Starting phenix.real_space_refine on Thu Aug 6 03:33:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z8n_39849/08_2026/8z8n_39849.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z8n_39849/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8z8n_39849/08_2026/8z8n_39849.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z8n_39849/08_2026/8z8n_39849.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z8n_39849/08_2026/8z8n_39849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z8n_39849/08_2026/8z8n_39849.map" } 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-2.2rc3-6140/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: 2.28, per 1000 atoms: 0.18 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: 0.89 Conformation dependent library (CDL) restraints added in 494.1 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: 0.36 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: 1.72 Time building geometry restraints manager: 1.17 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: 17058 1.83 - 3.67: 291 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=" O5' A D 7 " pdb=" C5' A D 7 " pdb=" C4' A D 7 " ideal model delta sigma weight residual 109.40 112.52 -3.12 8.00e-01 1.56e+00 1.52e+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=" O5' C E 16 " pdb=" C5' C E 16 " pdb=" C4' C E 16 " ideal model delta sigma weight residual 109.40 112.06 -2.66 8.00e-01 1.56e+00 1.11e+01 angle pdb=" O5' G E 15 " pdb=" C5' G E 15 " pdb=" C4' G E 15 " ideal model delta sigma weight residual 109.40 111.79 -2.39 8.00e-01 1.56e+00 8.96e+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: 1250 0.032 - 0.064: 476 0.064 - 0.096: 139 0.096 - 0.128: 66 0.128 - 0.160: 16 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.410 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.210 ------------------------------------------------------------------------------- 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= 0.116 Angle : 0.570 9.167 17385 Z= 0.304 Chirality : 0.041 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 0.00258 / 0.12 (12791) covalent geometry : angle 0.56958 / 0.30 (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 : 0.457 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: 0.6095 time to fit residues: 172.2807 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 : 0.298 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.151285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.119419 restraints weight = 17521.266| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.08 r_work: 0.3424 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12791 Z= 0.164 Angle : 0.630 7.623 17385 Z= 0.325 Chirality : 0.043 0.162 1947 Planarity : 0.006 0.066 2169 Dihedral : 8.482 75.665 1860 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.70 % Allowed : 10.49 % Favored : 87.81 % 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: -0.76 (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 0.014 0.001 TRP A 336 HIS 0.008 0.001 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (12791) covalent geometry : angle 0.63013 / 0.32 (17385) hydrogen bonds : bond 0.04748 / 3.31 ( 525) hydrogen bonds : angle 4.78892 / 3.45 ( 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 218 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 195 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7933 (pm20) REVERT: B 656 GLN cc_start: 0.7703 (tp-100) cc_final: 0.7399 (tp-100) REVERT: C 136 THR cc_start: 0.8113 (p) cc_final: 0.7896 (p) REVERT: C 142 ARG cc_start: 0.8030 (ppt170) cc_final: 0.7797 (ppt170) REVERT: C 161 GLU cc_start: 0.7836 (mp0) cc_final: 0.7493 (mp0) REVERT: C 194 GLU cc_start: 0.8583 (pp20) cc_final: 0.8262 (pp20) outliers start: 23 outliers final: 7 residues processed: 205 average time/residue: 0.6017 time to fit residues: 132.5577 Evaluate side-chains 180 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 106 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 11 ASN B 429 ASN B 476 HIS B 567 HIS C 120 ASN 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 = 0.143552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.108446 restraints weight = 16984.341| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.09 r_work: 0.3221 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 12791 Z= 0.274 Angle : 0.683 8.107 17385 Z= 0.353 Chirality : 0.047 0.166 1947 Planarity : 0.006 0.058 2169 Dihedral : 8.683 74.386 1860 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.69 % Allowed : 11.60 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.21), residues: 1494 helix: 0.53 (0.19), residues: 706 sheet: -0.96 (0.44), residues: 128 loop : -1.22 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 438 TYR 0.025 0.002 TYR B 533 PHE 0.026 0.002 PHE A 483 TRP 0.016 0.002 TRP A 336 HIS 0.008 0.001 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00649 / 0.27 (12791) covalent geometry : angle 0.68272 / 0.35 (17385) hydrogen bonds : bond 0.04866 / 3.40 ( 525) hydrogen bonds : angle 4.66325 / 3.34 ( 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 234 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 184 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8647 (ttp-170) cc_final: 0.8312 (ttm110) REVERT: A 142 LYS cc_start: 0.8154 (tmmt) cc_final: 0.7454 (ttmm) REVERT: A 150 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7680 (pm20) REVERT: B 11 ASN cc_start: 0.8641 (OUTLIER) cc_final: 0.8404 (m-40) REVERT: B 109 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8619 (mmtm) REVERT: B 656 GLN cc_start: 0.7787 (tp-100) cc_final: 0.7417 (tp-100) REVERT: C 120 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.7771 (m110) REVERT: C 136 THR cc_start: 0.8338 (p) cc_final: 0.8110 (p) REVERT: C 161 GLU cc_start: 0.7946 (mp0) cc_final: 0.7555 (mp0) REVERT: C 185 LYS cc_start: 0.7667 (tptt) cc_final: 0.7348 (tptt) outliers start: 50 outliers final: 14 residues processed: 215 average time/residue: 0.5743 time to fit residues: 132.5272 Evaluate side-chains 198 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 A residue 515 GLU Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 109 LYS 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 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 C residue 10 GLU Chi-restraints excluded: chain C residue 120 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN A 304 ASN B 429 ASN B 531 HIS C 120 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.144504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.109570 restraints weight = 16903.217| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.09 r_work: 0.3237 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12791 Z= 0.181 Angle : 0.613 7.865 17385 Z= 0.315 Chirality : 0.043 0.155 1947 Planarity : 0.005 0.056 2169 Dihedral : 8.651 74.843 1860 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.73 % Allowed : 14.11 % Favored : 83.16 % 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: -0.44 (0.21), residues: 1494 helix: 0.69 (0.20), residues: 707 sheet: -0.96 (0.43), residues: 128 loop : -1.21 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 582 TYR 0.021 0.002 TYR B 533 PHE 0.019 0.002 PHE C 41 TRP 0.015 0.001 TRP A 336 HIS 0.007 0.001 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (12791) covalent geometry : angle 0.61335 / 0.31 (17385) hydrogen bonds : bond 0.04183 / 2.90 ( 525) hydrogen bonds : angle 4.47517 / 3.20 ( 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 226 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6506 (mp0) REVERT: A 92 ARG cc_start: 0.8664 (ttp-170) cc_final: 0.8303 (mmm-85) REVERT: A 124 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7019 (mm-30) REVERT: A 150 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7584 (pm20) REVERT: B 109 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8634 (mmtm) REVERT: B 151 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7488 (mmt90) REVERT: B 229 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.7896 (pmm) REVERT: B 378 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7549 (ptt-90) REVERT: B 592 ARG cc_start: 0.8886 (mtm-85) cc_final: 0.8595 (mmm-85) REVERT: C 120 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.7936 (m110) REVERT: C 136 THR cc_start: 0.8303 (p) cc_final: 0.8069 (p) REVERT: C 142 ARG cc_start: 0.8189 (ppt170) cc_final: 0.7944 (ppt90) REVERT: C 160 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7152 (mm-30) REVERT: C 161 GLU cc_start: 0.7915 (mp0) cc_final: 0.7530 (mp0) REVERT: C 185 LYS cc_start: 0.7694 (tptt) cc_final: 0.7384 (tptt) REVERT: C 194 GLU cc_start: 0.8564 (pp20) cc_final: 0.8220 (pp20) REVERT: C 239 GLU cc_start: 0.7257 (tt0) cc_final: 0.6828 (pt0) outliers start: 37 outliers final: 12 residues processed: 210 average time/residue: 0.5561 time to fit residues: 125.6785 Evaluate side-chains 185 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU 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 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 378 ARG 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 C residue 10 GLU Chi-restraints excluded: chain C residue 120 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 148 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN B 429 ASN B 531 HIS B 656 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.144304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109328 restraints weight = 16900.023| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.10 r_work: 0.3235 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12791 Z= 0.180 Angle : 0.607 10.308 17385 Z= 0.311 Chirality : 0.043 0.168 1947 Planarity : 0.005 0.054 2169 Dihedral : 8.635 75.097 1860 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.55 % Allowed : 14.70 % Favored : 81.76 % 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: -0.43 (0.21), residues: 1494 helix: 0.71 (0.20), residues: 712 sheet: -0.92 (0.43), residues: 128 loop : -1.24 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 208 TYR 0.023 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 0.00426 / 0.18 (12791) covalent geometry : angle 0.60697 / 0.31 (17385) hydrogen bonds : bond 0.04060 / 2.81 ( 525) hydrogen bonds : angle 4.43827 / 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: 48 poor density : 177 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 69 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6437 (mp0) REVERT: A 92 ARG cc_start: 0.8669 (ttp-170) cc_final: 0.8288 (ttm110) REVERT: A 124 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7059 (mm-30) REVERT: A 150 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7546 (pm20) REVERT: B 109 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8621 (mmtm) REVERT: B 229 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.7941 (pmm) REVERT: C 120 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.8119 (m110) REVERT: C 136 THR cc_start: 0.8361 (p) cc_final: 0.8117 (p) REVERT: C 161 GLU cc_start: 0.7941 (mp0) cc_final: 0.7615 (mp0) outliers start: 48 outliers final: 16 residues processed: 208 average time/residue: 0.5661 time to fit residues: 126.9124 Evaluate side-chains 187 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 440 THR Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 493 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 438 LYS Chi-restraints excluded: chain B residue 503 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 C residue 120 ASN Chi-restraints excluded: chain C residue 141 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: 4.9990 chunk 29 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN B 429 ASN B 531 HIS B 656 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.143269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.109202 restraints weight = 16937.507| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.04 r_work: 0.3227 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12791 Z= 0.217 Angle : 0.636 9.756 17385 Z= 0.323 Chirality : 0.044 0.172 1947 Planarity : 0.005 0.053 2169 Dihedral : 8.672 75.125 1860 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.25 % Allowed : 16.32 % Favored : 80.43 % 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: -0.45 (0.21), residues: 1494 helix: 0.72 (0.20), residues: 707 sheet: -0.93 (0.43), residues: 128 loop : -1.27 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 134 TYR 0.024 0.002 TYR C 20 PHE 0.017 0.002 PHE C 41 TRP 0.015 0.002 TRP A 336 HIS 0.006 0.001 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 (12791) covalent geometry : angle 0.63599 / 0.32 (17385) hydrogen bonds : bond 0.04192 / 2.91 ( 525) hydrogen bonds : angle 4.46133 / 3.18 ( 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 215 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7718 (tpp-160) cc_final: 0.7038 (tpp-160) REVERT: A 68 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7952 (mp) REVERT: A 69 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6351 (mp0) REVERT: A 92 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8276 (ttm110) REVERT: A 124 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7126 (mm-30) REVERT: A 150 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7476 (pm20) REVERT: B 109 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8634 (mmtm) REVERT: B 141 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8067 (tp30) REVERT: B 229 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.7949 (pmm) REVERT: B 423 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7913 (t70) REVERT: C 120 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.7984 (m110) REVERT: C 161 GLU cc_start: 0.7967 (mp0) cc_final: 0.7593 (mp0) outliers start: 44 outliers final: 18 residues processed: 199 average time/residue: 0.5465 time to fit residues: 117.3779 Evaluate side-chains 188 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 92 ARG 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 440 THR Chi-restraints excluded: chain A residue 493 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 579 LEU Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 116 LEU 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 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: 3.9990 chunk 142 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN B 429 ASN B 531 HIS B 656 GLN C 209 GLN C 249 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.145940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111284 restraints weight = 16782.395| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.09 r_work: 0.3264 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12791 Z= 0.128 Angle : 0.600 12.679 17385 Z= 0.303 Chirality : 0.041 0.221 1947 Planarity : 0.005 0.055 2169 Dihedral : 8.609 75.620 1860 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.95 % Allowed : 17.21 % Favored : 79.84 % 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: -0.32 (0.21), residues: 1494 helix: 0.85 (0.20), residues: 706 sheet: -0.88 (0.43), residues: 128 loop : -1.23 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 582 TYR 0.026 0.002 TYR C 20 PHE 0.023 0.001 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 0.00300 / 0.13 (12791) covalent geometry : angle 0.59983 / 0.30 (17385) hydrogen bonds : bond 0.03695 / 2.53 ( 525) hydrogen bonds : angle 4.35446 / 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 212 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7692 (tpp-160) cc_final: 0.6967 (tpp-160) REVERT: A 68 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7935 (mp) REVERT: A 69 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6252 (mp0) REVERT: A 92 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8271 (ttm110) REVERT: A 124 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7125 (mm-30) REVERT: A 150 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7499 (pm20) REVERT: B 109 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8578 (mmtm) REVERT: B 229 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.7914 (pmm) REVERT: B 423 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7856 (t70) REVERT: B 593 ARG cc_start: 0.7137 (ttm110) cc_final: 0.6863 (ttp-110) REVERT: B 653 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7721 (pt0) REVERT: B 686 ARG cc_start: 0.7776 (mmm-85) cc_final: 0.7571 (mmm-85) REVERT: C 161 GLU cc_start: 0.7930 (mp0) cc_final: 0.7620 (mp0) outliers start: 40 outliers final: 13 residues processed: 196 average time/residue: 0.5510 time to fit residues: 116.9752 Evaluate side-chains 182 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 92 ARG 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 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 669 VAL Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 209 GLN 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: 1.9990 chunk 28 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 13 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 0.0030 chunk 35 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS 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 = 0.3835 r_free = 0.3835 target = 0.144974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.110264 restraints weight = 16766.855| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.08 r_work: 0.3250 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: 0.8688 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12791 Z= 0.170 Angle : 0.622 14.525 17385 Z= 0.313 Chirality : 0.043 0.189 1947 Planarity : 0.005 0.058 2169 Dihedral : 8.604 75.574 1860 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.88 % Allowed : 17.36 % Favored : 79.76 % 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: -0.29 (0.21), residues: 1494 helix: 0.90 (0.20), residues: 702 sheet: -0.88 (0.43), residues: 128 loop : -1.23 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 208 TYR 0.027 0.002 TYR C 20 PHE 0.020 0.001 PHE C 41 TRP 0.013 0.001 TRP A 336 HIS 0.006 0.001 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (12791) covalent geometry : angle 0.62159 / 0.31 (17385) hydrogen bonds : bond 0.03830 / 2.64 ( 525) hydrogen bonds : angle 4.34845 / 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 : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ARG cc_start: 0.7684 (tpp-160) cc_final: 0.6947 (tpp-160) REVERT: A 68 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7872 (mp) REVERT: A 69 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6218 (mp0) REVERT: A 92 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8267 (ttm110) REVERT: A 124 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7081 (mm-30) REVERT: A 150 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7510 (pm20) REVERT: A 397 ARG cc_start: 0.8323 (tpp80) cc_final: 0.8006 (mmt180) REVERT: B 109 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8586 (mmtm) REVERT: B 229 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.7917 (pmm) REVERT: B 593 ARG cc_start: 0.7164 (ttm110) cc_final: 0.6871 (ttp-110) REVERT: B 653 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7725 (pt0) REVERT: C 161 GLU cc_start: 0.7934 (mp0) cc_final: 0.7574 (mp0) REVERT: C 186 ARG cc_start: 0.8194 (mmp80) cc_final: 0.7951 (mmp80) outliers start: 39 outliers final: 16 residues processed: 195 average time/residue: 0.5622 time to fit residues: 117.9020 Evaluate side-chains 186 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 92 ARG 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 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 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 14 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 86 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3858 r_free = 0.3858 target = 0.146856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.112346 restraints weight = 16846.378| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.09 r_work: 0.3277 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12791 Z= 0.126 Angle : 0.606 14.109 17385 Z= 0.306 Chirality : 0.041 0.179 1947 Planarity : 0.005 0.062 2169 Dihedral : 8.557 76.055 1860 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.36 % Allowed : 18.09 % 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: -0.26 (0.21), residues: 1494 helix: 0.91 (0.20), residues: 707 sheet: -0.87 (0.43), residues: 128 loop : -1.21 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 208 TYR 0.030 0.002 TYR C 20 PHE 0.023 0.001 PHE C 41 TRP 0.013 0.001 TRP A 336 HIS 0.011 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (12791) covalent geometry : angle 0.60578 / 0.31 (17385) hydrogen bonds : bond 0.03563 / 2.44 ( 525) hydrogen bonds : angle 4.30591 / 3.06 ( 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 201 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8265 (ttm110) REVERT: A 124 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7040 (mm-30) REVERT: A 150 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7513 (pm20) REVERT: A 397 ARG cc_start: 0.8301 (tpp80) cc_final: 0.7970 (mmt180) REVERT: B 109 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8567 (mmtm) REVERT: B 229 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.7859 (pmm) REVERT: B 593 ARG cc_start: 0.7133 (ttm110) cc_final: 0.6845 (ttp-110) REVERT: B 686 ARG cc_start: 0.7851 (mmm-85) cc_final: 0.7558 (mmm-85) REVERT: C 21 ASN cc_start: 0.8082 (m-40) cc_final: 0.7867 (m-40) REVERT: C 120 ASN cc_start: 0.8420 (m-40) cc_final: 0.7987 (m110) REVERT: C 142 ARG cc_start: 0.7894 (ppt90) cc_final: 0.7649 (ppt90) REVERT: C 161 GLU cc_start: 0.7879 (mp0) cc_final: 0.7527 (mp0) REVERT: C 186 ARG cc_start: 0.8221 (mmp80) cc_final: 0.7985 (mmp80) outliers start: 32 outliers final: 14 residues processed: 191 average time/residue: 0.5719 time to fit residues: 117.3607 Evaluate side-chains 183 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 92 ARG 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 469 VAL 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 555 THR Chi-restraints excluded: chain C residue 14 ARG 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: 1.9990 chunk 96 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN B 429 ASN B 656 GLN C 209 GLN ** C 233 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 = 0.3816 r_free = 0.3816 target = 0.143937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109345 restraints weight = 17410.784| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.15 r_work: 0.3245 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2678 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= 0.220 Angle : 0.670 14.632 17385 Z= 0.340 Chirality : 0.045 0.176 1947 Planarity : 0.005 0.063 2169 Dihedral : 8.639 75.315 1860 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.14 % Allowed : 18.83 % Favored : 79.03 % 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: 0.82 (0.20), residues: 700 sheet: -0.92 (0.43), residues: 130 loop : -1.28 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 208 TYR 0.028 0.002 TYR C 20 PHE 0.016 0.002 PHE C 41 TRP 0.018 0.002 TRP A 62 HIS 0.007 0.001 HIS A 573 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.22 (12791) covalent geometry : angle 0.67010 / 0.34 (17385) hydrogen bonds : bond 0.04124 / 2.86 ( 525) hydrogen bonds : angle 4.41827 / 3.14 ( 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 198 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8407 (mmm-85) REVERT: A 124 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7035 (mm-30) REVERT: A 150 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7486 (pm20) REVERT: A 397 ARG cc_start: 0.8342 (tpp80) cc_final: 0.7945 (mmt180) REVERT: B 109 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8558 (mmtm) REVERT: B 229 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.7980 (pmm) REVERT: B 283 LYS cc_start: 0.8743 (ttmt) cc_final: 0.8530 (tppt) REVERT: B 593 ARG cc_start: 0.7129 (ttm110) cc_final: 0.6833 (ttp-110) REVERT: B 653 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7710 (pt0) REVERT: B 686 ARG cc_start: 0.7834 (mmm-85) cc_final: 0.7583 (mmm-85) REVERT: C 120 ASN cc_start: 0.8387 (m-40) cc_final: 0.7939 (m110) REVERT: C 161 GLU cc_start: 0.7927 (mp0) cc_final: 0.7599 (mp0) REVERT: C 186 ARG cc_start: 0.8214 (mmp80) cc_final: 0.7948 (mmp80) outliers start: 29 outliers final: 18 residues processed: 188 average time/residue: 0.5758 time to fit residues: 116.8266 Evaluate side-chains 187 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 92 ARG 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 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 555 THR Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 116 LEU 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: 0.7980 chunk 48 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 ASN B 429 ASN B 531 HIS B 656 GLN C 209 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.146674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.112112 restraints weight = 16808.367| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.09 r_work: 0.3277 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12791 Z= 0.128 Angle : 0.623 13.954 17385 Z= 0.315 Chirality : 0.042 0.231 1947 Planarity : 0.005 0.066 2169 Dihedral : 8.581 75.863 1860 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.44 % Allowed : 19.05 % Favored : 78.51 % 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: -0.28 (0.21), residues: 1494 helix: 0.93 (0.20), residues: 700 sheet: -0.89 (0.43), residues: 128 loop : -1.24 (0.22), residues: 666 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 0.023 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 0.00299 / 0.13 (12791) covalent geometry : angle 0.62264 / 0.32 (17385) hydrogen bonds : bond 0.03625 / 2.49 ( 525) hydrogen bonds : angle 4.36639 / 3.10 ( 1509) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3836.72 seconds wall clock time: 66 minutes 6.66 seconds (3966.66 seconds total)