7447 (tt0) REVERT: B 393 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.7171 (t80) outliers start: 19 outliers final: 12 residues processed: 61 average time/residue: 0.0714 time to fit residues: 6.2354 Evaluate side-chains 56 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 393 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 46 optimal weight: 0.3980 chunk 79 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 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 = 0.3665 r_free = 0.3665 target = 0.109756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.080773 restraints weight = 34590.723| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.45 r_work: 0.2963 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7946 Z= 0.171 Angle : 0.574 6.464 11112 Z= 0.294 Chirality : 0.039 0.211 1313 Planarity : 0.004 0.033 1148 Dihedral : 18.262 80.560 1991 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.46 % Allowed : 12.33 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -0.65 (0.31), residues: 769 helix: 0.75 (0.30), residues: 341 sheet: -0.62 (0.54), residues: 95 loop : -1.63 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 126 TYR 0.011 0.001 TYR B 354 PHE 0.014 0.002 PHE A 127 TRP 0.010 0.001 TRP A 240 HIS 0.004 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 7938) covalent geometry : angle 0.57135 / 0.29 (11106) hydrogen bonds : bond 0.06300 / 4.27 ( 305) hydrogen bonds : angle 4.59385 / 3.36 ( 801) metal coordination : bond 0.01387 / 0.50 ( 8) metal coordination : angle 2.51647 / 1.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 41 time to evaluate : 0.213 Fit side-chains REVERT: A 197 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8549 (tt) REVERT: B 1 MET cc_start: 0.5458 (mtm) cc_final: 0.4569 (mtp) REVERT: B 97 HIS cc_start: 0.8105 (OUTLIER) cc_final: 0.7367 (p90) REVERT: B 230 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8152 (mm-30) REVERT: B 249 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.5921 (mmt-90) REVERT: B 393 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.7207 (t80) outliers start: 23 outliers final: 15 residues processed: 63 average time/residue: 0.0753 time to fit residues: 6.5099 Evaluate side-chains 58 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 39 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 393 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.110148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.081178 restraints weight = 30504.221| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.27 r_work: 0.2990 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7946 Z= 0.155 Angle : 0.542 6.393 11112 Z= 0.279 Chirality : 0.038 0.215 1313 Planarity : 0.004 0.033 1148 Dihedral : 18.221 74.030 1991 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.76 % Allowed : 12.18 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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 (0.31), residues: 769 helix: 0.91 (0.31), residues: 335 sheet: -0.73 (0.50), residues: 107 loop : -1.64 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 126 TYR 0.010 0.001 TYR B 354 PHE 0.013 0.002 PHE A 127 TRP 0.012 0.001 TRP A 240 HIS 0.004 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 7938) covalent geometry : angle 0.53979 / 0.28 (11106) hydrogen bonds : bond 0.05863 / 3.97 ( 305) hydrogen bonds : angle 4.47248 / 3.27 ( 801) metal coordination : bond 0.01081 / 0.42 ( 8) metal coordination : angle 2.17452 / 1.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 42 time to evaluate : 0.255 Fit side-chains REVERT: A 197 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8541 (tt) REVERT: B 1 MET cc_start: 0.5419 (mtm) cc_final: 0.4543 (mtp) REVERT: B 97 HIS cc_start: 0.8067 (OUTLIER) cc_final: 0.7329 (p90) REVERT: B 230 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8147 (mm-30) REVERT: B 249 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.6188 (mmt-90) REVERT: B 393 TYR cc_start: 0.7864 (OUTLIER) cc_final: 0.7190 (t80) outliers start: 25 outliers final: 19 residues processed: 64 average time/residue: 0.0759 time to fit residues: 6.7989 Evaluate side-chains 62 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 39 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 393 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 25 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 72 optimal weight: 0.6980 chunk 44 optimal weight: 7.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.110645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.082508 restraints weight = 23723.254| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.85 r_work: 0.3028 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7946 Z= 0.135 Angle : 0.518 6.305 11112 Z= 0.265 Chirality : 0.037 0.223 1313 Planarity : 0.004 0.033 1148 Dihedral : 18.184 74.012 1991 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.76 % Allowed : 12.63 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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 (0.31), residues: 769 helix: 0.99 (0.31), residues: 335 sheet: -0.73 (0.49), residues: 112 loop : -1.57 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 349 TYR 0.009 0.001 TYR B 354 PHE 0.012 0.001 PHE A 127 TRP 0.012 0.001 TRP A 240 HIS 0.003 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 7938) covalent geometry : angle 0.51609 / 0.27 (11106) hydrogen bonds : bond 0.05498 / 3.73 ( 305) hydrogen bonds : angle 4.35142 / 3.18 ( 801) metal coordination : bond 0.00944 / 0.37 ( 8) metal coordination : angle 2.00145 / 1.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 43 time to evaluate : 0.228 Fit side-chains REVERT: A 197 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8513 (tt) REVERT: B 1 MET cc_start: 0.5422 (mtm) cc_final: 0.4580 (mtp) REVERT: B 97 HIS cc_start: 0.8036 (OUTLIER) cc_final: 0.7350 (p90) REVERT: B 230 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8140 (mm-30) REVERT: B 249 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.6223 (mmt-90) REVERT: B 341 GLN cc_start: 0.7718 (pt0) cc_final: 0.7413 (tt0) REVERT: B 393 TYR cc_start: 0.7852 (OUTLIER) cc_final: 0.7167 (t80) outliers start: 25 outliers final: 19 residues processed: 66 average time/residue: 0.0725 time to fit residues: 6.7722 Evaluate side-chains 63 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 40 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 393 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 6 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.108414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.079896 restraints weight = 31457.675| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.21 r_work: 0.2946 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7946 Z= 0.227 Angle : 0.608 6.494 11112 Z= 0.313 Chirality : 0.041 0.227 1313 Planarity : 0.004 0.035 1148 Dihedral : 18.253 74.115 1991 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.76 % Allowed : 12.93 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -0.79 (0.30), residues: 769 helix: 0.72 (0.30), residues: 335 sheet: -0.70 (0.52), residues: 97 loop : -1.76 (0.31), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 349 TYR 0.013 0.002 TYR B 354 PHE 0.017 0.002 PHE B 331 TRP 0.010 0.002 TRP A 240 HIS 0.005 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.23 ( 7938) covalent geometry : angle 0.60484 / 0.31 (11106) hydrogen bonds : bond 0.07146 / 4.87 ( 305) hydrogen bonds : angle 4.73483 / 3.44 ( 801) metal coordination : bond 0.01569 / 0.58 ( 8) metal coordination : angle 2.71858 / 1.64 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 38 time to evaluate : 0.171 Fit side-chains REVERT: B 1 MET cc_start: 0.5325 (mtm) cc_final: 0.4414 (mtp) REVERT: B 97 HIS cc_start: 0.8164 (OUTLIER) cc_final: 0.7405 (p90) REVERT: B 230 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8154 (mm-30) REVERT: B 249 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.5803 (mmt-90) REVERT: B 264 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7430 (mt) REVERT: B 393 TYR cc_start: 0.7912 (OUTLIER) cc_final: 0.7242 (t80) outliers start: 25 outliers final: 21 residues processed: 59 average time/residue: 0.0799 time to fit residues: 6.5932 Evaluate side-chains 61 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 36 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 393 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 58 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.110021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.082116 restraints weight = 21583.515| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.71 r_work: 0.3024 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7946 Z= 0.142 Angle : 0.528 6.308 11112 Z= 0.271 Chirality : 0.038 0.225 1313 Planarity : 0.004 0.034 1148 Dihedral : 18.198 74.052 1991 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.61 % Allowed : 13.38 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -0.61 (0.31), residues: 769 helix: 0.79 (0.30), residues: 342 sheet: -0.74 (0.51), residues: 102 loop : -1.58 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 349 TYR 0.010 0.001 TYR B 354 PHE 0.013 0.001 PHE A 127 TRP 0.013 0.001 TRP A 240 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 7938) covalent geometry : angle 0.52571 / 0.27 (11106) hydrogen bonds : bond 0.05789 / 3.93 ( 305) hydrogen bonds : angle 4.42893 / 3.23 ( 801) metal coordination : bond 0.00995 / 0.39 ( 8) metal coordination : angle 2.12548 / 1.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 40 time to evaluate : 0.178 Fit side-chains REVERT: B 1 MET cc_start: 0.5346 (mtm) cc_final: 0.4468 (mtp) REVERT: B 97 HIS cc_start: 0.8096 (OUTLIER) cc_final: 0.7366 (p90) REVERT: B 230 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8119 (mm-30) REVERT: B 249 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.6252 (mmt-90) REVERT: B 393 TYR cc_start: 0.7866 (OUTLIER) cc_final: 0.7165 (t80) outliers start: 24 outliers final: 20 residues processed: 61 average time/residue: 0.0746 time to fit residues: 6.4376 Evaluate side-chains 61 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 38 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 393 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 0.0010 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 0.0010 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 366 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.112903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.084909 restraints weight = 25104.241| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.95 r_work: 0.3075 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7946 Z= 0.092 Angle : 0.470 6.194 11112 Z= 0.239 Chirality : 0.036 0.241 1313 Planarity : 0.004 0.035 1148 Dihedral : 18.102 73.960 1991 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.41 % Allowed : 14.59 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -0.35 (0.31), residues: 769 helix: 1.03 (0.31), residues: 344 sheet: -0.82 (0.47), residues: 119 loop : -1.42 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 349 TYR 0.009 0.001 TYR B 354 PHE 0.012 0.001 PHE A 127 TRP 0.015 0.001 TRP A 240 HIS 0.003 0.000 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.09 ( 7938) covalent geometry : angle 0.46901 / 0.24 (11106) hydrogen bonds : bond 0.04363 / 2.98 ( 305) hydrogen bonds : angle 4.06488 / 2.98 ( 801) metal coordination : bond 0.00455 / 0.25 ( 8) metal coordination : angle 1.43607 / 0.86 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.214 Fit side-chains REVERT: B 1 MET cc_start: 0.5289 (mtm) cc_final: 0.4451 (mtp) REVERT: B 230 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8201 (mm-30) REVERT: B 249 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.6345 (mmt-90) REVERT: B 393 TYR cc_start: 0.7879 (OUTLIER) cc_final: 0.7184 (t80) outliers start: 16 outliers final: 13 residues processed: 55 average time/residue: 0.0732 time to fit residues: 5.8175 Evaluate side-chains 55 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 393 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.0870 chunk 30 optimal weight: 0.0670 chunk 17 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 40 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 overall best weight: 0.8298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.113036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.084241 restraints weight = 32491.513| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.42 r_work: 0.3049 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7946 Z= 0.092 Angle : 0.471 6.209 11112 Z= 0.239 Chirality : 0.035 0.241 1313 Planarity : 0.004 0.034 1148 Dihedral : 18.079 73.932 1988 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.11 % Allowed : 14.89 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -0.20 (0.31), residues: 769 helix: 1.21 (0.31), residues: 339 sheet: -0.78 (0.48), residues: 114 loop : -1.37 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 349 TYR 0.009 0.001 TYR B 354 PHE 0.010 0.001 PHE A 127 TRP 0.013 0.001 TRP A 240 HIS 0.002 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 ( 7938) covalent geometry : angle 0.46901 / 0.24 (11106) hydrogen bonds : bond 0.04417 / 3.04 ( 305) hydrogen bonds : angle 4.00789 / 2.93 ( 801) metal coordination : bond 0.00608 / 0.26 ( 8) metal coordination : angle 1.70212 / 1.02 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.185 Fit side-chains REVERT: A 197 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8473 (tt) REVERT: B 1 MET cc_start: 0.5308 (mtm) cc_final: 0.4477 (mtp) REVERT: B 230 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8228 (mm-30) REVERT: B 393 TYR cc_start: 0.7843 (OUTLIER) cc_final: 0.7097 (t80) outliers start: 14 outliers final: 12 residues processed: 52 average time/residue: 0.0737 time to fit residues: 5.5019 Evaluate side-chains 53 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 384 PHE Chi-restraints excluded: chain B residue 393 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 29 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 15 optimal weight: 0.3980 chunk 25 optimal weight: 0.4980 chunk 9 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.112068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.083471 restraints weight = 32382.292| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.42 r_work: 0.3024 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7946 Z= 0.109 Angle : 0.482 6.256 11112 Z= 0.245 Chirality : 0.036 0.241 1313 Planarity : 0.004 0.034 1148 Dihedral : 18.070 73.939 1984 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.11 % Allowed : 15.19 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -0.24 (0.31), residues: 769 helix: 1.09 (0.31), residues: 342 sheet: -0.69 (0.50), residues: 107 loop : -1.34 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 18 TYR 0.009 0.001 TYR B 354 PHE 0.011 0.001 PHE A 127 TRP 0.013 0.001 TRP A 240 HIS 0.003 0.001 HIS B 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 7938) covalent geometry : angle 0.48012 / 0.25 (11106) hydrogen bonds : bond 0.04884 / 3.36 ( 305) hydrogen bonds : angle 4.10197 / 2.99 ( 801) metal coordination : bond 0.00856 / 0.33 ( 8) metal coordination : angle 1.93929 / 1.19 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1602.24 seconds wall clock time: 28 minutes 2.82 seconds (1682.82 seconds total)