Starting phenix.real_space_refine on Fri Jul 3 09:01:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z8n_39849/07_2026/8z8n_39849.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z8n_39849/07_2026/8z8n_39849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z8n_39849/07_2026/8z8n_39849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z8n_39849/07_2026/8z8n_39849.map" model { file = "/net/cci-nas-00/data/ceres_data/8z8n_39849/07_2026/8z8n_39849.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z8n_39849/07_2026/8z8n_39849.cif" } resolution = 2.79 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= 0.004 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 1345 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: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 75 5.16 5 C 7868 2.51 5 N 2174 2.21 5 O 2354 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 12485 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 5020 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 31, 'TRANS': 589} Chain: "B" Number of atoms: 5254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5254 Classifications: {'peptide': 656} Link IDs: {'PTRANS': 33, 'TRANS': 622} Chain breaks: 3 Chain: "C" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1891 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 16, 'TRANS': 216} Chain breaks: 2 Chain: "D" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 237 Classifications: {'RNA': 11} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 7} Chain: "E" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pyr': 1} Link IDs: {'rna2p': 2, 'rna3p': 1} Time building chain proxies: 2.39, per 1000 atoms: 0.19 Number of scatterers: 12485 At special positions: 0 Unit cell: (90.7446, 103.323, 137.465, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 P 14 15.00 O 2354 8.00 N 2174 7.00 C 7868 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: 1.00 Conformation dependent library (CDL) restraints added in 625.9 milliseconds 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2882 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 14 sheets defined 49.5% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 removed outlier: 4.411A pdb=" N THR A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 46 Processing helix chain 'A' and resid 64 through 75 removed outlier: 3.669A pdb=" N ILE A 68 " --> pdb=" O ASP A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 134 through 155 removed outlier: 3.639A pdb=" N ASN A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 167 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 273 through 286 removed outlier: 3.569A pdb=" N LEU A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 302 removed outlier: 4.416A pdb=" N ILE A 299 " --> pdb=" O HIS A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 335 through 345 removed outlier: 4.032A pdb=" N GLU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG A 345 " --> pdb=" O MET A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 4.437A pdb=" N ARG A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.739A pdb=" N GLN A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 492 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 498 through 516 Processing helix chain 'A' and resid 540 through 557 Processing helix chain 'A' and resid 559 through 581 removed outlier: 4.505A pdb=" N ARG A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 599 removed outlier: 3.883A pdb=" N LYS A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 597 " --> pdb=" O PRO A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 616 Processing helix chain 'B' and resid 1 through 5 removed outlier: 3.544A pdb=" N THR B 5 " --> pdb=" O ASN B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 20 removed outlier: 3.548A pdb=" N TYR B 20 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 47 Proline residue: B 44 - end of helix Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 80 through 94 Processing helix chain 'B' and resid 95 through 108 removed outlier: 3.582A pdb=" N LEU B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 120 removed outlier: 3.821A pdb=" N GLU B 117 " --> pdb=" O LYS B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 Processing helix chain 'B' and resid 157 through 169 removed outlier: 3.711A pdb=" N MET B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 247 through 266 removed outlier: 4.421A pdb=" N GLY B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N PHE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 285 removed outlier: 4.239A pdb=" N ALA B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 removed outlier: 3.773A pdb=" N LEU B 309 " --> pdb=" O PHE B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 325 removed outlier: 3.828A pdb=" N MET B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 344 Proline residue: B 338 - end of helix removed outlier: 3.535A pdb=" N SER B 344 " --> pdb=" O MET B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 378 removed outlier: 3.546A pdb=" N VAL B 377 " --> pdb=" O ASP B 374 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG B 378 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 407 removed outlier: 4.073A pdb=" N SER B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 449 removed outlier: 3.604A pdb=" N LYS B 448 " --> pdb=" O ARG B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 514 removed outlier: 3.515A pdb=" N ALA B 502 " --> pdb=" O MET B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 537 Processing helix chain 'B' and resid 543 through 552 Processing helix chain 'B' and resid 575 through 583 Processing helix chain 'B' and resid 588 through 595 removed outlier: 3.502A pdb=" N ARG B 593 " --> pdb=" O GLU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 647 No H-bonds generated for 'chain 'B' and resid 645 through 647' Processing helix chain 'B' and resid 648 through 666 Processing helix chain 'B' and resid 679 through 694 Processing helix chain 'B' and resid 698 through 708 removed outlier: 3.933A pdb=" N ARG B 708 " --> pdb=" O ARG B 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 27 Processing helix chain 'C' and resid 27 through 32 removed outlier: 3.618A pdb=" N SER C 32 " --> pdb=" O PRO C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 36 removed outlier: 6.265A pdb=" N THR C 36 " --> pdb=" O LYS C 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 33 through 36' Processing helix chain 'C' and resid 37 through 42 Processing helix chain 'C' and resid 52 through 55 Processing helix chain 'C' and resid 56 through 62 removed outlier: 3.741A pdb=" N ARG C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 115 through 122 Processing helix chain 'C' and resid 124 through 134 Processing helix chain 'C' and resid 163 through 165 No H-bonds generated for 'chain 'C' and resid 163 through 165' Processing helix chain 'C' and resid 166 through 176 Processing helix chain 'C' and resid 181 through 187 Processing helix chain 'C' and resid 191 through 207 Proline residue: C 202 - end of helix removed outlier: 3.849A pdb=" N LYS C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 206 " --> pdb=" O PRO C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 234 through 240 removed outlier: 3.985A pdb=" N MET C 240 " --> pdb=" O ARG C 236 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 59 removed outlier: 6.321A pdb=" N ALA A 95 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU A 117 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYS A 97 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 211 Processing sheet with id=AA4, first strand: chain 'A' and resid 210 through 211 removed outlier: 4.375A pdb=" N ASN B 453 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 237 through 238 removed outlier: 4.557A pdb=" N ILE A 450 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 430 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N TRP A 426 " --> pdb=" O ILE A 450 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 423 through 431 current: chain 'A' and resid 464 through 468 removed outlier: 6.535A pdb=" N VAL A 464 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 240 through 242 removed outlier: 7.712A pdb=" N TRP A 426 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 430 " --> pdb=" O LEU A 446 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 442 through 451 current: chain 'A' and resid 290 through 291 Processing sheet with id=AA7, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA8, first strand: chain 'A' and resid 526 through 531 Processing sheet with id=AA9, first strand: chain 'B' and resid 124 through 126 removed outlier: 3.640A pdb=" N ARG B 131 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 173 through 175 Processing sheet with id=AB2, first strand: chain 'B' and resid 242 through 245 removed outlier: 3.506A pdb=" N ASN B 227 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU B 226 " --> pdb=" O ASP B 348 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 467 through 470 Processing sheet with id=AB4, first strand: chain 'C' and resid 142 through 143 Processing sheet with id=AB5, first strand: chain 'C' and resid 151 through 154 537 hydrogen bonds defined for protein. 1509 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.05 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3906 1.34 - 1.45: 1765 1.45 - 1.57: 6971 1.57 - 1.69: 27 1.69 - 1.81: 122 Bond restraints: 12791 Sorted by residual: bond pdb=" CB PRO C 53 " pdb=" CG PRO C 53 " ideal model delta sigma weight residual 1.492 1.552 -0.060 5.00e-02 4.00e+02 1.44e+00 bond pdb=" CG GLU A 150 " pdb=" CD GLU A 150 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.18e+00 bond pdb=" C SER B 463 " pdb=" N PRO B 464 " ideal model delta sigma weight residual 1.334 1.358 -0.025 2.34e-02 1.83e+03 1.10e+00 bond pdb=" CB PRO A 525 " pdb=" CG PRO A 525 " ideal model delta sigma weight residual 1.492 1.545 -0.053 5.00e-02 4.00e+02 1.10e+00 bond pdb=" C VAL B 273 " pdb=" N PRO B 274 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.09e+00 ... (remaining 12786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 17090 1.83 - 3.67: 259 3.67 - 5.50: 29 5.50 - 7.33: 5 7.33 - 9.17: 2 Bond angle restraints: 17385 Sorted by residual: angle pdb=" N GLU A 150 " pdb=" CA GLU A 150 " pdb=" CB GLU A 150 " ideal model delta sigma weight residual 110.39 117.27 -6.88 1.66e+00 3.63e-01 1.72e+01 angle pdb=" C LEU A 149 " pdb=" N GLU A 150 " pdb=" CA GLU A 150 " ideal model delta sigma weight residual 120.72 114.70 6.02 1.67e+00 3.59e-01 1.30e+01 angle pdb=" CA GLU A 150 " pdb=" CB GLU A 150 " pdb=" CG GLU A 150 " ideal model delta sigma weight residual 114.10 119.46 -5.36 2.00e+00 2.50e-01 7.19e+00 angle pdb=" C ASN A 155 " pdb=" N ASN A 156 " pdb=" CA ASN A 156 " ideal model delta sigma weight residual 122.82 126.58 -3.76 1.42e+00 4.96e-01 7.03e+00 angle pdb=" C SER B 8 " pdb=" N GLU B 9 " pdb=" CA GLU B 9 " ideal model delta sigma weight residual 121.54 126.57 -5.03 1.91e+00 2.74e-01 6.94e+00 ... (remaining 17380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 7129 17.12 - 34.24: 552 34.24 - 51.36: 87 51.36 - 68.49: 24 68.49 - 85.61: 13 Dihedral angle restraints: 7805 sinusoidal: 3370 harmonic: 4435 Sorted by residual: dihedral pdb=" CA GLU A 81 " pdb=" C GLU A 81 " pdb=" N ARG A 82 " pdb=" CA ARG A 82 " ideal model delta harmonic sigma weight residual -180.00 -162.06 -17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA LEU A 157 " pdb=" C LEU A 157 " pdb=" N THR A 158 " pdb=" CA THR A 158 " ideal model delta harmonic sigma weight residual 180.00 -162.08 -17.92 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CB GLU C 26 " pdb=" CG GLU C 26 " pdb=" CD GLU C 26 " pdb=" OE1 GLU C 26 " ideal model delta sinusoidal sigma weight residual 0.00 85.61 -85.61 1 3.00e+01 1.11e-03 9.85e+00 ... (remaining 7802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1266 0.032 - 0.064: 475 0.064 - 0.096: 133 0.096 - 0.128: 65 0.128 - 0.160: 8 Chirality restraints: 1947 Sorted by residual: chirality pdb=" CA ASN A 156 " pdb=" N ASN A 156 " pdb=" C ASN A 156 " pdb=" CB ASN A 156 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.40e-01 chirality pdb=" CB ILE B 10 " pdb=" CA ILE B 10 " pdb=" CG1 ILE B 10 " pdb=" CG2 ILE B 10 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA GLU A 150 " pdb=" N GLU A 150 " pdb=" C GLU A 150 " pdb=" CB GLU A 150 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.11e-01 ... (remaining 1944 not shown) Planarity restraints: 2169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 52 " 0.064 5.00e-02 4.00e+02 9.59e-02 1.47e+01 pdb=" N PRO C 53 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO C 53 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 53 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 288 " 0.052 5.00e-02 4.00e+02 7.78e-02 9.70e+00 pdb=" N PRO A 289 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 289 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 289 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 96 " -0.033 5.00e-02 4.00e+02 5.06e-02 4.09e+00 pdb=" N PRO B 97 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 97 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 97 " -0.028 5.00e-02 4.00e+02 ... (remaining 2166 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 238 2.67 - 3.23: 12118 3.23 - 3.79: 19892 3.79 - 4.34: 27804 4.34 - 4.90: 45217 Nonbonded interactions: 105269 Sorted by model distance: nonbonded pdb=" OE1 GLU B 141 " pdb=" OH TYR B 176 " model vdw 2.114 3.040 nonbonded pdb=" OG1 THR B 679 " pdb=" OE1 GLU B 682 " model vdw 2.119 3.040 nonbonded pdb=" OG SER A 400 " pdb=" OE1 GLN A 401 " model vdw 2.151 3.040 nonbonded pdb=" OD2 ASP B 500 " pdb=" OH TYR B 537 " model vdw 2.151 3.040 nonbonded pdb=" OD2 ASP A 21 " pdb=" OG1 THR A 24 " model vdw 2.182 3.040 ... (remaining 105264 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.670 Find NCS groups from input model: 0.080 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:7.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12791 Z= 0.115 Angle : 0.559 9.167 17385 Z= 0.291 Chirality : 0.040 0.160 1947 Planarity : 0.006 0.096 2169 Dihedral : 12.853 85.607 4923 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.21), residues: 1494 helix: 0.75 (0.20), residues: 684 sheet: -0.63 (0.45), residues: 119 loop : -1.21 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 198 TYR 0.015 0.001 TYR B 176 PHE 0.023 0.001 PHE A 483 TRP 0.021 0.001 TRP A 62 HIS 0.006 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (12791) covalent geometry : angle 0.55928 / 0.29 (17385) hydrogen bonds : bond 0.17467 / 12.33 ( 525) hydrogen bonds : angle 6.07634 / 4.39 ( 1509) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ILE cc_start: 0.7762 (mp) cc_final: 0.7151 (mp) REVERT: A 142 LYS cc_start: 0.7635 (ttmm) cc_final: 0.7272 (ttmm) REVERT: B 592 ARG cc_start: 0.8394 (mtt180) cc_final: 0.8181 (mmm-85) REVERT: B 656 GLN cc_start: 0.7387 (tp-100) cc_final: 0.7104 (tp-100) REVERT: C 161 GLU cc_start: 0.7366 (mp0) cc_final: 0.6986 (mp0) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.6208 time to fit residues: 175.3977 Evaluate side-chains 177 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 40.0000 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN A 486 ASN B 302 GLN B 471 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.151153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.119289 restraints weight = 17513.491| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.07 r_work: 0.3421 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12791 Z= 0.163 Angle : 0.631 7.561 17385 Z= 0.325 Chirality : 0.043 0.160 1947 Planarity : 0.006 0.065 2169 Dihedral : 8.507 76.846 1860 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.70 % Allowed : 10.56 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.21), residues: 1494 helix: 0.81 (0.20), residues: 698 sheet: -0.75 (0.44), residues: 128 loop : -1.23 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 92 TYR 0.022 0.002 TYR B 533 PHE 0.021 0.002 PHE A 483 TRP 0.015 0.001 TRP A 426 HIS 0.008 0.001 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (12791) covalent geometry : angle 0.63055 / 0.32 (17385) hydrogen bonds : bond 0.04730 / 3.29 ( 525) hydrogen bonds : angle 4.76491 / 3.43 ( 1509) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7906 (pm20) REVERT: B 592 ARG cc_start: 0.8879 (mtt180) cc_final: 0.8672 (mmm-85) REVERT: C 136 THR cc_start: 0.8106 (p) cc_final: 0.7887 (p) REVERT: C 142 ARG cc_start: 0.7988 (ppt170) cc_final: 0.7745 (ppt170) REVERT: C 161 GLU cc_start: 0.7856 (mp0) cc_final: 0.7426 (mp0) outliers start: 23 outliers final: 8 residues processed: 200 average time/residue: 0.6109 time to fit residues: 131.4992 Evaluate side-chains 181 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 172 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 550 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 55 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN B 429 ASN B 476 HIS B 567 HIS B 656 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.141668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.106073 restraints weight = 17030.509| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.10 r_work: 0.3183 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 12791 Z= 0.346 Angle : 0.749 8.423 17385 Z= 0.391 Chirality : 0.050 0.186 1947 Planarity : 0.007 0.062 2169 Dihedral : 8.895 74.227 1860 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.47 % Allowed : 12.19 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.20), residues: 1494 helix: 0.28 (0.19), residues: 705 sheet: -1.08 (0.47), residues: 112 loop : -1.32 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 438 TYR 0.027 0.003 TYR B 537 PHE 0.027 0.003 PHE A 483 TRP 0.018 0.003 TRP A 336 HIS 0.008 0.002 HIS A 462 Details of bonding type rmsd/Z covalent geometry : bond 0.00814 / 0.35 (12791) covalent geometry : angle 0.74890 / 0.39 (17385) hydrogen bonds : bond 0.05392 / 3.78 ( 525) hydrogen bonds : angle 4.75712 / 3.41 ( 1509) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 186 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7056 (mm-30) REVERT: A 150 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7560 (pm20) REVERT: A 401 GLN cc_start: 0.8594 (mp10) cc_final: 0.8326 (mp10) REVERT: B 109 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8687 (mmtm) REVERT: B 332 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8333 (mtt) REVERT: B 378 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7571 (ptt-90) REVERT: B 395 MET cc_start: 0.8762 (mtp) cc_final: 0.8538 (mtp) REVERT: B 549 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.6968 (mpt) REVERT: B 592 ARG cc_start: 0.8968 (mtt180) cc_final: 0.8638 (mmm-85) REVERT: C 120 ASN cc_start: 0.8385 (m-40) cc_final: 0.7920 (m110) REVERT: C 161 GLU cc_start: 0.8002 (mp0) cc_final: 0.7647 (mp0) REVERT: C 185 LYS cc_start: 0.7687 (tptt) cc_final: 0.7370 (tptt) outliers start: 47 outliers final: 14 residues processed: 217 average time/residue: 0.6497 time to fit residues: 151.2690 Evaluate side-chains 186 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 378 ARG Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 41 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 145 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 127 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 87 optimal weight: 0.4980 chunk 112 optimal weight: 0.7980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 429 ASN B 531 HIS B 656 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.145207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.111473 restraints weight = 16840.650| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.03 r_work: 0.3261 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12791 Z= 0.132 Angle : 0.595 7.841 17385 Z= 0.304 Chirality : 0.042 0.152 1947 Planarity : 0.005 0.056 2169 Dihedral : 8.731 75.822 1860 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.58 % Allowed : 14.62 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.21), residues: 1494 helix: 0.64 (0.20), residues: 710 sheet: -0.95 (0.43), residues: 128 loop : -1.20 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 582 TYR 0.019 0.002 TYR B 533 PHE 0.021 0.001 PHE C 41 TRP 0.014 0.001 TRP A 336 HIS 0.008 0.001 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (12791) covalent geometry : angle 0.59464 / 0.30 (17385) hydrogen bonds : bond 0.03964 / 2.73 ( 525) hydrogen bonds : angle 4.44514 / 3.17 ( 1509) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8601 (ttp-170) cc_final: 0.8333 (ttm110) REVERT: A 124 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7066 (mm-30) REVERT: A 150 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7531 (pm20) REVERT: A 401 GLN cc_start: 0.8490 (mp10) cc_final: 0.8281 (mp10) REVERT: A 470 GLU cc_start: 0.7221 (mp0) cc_final: 0.6955 (mp0) REVERT: A 507 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8899 (mt0) REVERT: B 23 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8360 (m) REVERT: B 104 TYR cc_start: 0.8686 (t80) cc_final: 0.8442 (t80) REVERT: B 109 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8639 (mmtm) REVERT: B 229 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.7898 (pmm) REVERT: B 395 MET cc_start: 0.8706 (mtp) cc_final: 0.8480 (mtp) REVERT: B 592 ARG cc_start: 0.8906 (mtt180) cc_final: 0.8649 (mmm-85) REVERT: B 686 ARG cc_start: 0.7933 (mtp85) cc_final: 0.7666 (mmm-85) REVERT: C 142 ARG cc_start: 0.8159 (ppt170) cc_final: 0.7894 (ppt90) REVERT: C 161 GLU cc_start: 0.7927 (mp0) cc_final: 0.7546 (mp0) outliers start: 35 outliers final: 10 residues processed: 213 average time/residue: 0.6042 time to fit residues: 138.3395 Evaluate side-chains 186 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain C residue 10 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 148 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN A 304 ASN B 429 ASN B 531 HIS B 656 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.142936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.107875 restraints weight = 16945.841| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.09 r_work: 0.3214 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12791 Z= 0.221 Angle : 0.636 10.789 17385 Z= 0.324 Chirality : 0.044 0.166 1947 Planarity : 0.005 0.055 2169 Dihedral : 8.712 75.817 1860 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.91 % Allowed : 15.44 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.21), residues: 1494 helix: 0.64 (0.20), residues: 713 sheet: -0.88 (0.45), residues: 118 loop : -1.28 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 208 TYR 0.022 0.002 TYR B 533 PHE 0.017 0.002 PHE C 41 TRP 0.014 0.002 TRP A 336 HIS 0.007 0.001 HIS A 573 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.22 (12791) covalent geometry : angle 0.63601 / 0.32 (17385) hydrogen bonds : bond 0.04236 / 2.94 ( 525) hydrogen bonds : angle 4.43469 / 3.17 ( 1509) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 172 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 68 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7929 (mp) REVERT: A 69 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6409 (mp0) REVERT: A 92 ARG cc_start: 0.8602 (ttp-170) cc_final: 0.8352 (ttm110) REVERT: A 124 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7132 (mm-30) REVERT: A 150 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7469 (pm20) REVERT: A 401 GLN cc_start: 0.8574 (mp10) cc_final: 0.8276 (mp10) REVERT: B 109 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8661 (mmtm) REVERT: B 151 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7426 (mmt90) REVERT: B 229 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.7970 (pmm) REVERT: B 395 MET cc_start: 0.8721 (mtp) cc_final: 0.8468 (mtp) REVERT: B 423 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7901 (t70) REVERT: B 592 ARG cc_start: 0.8920 (mtt180) cc_final: 0.8613 (mmm-85) REVERT: B 686 ARG cc_start: 0.7883 (mtp85) cc_final: 0.7636 (mmm-85) REVERT: C 120 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.7807 (m110) REVERT: C 142 ARG cc_start: 0.8193 (ppt170) cc_final: 0.7784 (ppt90) REVERT: C 161 GLU cc_start: 0.7947 (mp0) cc_final: 0.7600 (mp0) outliers start: 53 outliers final: 18 residues processed: 205 average time/residue: 0.6119 time to fit residues: 134.9990 Evaluate side-chains 193 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 621 MET Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 93 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN B 429 ASN B 531 HIS B 656 GLN C 249 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.143897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.108831 restraints weight = 16904.067| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.09 r_work: 0.3222 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12791 Z= 0.172 Angle : 0.617 11.685 17385 Z= 0.313 Chirality : 0.042 0.224 1947 Planarity : 0.005 0.053 2169 Dihedral : 8.684 76.121 1860 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.40 % Allowed : 16.99 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.21), residues: 1494 helix: 0.74 (0.20), residues: 707 sheet: -0.90 (0.43), residues: 128 loop : -1.23 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 208 TYR 0.024 0.002 TYR C 20 PHE 0.020 0.002 PHE C 41 TRP 0.014 0.001 TRP A 336 HIS 0.007 0.001 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (12791) covalent geometry : angle 0.61707 / 0.31 (17385) hydrogen bonds : bond 0.03964 / 2.74 ( 525) hydrogen bonds : angle 4.37951 / 3.12 ( 1509) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 175 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7735 (tpp-160) cc_final: 0.6987 (tpp-160) REVERT: A 68 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7879 (mp) REVERT: A 69 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6206 (mp0) REVERT: A 92 ARG cc_start: 0.8594 (ttp-170) cc_final: 0.8321 (ttm110) REVERT: A 124 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7152 (mm-30) REVERT: A 150 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7497 (pm20) REVERT: A 397 ARG cc_start: 0.8361 (tpp80) cc_final: 0.7892 (mmt180) REVERT: A 401 GLN cc_start: 0.8532 (mp10) cc_final: 0.8239 (mp10) REVERT: B 109 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8608 (mmtm) REVERT: B 229 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.7995 (pmm) REVERT: B 395 MET cc_start: 0.8723 (mtp) cc_final: 0.8474 (mtp) REVERT: B 423 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7889 (t70) REVERT: B 592 ARG cc_start: 0.8894 (mtt180) cc_final: 0.8588 (mmm-85) REVERT: C 120 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.7919 (m110) REVERT: C 161 GLU cc_start: 0.7916 (mp0) cc_final: 0.7534 (mp0) outliers start: 46 outliers final: 18 residues processed: 205 average time/residue: 0.5998 time to fit residues: 132.3922 Evaluate side-chains 191 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 71 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN B 429 ASN B 531 HIS B 656 GLN C 233 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.143065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.108891 restraints weight = 16863.756| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.04 r_work: 0.3217 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12791 Z= 0.194 Angle : 0.632 12.517 17385 Z= 0.319 Chirality : 0.043 0.196 1947 Planarity : 0.005 0.054 2169 Dihedral : 8.685 76.072 1860 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.25 % Allowed : 17.21 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.21), residues: 1494 helix: 0.75 (0.20), residues: 707 sheet: -0.91 (0.43), residues: 128 loop : -1.21 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 438 TYR 0.025 0.002 TYR C 20 PHE 0.019 0.002 PHE C 41 TRP 0.014 0.001 TRP A 336 HIS 0.006 0.001 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.19 (12791) covalent geometry : angle 0.63182 / 0.32 (17385) hydrogen bonds : bond 0.04010 / 2.78 ( 525) hydrogen bonds : angle 4.35666 / 3.10 ( 1509) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 49 HIS cc_start: 0.7904 (OUTLIER) cc_final: 0.7557 (t-90) REVERT: A 65 ARG cc_start: 0.7693 (tpp-160) cc_final: 0.6945 (tpp-160) REVERT: A 68 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7824 (mp) REVERT: A 69 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6399 (mp0) REVERT: A 92 ARG cc_start: 0.8594 (ttp-170) cc_final: 0.8312 (ttm110) REVERT: A 124 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7161 (mm-30) REVERT: A 150 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7515 (pm20) REVERT: A 397 ARG cc_start: 0.8375 (tpp80) cc_final: 0.7872 (mmt180) REVERT: A 401 GLN cc_start: 0.8578 (mp10) cc_final: 0.8260 (mp10) REVERT: B 11 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8430 (m110) REVERT: B 109 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8616 (mmtm) REVERT: B 229 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.7991 (pmm) REVERT: B 395 MET cc_start: 0.8707 (mtp) cc_final: 0.8459 (mtp) REVERT: B 423 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7895 (t70) REVERT: B 592 ARG cc_start: 0.8865 (mtt180) cc_final: 0.8651 (mmm-85) REVERT: C 120 ASN cc_start: 0.8400 (m-40) cc_final: 0.7877 (m110) REVERT: C 161 GLU cc_start: 0.7940 (mp0) cc_final: 0.7618 (mp0) outliers start: 44 outliers final: 19 residues processed: 201 average time/residue: 0.6119 time to fit residues: 132.4122 Evaluate side-chains 190 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 77 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN B 429 ASN B 531 HIS C 209 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.145005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.110276 restraints weight = 16739.370| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.08 r_work: 0.3249 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12791 Z= 0.143 Angle : 0.615 13.425 17385 Z= 0.310 Chirality : 0.042 0.170 1947 Planarity : 0.005 0.059 2169 Dihedral : 8.652 76.500 1860 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.88 % Allowed : 18.17 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.21), residues: 1494 helix: 0.84 (0.20), residues: 700 sheet: -0.86 (0.43), residues: 128 loop : -1.19 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 208 TYR 0.026 0.002 TYR C 20 PHE 0.022 0.001 PHE C 41 TRP 0.014 0.001 TRP A 336 HIS 0.006 0.001 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (12791) covalent geometry : angle 0.61514 / 0.31 (17385) hydrogen bonds : bond 0.03764 / 2.61 ( 525) hydrogen bonds : angle 4.34299 / 3.09 ( 1509) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.7935 (OUTLIER) cc_final: 0.7567 (t-90) REVERT: A 65 ARG cc_start: 0.7703 (tpp-160) cc_final: 0.7033 (tpp-160) REVERT: A 68 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7785 (mp) REVERT: A 69 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6520 (mp0) REVERT: A 92 ARG cc_start: 0.8565 (ttp-170) cc_final: 0.8282 (ttm110) REVERT: A 124 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7148 (mm-30) REVERT: A 150 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7513 (pm20) REVERT: A 163 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8104 (pp20) REVERT: A 397 ARG cc_start: 0.8341 (tpp80) cc_final: 0.7833 (mmt180) REVERT: A 401 GLN cc_start: 0.8482 (mp10) cc_final: 0.8191 (mp10) REVERT: B 109 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8598 (mmtm) REVERT: B 229 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.7936 (pmm) REVERT: B 395 MET cc_start: 0.8701 (mtp) cc_final: 0.8451 (mtp) REVERT: B 423 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7893 (t70) REVERT: B 592 ARG cc_start: 0.8865 (mtt180) cc_final: 0.8648 (mmm-85) REVERT: C 120 ASN cc_start: 0.8415 (m-40) cc_final: 0.7985 (m110) REVERT: C 161 GLU cc_start: 0.7924 (mp0) cc_final: 0.7595 (mp0) REVERT: C 186 ARG cc_start: 0.8171 (mmp80) cc_final: 0.7928 (mmp80) outliers start: 39 outliers final: 21 residues processed: 192 average time/residue: 0.6089 time to fit residues: 126.0863 Evaluate side-chains 189 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 209 GLN Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 86 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 127 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN B 429 ASN B 531 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.145551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.111945 restraints weight = 16862.598| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.03 r_work: 0.3265 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12791 Z= 0.129 Angle : 0.613 16.520 17385 Z= 0.308 Chirality : 0.041 0.159 1947 Planarity : 0.005 0.061 2169 Dihedral : 8.601 76.755 1860 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.73 % Allowed : 18.46 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.21), residues: 1494 helix: 0.91 (0.20), residues: 701 sheet: -0.82 (0.44), residues: 128 loop : -1.16 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 208 TYR 0.026 0.002 TYR C 20 PHE 0.022 0.001 PHE C 41 TRP 0.013 0.001 TRP A 336 HIS 0.007 0.001 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (12791) covalent geometry : angle 0.61341 / 0.31 (17385) hydrogen bonds : bond 0.03631 / 2.50 ( 525) hydrogen bonds : angle 4.27375 / 3.03 ( 1509) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.7929 (OUTLIER) cc_final: 0.7585 (t-90) REVERT: A 65 ARG cc_start: 0.7695 (tpp-160) cc_final: 0.7026 (tpp-160) REVERT: A 68 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7734 (mp) REVERT: A 69 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6522 (mp0) REVERT: A 92 ARG cc_start: 0.8558 (ttp-170) cc_final: 0.8271 (ttm110) REVERT: A 124 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7135 (mm-30) REVERT: A 150 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7513 (pm20) REVERT: A 163 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.8036 (pp20) REVERT: A 397 ARG cc_start: 0.8325 (tpp80) cc_final: 0.7803 (mmt180) REVERT: A 401 GLN cc_start: 0.8477 (mp10) cc_final: 0.8175 (mp10) REVERT: B 109 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8576 (mmtm) REVERT: B 229 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.7882 (pmm) REVERT: B 395 MET cc_start: 0.8691 (mtp) cc_final: 0.8477 (mtp) REVERT: B 423 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7874 (t70) REVERT: B 592 ARG cc_start: 0.8849 (mtt180) cc_final: 0.8629 (mmm-85) REVERT: B 593 ARG cc_start: 0.7145 (ttm110) cc_final: 0.6909 (ttp-110) REVERT: B 686 ARG cc_start: 0.7844 (mmm160) cc_final: 0.7591 (mmm-85) REVERT: C 120 ASN cc_start: 0.8411 (m-40) cc_final: 0.7920 (m110) REVERT: C 161 GLU cc_start: 0.7939 (mp0) cc_final: 0.7564 (mp0) REVERT: C 186 ARG cc_start: 0.8182 (mmp80) cc_final: 0.7940 (mmp80) outliers start: 37 outliers final: 18 residues processed: 194 average time/residue: 0.5878 time to fit residues: 122.4564 Evaluate side-chains 189 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 88 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 79 optimal weight: 0.0270 chunk 140 optimal weight: 20.0000 chunk 50 optimal weight: 0.6980 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN B 429 ASN B 656 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.145477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.111425 restraints weight = 17434.058| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.15 r_work: 0.3280 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12791 Z= 0.143 Angle : 0.622 16.629 17385 Z= 0.312 Chirality : 0.042 0.168 1947 Planarity : 0.005 0.064 2169 Dihedral : 8.563 76.739 1860 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.22 % Allowed : 19.20 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.21), residues: 1494 helix: 0.91 (0.20), residues: 701 sheet: -0.81 (0.43), residues: 128 loop : -1.15 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 208 TYR 0.027 0.002 TYR C 20 PHE 0.020 0.001 PHE C 41 TRP 0.014 0.001 TRP A 62 HIS 0.006 0.001 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (12791) covalent geometry : angle 0.62210 / 0.31 (17385) hydrogen bonds : bond 0.03673 / 2.53 ( 525) hydrogen bonds : angle 4.26775 / 3.03 ( 1509) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.7915 (OUTLIER) cc_final: 0.7605 (t-90) REVERT: A 65 ARG cc_start: 0.7649 (tpp-160) cc_final: 0.6997 (tpp-160) REVERT: A 68 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7630 (mp) REVERT: A 69 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6522 (mp0) REVERT: A 92 ARG cc_start: 0.8565 (ttp-170) cc_final: 0.8344 (mmm-85) REVERT: A 124 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7035 (mm-30) REVERT: A 150 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7494 (pm20) REVERT: A 397 ARG cc_start: 0.8335 (tpp80) cc_final: 0.7733 (mmt180) REVERT: A 401 GLN cc_start: 0.8479 (mp10) cc_final: 0.8114 (mp10) REVERT: B 109 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8542 (mmtm) REVERT: B 229 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.7958 (pmm) REVERT: B 395 MET cc_start: 0.8677 (mtp) cc_final: 0.8463 (mtp) REVERT: B 423 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7872 (t70) REVERT: B 686 ARG cc_start: 0.7843 (mmm160) cc_final: 0.7597 (mmm-85) REVERT: C 21 ASN cc_start: 0.8034 (m-40) cc_final: 0.7830 (m-40) REVERT: C 120 ASN cc_start: 0.8327 (m-40) cc_final: 0.7873 (m110) REVERT: C 161 GLU cc_start: 0.7942 (mp0) cc_final: 0.7567 (mp0) REVERT: C 186 ARG cc_start: 0.8205 (mmp80) cc_final: 0.7823 (mpp80) outliers start: 30 outliers final: 18 residues processed: 188 average time/residue: 0.6052 time to fit residues: 122.5609 Evaluate side-chains 187 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 251 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 102 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN B 429 ASN B 531 HIS C 209 GLN ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.146392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.112315 restraints weight = 17536.777| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.17 r_work: 0.3282 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12791 Z= 0.126 Angle : 0.615 16.290 17385 Z= 0.309 Chirality : 0.041 0.251 1947 Planarity : 0.005 0.065 2169 Dihedral : 8.519 77.026 1860 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.36 % Allowed : 18.98 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.22), residues: 1494 helix: 0.92 (0.20), residues: 707 sheet: -0.77 (0.43), residues: 128 loop : -1.19 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 208 TYR 0.027 0.001 TYR C 20 PHE 0.022 0.001 PHE C 41 TRP 0.013 0.001 TRP A 336 HIS 0.005 0.001 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (12791) covalent geometry : angle 0.61535 / 0.31 (17385) hydrogen bonds : bond 0.03526 / 2.42 ( 525) hydrogen bonds : angle 4.25166 / 3.02 ( 1509) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4337.80 seconds wall clock time: 74 minutes 39.60 seconds (4479.60 seconds total)