Starting phenix.real_space_refine on Sat Oct 11 11:04:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8omr_16976/10_2025/8omr_16976.cif Found real_map, /net/cci-nas-00/data/ceres_data/8omr_16976/10_2025/8omr_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_16976/10_2025/8omr_16976.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8omr_16976/10_2025/8omr_16976.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8omr_16976/10_2025/8omr_16976.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8omr_16976/10_2025/8omr_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-2.0-5842/lib/python3.9/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: 2.22, per 1000 atoms: 0.29 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: 0.79 Conformation dependent library (CDL) restraints added in 347.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.05 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: 1.22 Time building geometry restraints manager: 0.97 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: 4618 29.64 - 59.28: 208 59.28 - 88.93: 81 88.93 - 118.57: 0 118.57 - 148.21: 1 Dihedral angle restraints: 4908 sinusoidal: 2691 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 4905 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.500 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 : 17.486 148.211 3480 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 aren 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 covalent geometry : bond 0.00951 ( 7938) covalent geometry : angle 1.00378 (11106) hydrogen bonds : bond 0.16748 ( 305) hydrogen bonds : angle 6.65423 ( 801) metal coordination : bond 0.02265 ( 8) metal coordination : angle 4.59186 ( 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 : 0.181 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: 0.0965 time to fit residues: 11.5867 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 : 0.266 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3736 r_free = 0.3736 target = 0.113201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.083588 restraints weight = 35620.950| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.58 r_work: 0.3044 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 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 = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7946 Z= 0.117 Angle : 0.571 7.036 11112 Z= 0.292 Chirality : 0.038 0.198 1313 Planarity : 0.004 0.040 1148 Dihedral : 19.031 129.320 2095 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.01 % Allowed : 10.68 % 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 aren not related in a simple way. whole: -0.72 (0.30), residues: 769 helix: 0.75 (0.30), residues: 325 sheet: -0.72 (0.54), residues: 100 loop : -1.60 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 349 TYR 0.012 0.001 TYR B 354 PHE 0.012 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 covalent geometry : bond 0.00232 ( 7938) covalent geometry : angle 0.56866 (11106) hydrogen bonds : bond 0.05246 ( 305) hydrogen bonds : angle 4.75576 ( 801) metal coordination : bond 0.00721 ( 8) metal coordination : angle 2.06282 ( 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 69 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.228 Fit side-chains REVERT: B 1 MET cc_start: 0.5463 (mtm) cc_final: 0.4477 (mtp) REVERT: B 97 HIS cc_start: 0.8197 (OUTLIER) cc_final: 0.7381 (p90) REVERT: B 173 ASN cc_start: 0.8707 (m-40) cc_final: 0.8455 (m-40) REVERT: B 249 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.5493 (mmt-90) REVERT: B 393 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.7323 (t80) outliers start: 20 outliers final: 11 residues processed: 66 average time/residue: 0.0829 time to fit residues: 7.4604 Evaluate side-chains 55 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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: 7.9990 chunk 38 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.112062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.082823 restraints weight = 34848.886| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.52 r_work: 0.3014 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1863 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= 0.112 Angle : 0.533 6.365 11112 Z= 0.270 Chirality : 0.037 0.200 1313 Planarity : 0.004 0.032 1148 Dihedral : 18.893 103.739 2058 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.56 % Allowed : 11.58 % Favored : 85.86 % 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 aren not related in a simple way. whole: -0.50 (0.31), residues: 769 helix: 0.90 (0.31), residues: 335 sheet: -0.77 (0.50), residues: 112 loop : -1.48 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 126 TYR 0.009 0.001 TYR B 354 PHE 0.013 0.001 PHE A 127 TRP 0.011 0.001 TRP A 240 HIS 0.003 0.001 HIS B 365 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 7938) covalent geometry : angle 0.53159 (11106) hydrogen bonds : bond 0.05007 ( 305) hydrogen bonds : angle 4.44440 ( 801) metal coordination : bond 0.00726 ( 8) metal coordination : angle 1.84143 ( 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 61 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.263 Fit side-chains REVERT: B 1 MET cc_start: 0.5439 (mtm) cc_final: 0.4524 (mtp) REVERT: B 97 HIS cc_start: 0.8108 (OUTLIER) cc_final: 0.7360 (p90) REVERT: B 230 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8163 (mm-30) REVERT: B 249 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.5571 (mmt-90) REVERT: B 341 GLN cc_start: 0.7723 (pt0) cc_final: 0.7456 (tt0) REVERT: B 393 TYR cc_start: 0.7876 (OUTLIER) cc_final: 0.7160 (t80) outliers start: 17 outliers final: 11 residues processed: 59 average time/residue: 0.0871 time to fit residues: 7.2644 Evaluate side-chains 55 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.200 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 22 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 46 optimal weight: 0.3980 chunk 79 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.111702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.082716 restraints weight = 34637.902| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.58 r_work: 0.3000 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7946 Z= 0.120 Angle : 0.515 6.354 11112 Z= 0.262 Chirality : 0.037 0.207 1313 Planarity : 0.004 0.032 1148 Dihedral : 18.893 80.375 2055 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.46 % Allowed : 10.98 % Favored : 85.56 % 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 aren not related in a simple way. whole: -0.44 (0.31), residues: 769 helix: 0.93 (0.31), residues: 341 sheet: -0.72 (0.50), residues: 112 loop : -1.47 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 126 TYR 0.009 0.001 TYR B 354 PHE 0.012 0.001 PHE A 127 TRP 0.010 0.001 TRP A 240 HIS 0.003 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 7938) covalent geometry : angle 0.51279 (11106) hydrogen bonds : bond 0.05173 ( 305) hydrogen bonds : angle 4.30391 ( 801) metal coordination : bond 0.00946 ( 8) metal coordination : angle 1.96277 ( 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 66 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 43 time to evaluate : 0.275 Fit side-chains REVERT: A 197 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8537 (tt) REVERT: B 1 MET cc_start: 0.5391 (mtm) cc_final: 0.4497 (mtp) REVERT: B 97 HIS cc_start: 0.8038 (OUTLIER) cc_final: 0.7295 (p90) REVERT: B 230 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8161 (mm-30) REVERT: B 249 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.6504 (mmt-90) REVERT: B 393 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.7245 (t80) outliers start: 23 outliers final: 14 residues processed: 65 average time/residue: 0.0955 time to fit residues: 8.5551 Evaluate side-chains 61 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 69 optimal weight: 0.1980 chunk 29 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.111066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.082322 restraints weight = 28858.184| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.18 r_work: 0.3015 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7946 Z= 0.134 Angle : 0.519 6.361 11112 Z= 0.265 Chirality : 0.037 0.218 1313 Planarity : 0.004 0.032 1148 Dihedral : 18.891 74.021 2055 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.31 % Allowed : 12.33 % Favored : 84.36 % 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 aren not related in a simple way. whole: -0.47 (0.31), residues: 769 helix: 0.89 (0.31), residues: 341 sheet: -0.69 (0.50), residues: 112 loop : -1.48 (0.32), residues: 316 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 0.010 0.001 TRP A 240 HIS 0.003 0.001 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7938) covalent geometry : angle 0.51729 (11106) hydrogen bonds : bond 0.05381 ( 305) hydrogen bonds : angle 4.33960 ( 801) metal coordination : bond 0.01013 ( 8) metal coordination : angle 2.01269 ( 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 65 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 43 time to evaluate : 0.263 Fit side-chains REVERT: A 197 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8553 (tt) REVERT: B 1 MET cc_start: 0.5478 (mtm) cc_final: 0.4615 (mtp) REVERT: B 97 HIS cc_start: 0.8054 (OUTLIER) cc_final: 0.7336 (p90) REVERT: B 230 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8198 (mm-30) REVERT: B 249 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.6240 (mmt-90) REVERT: B 341 GLN cc_start: 0.7715 (pt0) cc_final: 0.7451 (tt0) REVERT: B 393 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.7241 (t80) outliers start: 22 outliers final: 16 residues processed: 63 average time/residue: 0.0835 time to fit residues: 7.2868 Evaluate side-chains 61 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 155 THR 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=3.00 ------------------------------------------------------------------------------- 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: 0.1980 chunk 77 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.109543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.081143 restraints weight = 25867.637| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.95 r_work: 0.2993 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7946 Z= 0.179 Angle : 0.563 6.434 11112 Z= 0.289 Chirality : 0.039 0.225 1313 Planarity : 0.004 0.033 1148 Dihedral : 18.968 74.101 2055 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.91 % Allowed : 11.88 % 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 aren not related in a simple way. whole: -0.62 (0.30), residues: 769 helix: 0.85 (0.30), residues: 335 sheet: -0.81 (0.50), residues: 107 loop : -1.60 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 126 TYR 0.011 0.001 TYR B 354 PHE 0.014 0.002 PHE A 127 TRP 0.009 0.001 TRP A 240 HIS 0.004 0.001 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 7938) covalent geometry : angle 0.56069 (11106) hydrogen bonds : bond 0.06340 ( 305) hydrogen bonds : angle 4.55801 ( 801) metal coordination : bond 0.01317 ( 8) metal coordination : angle 2.39469 ( 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 69 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 43 time to evaluate : 0.238 Fit side-chains REVERT: A 197 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8551 (tt) REVERT: B 1 MET cc_start: 0.5437 (mtm) cc_final: 0.4578 (mtp) REVERT: B 97 HIS cc_start: 0.8124 (OUTLIER) cc_final: 0.7364 (p90) REVERT: B 230 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8170 (mm-30) REVERT: B 249 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.6279 (mmt-90) REVERT: B 341 GLN cc_start: 0.7729 (pt0) cc_final: 0.7398 (tt0) REVERT: B 393 TYR cc_start: 0.7918 (OUTLIER) cc_final: 0.7249 (t80) outliers start: 26 outliers final: 20 residues processed: 67 average time/residue: 0.0925 time to fit residues: 8.5386 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 : 0.275 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 6 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 3 optimal weight: 0.3980 chunk 21 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.108322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.079419 restraints weight = 31552.789| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.29 r_work: 0.2949 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 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 = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 7946 Z= 0.218 Angle : 0.608 6.498 11112 Z= 0.314 Chirality : 0.041 0.226 1313 Planarity : 0.004 0.034 1148 Dihedral : 18.991 74.106 2055 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.61 % Allowed : 12.78 % 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 aren not related in a simple way. whole: -0.82 (0.30), residues: 769 helix: 0.67 (0.30), residues: 334 sheet: -0.60 (0.54), residues: 95 loop : -1.78 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 349 TYR 0.012 0.002 TYR B 354 PHE 0.016 0.002 PHE B 331 TRP 0.010 0.002 TRP A 240 HIS 0.005 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 7938) covalent geometry : angle 0.60508 (11106) hydrogen bonds : bond 0.07165 ( 305) hydrogen bonds : angle 4.77018 ( 801) metal coordination : bond 0.01426 ( 8) metal coordination : angle 2.61570 ( 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 64 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 40 time to evaluate : 0.265 Fit side-chains REVERT: B 1 MET cc_start: 0.5374 (mtm) cc_final: 0.4485 (mtp) REVERT: B 97 HIS cc_start: 0.8207 (OUTLIER) cc_final: 0.7501 (p90) REVERT: B 230 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8190 (mm-30) REVERT: B 249 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.5698 (mmt-90) REVERT: B 393 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7194 (t80) outliers start: 24 outliers final: 21 residues processed: 62 average time/residue: 0.0873 time to fit residues: 7.5304 Evaluate side-chains 62 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 38 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 57 ILE Chi-restraints excluded: chain A residue 71 LEU 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 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: 4.9990 chunk 22 optimal weight: 0.9980 chunk 83 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.110149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.082357 restraints weight = 21650.677| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.69 r_work: 0.3028 rms_B_bonded: 3.54 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 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7946 Z= 0.140 Angle : 0.524 6.299 11112 Z= 0.269 Chirality : 0.038 0.220 1313 Planarity : 0.004 0.034 1148 Dihedral : 18.936 74.071 2055 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.46 % Allowed : 13.68 % Favored : 82.86 % 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 aren not related in a simple way. whole: -0.59 (0.31), residues: 769 helix: 0.80 (0.30), residues: 341 sheet: -0.72 (0.50), residues: 112 loop : -1.57 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 covalent geometry : bond 0.00315 ( 7938) covalent geometry : angle 0.52252 (11106) hydrogen bonds : bond 0.05684 ( 305) hydrogen bonds : angle 4.43382 ( 801) metal coordination : bond 0.00923 ( 8) metal coordination : angle 1.98433 ( 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 63 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 40 time to evaluate : 0.297 Fit side-chains REVERT: A 197 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8560 (tt) REVERT: A 250 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8254 (mm) REVERT: B 1 MET cc_start: 0.5336 (mtm) cc_final: 0.4455 (mtp) REVERT: B 97 HIS cc_start: 0.8089 (OUTLIER) cc_final: 0.7398 (p90) REVERT: B 230 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8123 (mm-30) REVERT: B 249 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.6174 (mmt-90) REVERT: B 393 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.7151 (t80) outliers start: 23 outliers final: 16 residues processed: 61 average time/residue: 0.0894 time to fit residues: 7.6963 Evaluate side-chains 61 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 40 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 250 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 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: 1.9990 chunk 49 optimal weight: 20.0000 chunk 28 optimal weight: 0.0970 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 0.0980 chunk 37 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.112218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.084163 restraints weight = 25649.501| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.97 r_work: 0.3059 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 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 = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7946 Z= 0.100 Angle : 0.484 6.236 11112 Z= 0.246 Chirality : 0.036 0.244 1313 Planarity : 0.004 0.034 1148 Dihedral : 18.866 73.976 2055 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.86 % Allowed : 14.29 % Favored : 82.86 % 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 aren not related in a simple way. whole: -0.42 (0.31), residues: 769 helix: 0.93 (0.31), residues: 347 sheet: -0.66 (0.50), residues: 112 loop : -1.52 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 349 TYR 0.008 0.001 TYR B 354 PHE 0.011 0.001 PHE A 127 TRP 0.014 0.001 TRP A 240 HIS 0.002 0.001 HIS B 365 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 7938) covalent geometry : angle 0.48242 (11106) hydrogen bonds : bond 0.04649 ( 305) hydrogen bonds : angle 4.16113 ( 801) metal coordination : bond 0.00556 ( 8) metal coordination : angle 1.52259 ( 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 61 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.364 Fit side-chains REVERT: A 197 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8547 (tt) REVERT: A 250 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8092 (mm) REVERT: B 1 MET cc_start: 0.5373 (mtm) cc_final: 0.4511 (mtp) REVERT: B 97 HIS cc_start: 0.8028 (OUTLIER) cc_final: 0.7352 (p90) REVERT: B 230 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8142 (mm-30) REVERT: B 249 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.6390 (mmt-90) REVERT: B 393 TYR cc_start: 0.7832 (OUTLIER) cc_final: 0.7151 (t80) outliers start: 19 outliers final: 13 residues processed: 59 average time/residue: 0.0874 time to fit residues: 7.4223 Evaluate side-chains 59 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 250 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 97 HIS Chi-restraints excluded: chain B residue 155 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 73 optimal weight: 0.0870 overall best weight: 1.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.110970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.082060 restraints weight = 32713.051| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.39 r_work: 0.3007 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 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 = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7946 Z= 0.135 Angle : 0.516 6.301 11112 Z= 0.264 Chirality : 0.037 0.240 1313 Planarity : 0.004 0.034 1148 Dihedral : 18.878 73.982 2054 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.01 % Allowed : 14.29 % 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 aren not related in a simple way. whole: -0.37 (0.31), residues: 769 helix: 1.01 (0.31), residues: 341 sheet: -0.71 (0.51), residues: 107 loop : -1.45 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 349 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 A 344 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7938) covalent geometry : angle 0.51416 (11106) hydrogen bonds : bond 0.05439 ( 305) hydrogen bonds : angle 4.28041 ( 801) metal coordination : bond 0.01034 ( 8) metal coordination : angle 2.08906 ( 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 60 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 40 time to evaluate : 0.276 Fit side-chains REVERT: A 197 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8540 (tt) REVERT: A 250 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8228 (mm) REVERT: B 1 MET cc_start: 0.5320 (mtm) cc_final: 0.4452 (mtp) REVERT: B 97 HIS cc_start: 0.8042 (OUTLIER) cc_final: 0.7327 (p90) REVERT: B 230 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8184 (mm-30) REVERT: B 249 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.6215 (mmt-90) REVERT: B 393 TYR cc_start: 0.7823 (OUTLIER) cc_final: 0.7143 (t80) outliers start: 20 outliers final: 14 residues processed: 58 average time/residue: 0.0788 time to fit residues: 6.5059 Evaluate side-chains 59 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 250 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 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 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: 0.2980 chunk 66 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 15 optimal weight: 0.0970 chunk 25 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 49 optimal weight: 0.0270 chunk 45 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.114689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.086105 restraints weight = 32664.157| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.42 r_work: 0.3091 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7946 Z= 0.085 Angle : 0.457 6.124 11112 Z= 0.232 Chirality : 0.035 0.240 1313 Planarity : 0.004 0.033 1148 Dihedral : 18.820 73.958 2054 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.95 % Allowed : 15.64 % Favored : 82.41 % 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 aren not related in a simple way. whole: -0.21 (0.31), residues: 769 helix: 1.12 (0.30), residues: 344 sheet: -0.65 (0.50), residues: 108 loop : -1.35 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 349 TYR 0.006 0.001 TYR B 354 PHE 0.012 0.001 PHE A 127 TRP 0.016 0.001 TRP A 240 HIS 0.003 0.000 HIS B 365 Details of bonding type rmsd covalent geometry : bond 0.00172 ( 7938) covalent geometry : angle 0.45686 (11106) hydrogen bonds : bond 0.03934 ( 305) hydrogen bonds : angle 3.93815 ( 801) metal coordination : bond 0.00314 ( 8) metal coordination : angle 1.00304 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2000.38 seconds wall clock time: 34 minutes 51.98 seconds (2091.98 seconds total)