Starting phenix.real_space_refine on Wed Aug 5 03:04:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w6c_37320/08_2026/8w6c_37320.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w6c_37320/08_2026/8w6c_37320.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w6c_37320/08_2026/8w6c_37320.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w6c_37320/08_2026/8w6c_37320.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w6c_37320/08_2026/8w6c_37320.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w6c_37320/08_2026/8w6c_37320.map" } resolution = 2.7 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 58 5.16 5 Na 4 4.78 5 C 5594 2.51 5 N 1290 2.21 5 O 1412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 8360 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4081 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 33, 'TRANS': 496} Chain breaks: 1 Chain: "B" Number of atoms: 4081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4081 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 33, 'TRANS': 496} Chain breaks: 1 Chain: "A" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 133 Unusual residues: {' NA': 2, '3PH': 1, 'CIT': 1, 'Y01': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Unusual residues: {' NA': 2, '3PH': 1, 'CIT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.93, per 1000 atoms: 0.23 Number of scatterers: 8360 At special positions: 0 Unit cell: (96.743, 107.613, 90.221, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 2 15.00 Na 4 11.00 O 1412 8.00 N 1290 7.00 C 5594 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: 0.73 Conformation dependent library (CDL) restraints added in 216.9 milliseconds 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1988 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 0 sheets defined 76.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 4.007A pdb=" N GLN A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 7 " --> pdb=" O THR A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 24 Proline residue: A 21 - end of helix Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 33 through 51 removed outlier: 3.588A pdb=" N ALA A 41 " --> pdb=" O TYR A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 61 through 67 removed outlier: 3.970A pdb=" N ILE A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.580A pdb=" N VAL A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 103 removed outlier: 3.673A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 118 removed outlier: 3.848A pdb=" N ARG A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 137 Processing helix chain 'A' and resid 140 through 163 Proline residue: A 150 - end of helix removed outlier: 3.708A pdb=" N GLN A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 233 removed outlier: 3.853A pdb=" N GLN A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 222 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 230 " --> pdb=" O CYS A 226 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 254 removed outlier: 3.970A pdb=" N LEU A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 290 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 304 through 321 Processing helix chain 'A' and resid 326 through 345 Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 369 through 381 Processing helix chain 'A' and resid 409 through 417 Processing helix chain 'A' and resid 418 through 438 removed outlier: 3.591A pdb=" N VAL A 422 " --> pdb=" O PRO A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 447 through 453 Proline residue: A 450 - end of helix removed outlier: 4.117A pdb=" N SER A 453 " --> pdb=" O PRO A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 447 through 453' Processing helix chain 'A' and resid 455 through 471 removed outlier: 3.723A pdb=" N ALA A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 461 " --> pdb=" O PRO A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 494 Proline residue: A 485 - end of helix removed outlier: 3.515A pdb=" N SER A 489 " --> pdb=" O PRO A 485 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 494 " --> pdb=" O MET A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 509 removed outlier: 3.569A pdb=" N CYS A 505 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A 509 " --> pdb=" O CYS A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 525 removed outlier: 3.595A pdb=" N ALA A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A 525 " --> pdb=" O PRO A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 557 removed outlier: 4.688A pdb=" N LEU A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE A 545 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A 556 " --> pdb=" O ALA A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.579A pdb=" N GLN A 573 " --> pdb=" O SER A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 11 removed outlier: 4.007A pdb=" N GLN B 6 " --> pdb=" O ALA B 2 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA B 7 " --> pdb=" O THR B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 24 Proline residue: B 21 - end of helix Processing helix chain 'B' and resid 25 through 31 Processing helix chain 'B' and resid 33 through 51 removed outlier: 3.589A pdb=" N ALA B 41 " --> pdb=" O TYR B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 61 through 67 removed outlier: 3.971A pdb=" N ILE B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 80 removed outlier: 3.580A pdb=" N VAL B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 103 removed outlier: 3.672A pdb=" N ALA B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 118 removed outlier: 3.848A pdb=" N ARG B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 137 Processing helix chain 'B' and resid 140 through 163 Proline residue: B 150 - end of helix removed outlier: 3.708A pdb=" N GLN B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 233 removed outlier: 3.854A pdb=" N GLN B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER B 222 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER B 230 " --> pdb=" O CYS B 226 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 254 removed outlier: 3.968A pdb=" N LEU B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 290 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 304 through 321 Processing helix chain 'B' and resid 326 through 345 Processing helix chain 'B' and resid 353 through 358 Processing helix chain 'B' and resid 369 through 381 Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'B' and resid 418 through 438 removed outlier: 3.590A pdb=" N VAL B 422 " --> pdb=" O PRO B 418 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 446 Processing helix chain 'B' and resid 447 through 453 Proline residue: B 450 - end of helix removed outlier: 4.117A pdb=" N SER B 453 " --> pdb=" O PRO B 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 447 through 453' Processing helix chain 'B' and resid 455 through 471 removed outlier: 3.723A pdb=" N ALA B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE B 461 " --> pdb=" O PRO B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 494 Proline residue: B 485 - end of helix removed outlier: 3.516A pdb=" N SER B 489 " --> pdb=" O PRO B 485 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE B 494 " --> pdb=" O MET B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 509 removed outlier: 3.570A pdb=" N CYS B 505 " --> pdb=" O VAL B 501 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B 509 " --> pdb=" O CYS B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 525 removed outlier: 3.596A pdb=" N ALA B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL B 525 " --> pdb=" O PRO B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 557 removed outlier: 4.688A pdb=" N LEU B 542 " --> pdb=" O ARG B 538 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE B 545 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN B 556 " --> pdb=" O ALA B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 564 Processing helix chain 'B' and resid 569 through 573 removed outlier: 3.579A pdb=" N GLN B 573 " --> pdb=" O SER B 570 " (cutoff:3.500A) 487 hydrogen bonds defined for protein. 1455 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: 1.20 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1267 1.32 - 1.44: 2253 1.44 - 1.56: 4966 1.56 - 1.69: 2 1.69 - 1.81: 96 Bond restraints: 8584 Sorted by residual: bond pdb=" O11 3PH A 806 " pdb=" P 3PH A 806 " ideal model delta sigma weight residual 1.703 1.606 0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" O11 3PH B1101 " pdb=" P 3PH B1101 " ideal model delta sigma weight residual 1.703 1.608 0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C1 3PH A 806 " pdb=" O11 3PH A 806 " ideal model delta sigma weight residual 1.385 1.453 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C1 3PH B1101 " pdb=" O11 3PH B1101 " ideal model delta sigma weight residual 1.385 1.452 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C PHE A 359 " pdb=" N PRO A 360 " ideal model delta sigma weight residual 1.329 1.365 -0.036 1.22e-02 6.72e+03 8.51e+00 ... (remaining 8579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 11263 2.30 - 4.59: 363 4.59 - 6.89: 72 6.89 - 9.18: 20 9.18 - 11.48: 6 Bond angle restraints: 11724 Sorted by residual: angle pdb=" C GLU A 396 " pdb=" N ASN A 397 " pdb=" CA ASN A 397 " ideal model delta sigma weight residual 121.80 131.71 -9.91 2.44e+00 1.68e-01 1.65e+01 angle pdb=" C GLU B 396 " pdb=" N ASN B 397 " pdb=" CA ASN B 397 " ideal model delta sigma weight residual 121.80 131.63 -9.83 2.44e+00 1.68e-01 1.62e+01 angle pdb=" C LEU A 61 " pdb=" N PHE A 62 " pdb=" CA PHE A 62 " ideal model delta sigma weight residual 120.06 124.85 -4.79 1.19e+00 7.06e-01 1.62e+01 angle pdb=" C LEU B 61 " pdb=" N PHE B 62 " pdb=" CA PHE B 62 " ideal model delta sigma weight residual 120.06 124.84 -4.78 1.19e+00 7.06e-01 1.61e+01 angle pdb=" C GLU A 302 " pdb=" N LYS A 303 " pdb=" CA LYS A 303 " ideal model delta sigma weight residual 125.66 131.99 -6.33 1.85e+00 2.92e-01 1.17e+01 ... (remaining 11719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.13: 4674 18.13 - 36.26: 359 36.26 - 54.39: 57 54.39 - 72.52: 22 72.52 - 90.65: 8 Dihedral angle restraints: 5120 sinusoidal: 2058 harmonic: 3062 Sorted by residual: dihedral pdb=" CA LYS B 400 " pdb=" C LYS B 400 " pdb=" N LEU B 401 " pdb=" CA LEU B 401 " ideal model delta harmonic sigma weight residual 180.00 160.21 19.79 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA LYS A 400 " pdb=" C LYS A 400 " pdb=" N LEU A 401 " pdb=" CA LEU A 401 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA LEU B 499 " pdb=" C LEU B 499 " pdb=" N TYR B 500 " pdb=" CA TYR B 500 " ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 5117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 865 0.044 - 0.088: 382 0.088 - 0.132: 110 0.132 - 0.176: 27 0.176 - 0.220: 10 Chirality restraints: 1394 Sorted by residual: chirality pdb=" CB VAL A 73 " pdb=" CA VAL A 73 " pdb=" CG1 VAL A 73 " pdb=" CG2 VAL A 73 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB VAL B 73 " pdb=" CA VAL B 73 " pdb=" CG1 VAL B 73 " pdb=" CG2 VAL B 73 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA VAL A 454 " pdb=" N VAL A 454 " pdb=" C VAL A 454 " pdb=" CB VAL A 454 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1391 not shown) Planarity restraints: 1414 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 25 " -0.052 5.00e-02 4.00e+02 7.71e-02 9.50e+00 pdb=" N PRO A 26 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 26 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 26 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 25 " 0.051 5.00e-02 4.00e+02 7.68e-02 9.44e+00 pdb=" N PRO B 26 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 26 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 26 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 519 " -0.050 5.00e-02 4.00e+02 7.59e-02 9.22e+00 pdb=" N PRO A 520 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 520 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 520 " -0.042 5.00e-02 4.00e+02 ... (remaining 1411 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 273 2.71 - 3.26: 7857 3.26 - 3.81: 13065 3.81 - 4.35: 17801 4.35 - 4.90: 29368 Nonbonded interactions: 68364 Sorted by model distance: nonbonded pdb=" O1 CIT B1104 " pdb=" O7 CIT B1104 " model vdw 2.163 3.040 nonbonded pdb=" O3 CIT A 804 " pdb=" O7 CIT A 804 " model vdw 2.164 3.040 nonbonded pdb=" OG SER B 140 " pdb=" O6 CIT B1104 " model vdw 2.280 3.040 nonbonded pdb=" OG SER A 140 " pdb=" O6 CIT A 804 " model vdw 2.281 3.040 nonbonded pdb=" O GLN B 158 " pdb=" OG SER B 162 " model vdw 2.302 3.040 ... (remaining 68359 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 578 or resid 802 or resid 804)) selection = (chain 'B' and (resid 1 through 578 or resid 1102 or resid 1104)) } 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.830 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 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 : 0.007 0.097 8584 Z= 0.295 Angle : 1.049 11.479 11724 Z= 0.560 Chirality : 0.055 0.220 1394 Planarity : 0.009 0.077 1414 Dihedral : 14.215 90.646 3132 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.13 % Allowed : 4.76 % Favored : 94.10 % 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: -3.18 (0.21), residues: 1052 helix: -1.80 (0.15), residues: 756 sheet: None (None), residues: 0 loop : -2.47 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 108 TYR 0.008 0.002 TYR A 500 PHE 0.022 0.002 PHE A 359 TRP 0.028 0.002 TRP B 410 HIS 0.006 0.001 HIS B 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.29 ( 8584) covalent geometry : angle 1.04949 / 0.56 (11724) hydrogen bonds : bond 0.16915 / 11.19 ( 487) hydrogen bonds : angle 6.24429 / 4.50 ( 1455) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8573 (mtp) cc_final: 0.8329 (mtm) REVERT: A 129 MET cc_start: 0.9117 (mtp) cc_final: 0.8600 (mtp) REVERT: A 286 GLN cc_start: 0.8403 (tt0) cc_final: 0.8157 (tt0) REVERT: A 295 ARG cc_start: 0.7066 (mtp-110) cc_final: 0.6582 (mpt180) REVERT: A 320 ARG cc_start: 0.7362 (ttm110) cc_final: 0.7087 (ttp-170) REVERT: A 433 LYS cc_start: 0.8507 (tptt) cc_final: 0.8199 (tptm) REVERT: A 514 MET cc_start: 0.8702 (mtm) cc_final: 0.8409 (mtm) REVERT: B 69 MET cc_start: 0.8619 (mtp) cc_final: 0.8368 (mtm) REVERT: B 129 MET cc_start: 0.9128 (mtp) cc_final: 0.8595 (mtp) REVERT: B 295 ARG cc_start: 0.7078 (mtp-110) cc_final: 0.6642 (mpt180) REVERT: B 433 LYS cc_start: 0.8500 (tptt) cc_final: 0.8181 (tptp) REVERT: B 514 MET cc_start: 0.8705 (mtm) cc_final: 0.8407 (mtm) outliers start: 10 outliers final: 2 residues processed: 143 average time/residue: 0.4441 time to fit residues: 67.6665 Evaluate side-chains 112 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain B residue 240 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN A 257 ASN A 297 ASN A 308 GLN A 356 ASN A 414 ASN A 556 ASN B 6 GLN B 257 ASN B 286 GLN B 297 ASN B 308 GLN B 356 ASN B 414 ASN B 556 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.125387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.101016 restraints weight = 9053.117| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.37 r_work: 0.2921 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8584 Z= 0.138 Angle : 0.666 7.613 11724 Z= 0.321 Chirality : 0.042 0.152 1394 Planarity : 0.007 0.058 1414 Dihedral : 8.272 59.945 1316 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.49 % Allowed : 9.07 % Favored : 88.44 % 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: -0.66 (0.26), residues: 1052 helix: 0.30 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -2.31 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 346 TYR 0.007 0.001 TYR B 500 PHE 0.013 0.001 PHE B 351 TRP 0.019 0.002 TRP A 410 HIS 0.002 0.001 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 8584) covalent geometry : angle 0.66584 / 0.32 (11724) hydrogen bonds : bond 0.04945 / 3.19 ( 487) hydrogen bonds : angle 4.18499 / 3.03 ( 1455) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9118 (mtp) cc_final: 0.8846 (mtm) REVERT: A 88 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8476 (mm) REVERT: A 129 MET cc_start: 0.9145 (mtp) cc_final: 0.8640 (mtp) REVERT: A 286 GLN cc_start: 0.8541 (tt0) cc_final: 0.8248 (tt0) REVERT: A 295 ARG cc_start: 0.7601 (mtp-110) cc_final: 0.6769 (mmt180) REVERT: A 313 CYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7713 (m) REVERT: A 433 LYS cc_start: 0.8736 (tptt) cc_final: 0.8337 (tptp) REVERT: A 514 MET cc_start: 0.9019 (mtm) cc_final: 0.8729 (mtm) REVERT: B 69 MET cc_start: 0.9140 (mtp) cc_final: 0.8873 (mtm) REVERT: B 88 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8491 (mm) REVERT: B 129 MET cc_start: 0.9146 (mtp) cc_final: 0.8626 (mtp) REVERT: B 295 ARG cc_start: 0.7644 (mtp-110) cc_final: 0.6783 (mmt180) REVERT: B 313 CYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7722 (m) REVERT: B 411 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8128 (mppt) REVERT: B 433 LYS cc_start: 0.8733 (tptt) cc_final: 0.8298 (tptm) REVERT: B 446 ASN cc_start: 0.8744 (m-40) cc_final: 0.8541 (m-40) REVERT: B 514 MET cc_start: 0.9008 (mtm) cc_final: 0.8747 (mtm) outliers start: 22 outliers final: 9 residues processed: 127 average time/residue: 0.4264 time to fit residues: 58.0493 Evaluate side-chains 122 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 411 LYS Chi-restraints excluded: chain B residue 519 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 40 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN A 286 GLN B 6 GLN B 286 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.125996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.101561 restraints weight = 8921.821| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.37 r_work: 0.2928 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8584 Z= 0.127 Angle : 0.622 7.382 11724 Z= 0.301 Chirality : 0.041 0.155 1394 Planarity : 0.006 0.054 1414 Dihedral : 8.002 58.682 1314 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.72 % Allowed : 10.54 % Favored : 86.73 % 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 (0.27), residues: 1052 helix: 1.19 (0.19), residues: 760 sheet: None (None), residues: 0 loop : -2.06 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 112 TYR 0.005 0.001 TYR B 500 PHE 0.012 0.001 PHE B 350 TRP 0.019 0.001 TRP A 410 HIS 0.002 0.001 HIS B 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 8584) covalent geometry : angle 0.62204 / 0.30 (11724) hydrogen bonds : bond 0.04335 / 2.80 ( 487) hydrogen bonds : angle 3.86066 / 2.78 ( 1455) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9120 (mtp) cc_final: 0.8876 (mtm) REVERT: A 129 MET cc_start: 0.9142 (mtp) cc_final: 0.8656 (mtp) REVERT: A 286 GLN cc_start: 0.8463 (tt0) cc_final: 0.8251 (tt0) REVERT: A 295 ARG cc_start: 0.7755 (mtp-110) cc_final: 0.6965 (mpt180) REVERT: A 409 ASP cc_start: 0.8694 (p0) cc_final: 0.8295 (p0) REVERT: A 411 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8201 (tttt) REVERT: A 433 LYS cc_start: 0.8734 (tptt) cc_final: 0.8322 (tptp) REVERT: A 514 MET cc_start: 0.8994 (mtm) cc_final: 0.8752 (mtm) REVERT: B 69 MET cc_start: 0.9127 (mtp) cc_final: 0.8884 (mtm) REVERT: B 129 MET cc_start: 0.9133 (mtp) cc_final: 0.8640 (mtp) REVERT: B 286 GLN cc_start: 0.8500 (tt0) cc_final: 0.8273 (tt0) REVERT: B 295 ARG cc_start: 0.7747 (mtp-110) cc_final: 0.6976 (mpt180) REVERT: B 409 ASP cc_start: 0.8671 (p0) cc_final: 0.8273 (p0) REVERT: B 411 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8183 (tttt) REVERT: B 433 LYS cc_start: 0.8792 (tptt) cc_final: 0.8341 (tptm) REVERT: B 514 MET cc_start: 0.8965 (mtm) cc_final: 0.8703 (mtm) outliers start: 24 outliers final: 16 residues processed: 123 average time/residue: 0.4407 time to fit residues: 57.9005 Evaluate side-chains 129 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 411 LYS Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 519 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 90 optimal weight: 1.9990 chunk 47 optimal weight: 0.0570 chunk 6 optimal weight: 2.9990 chunk 42 optimal weight: 0.0670 chunk 12 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.128515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.104133 restraints weight = 9044.765| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.39 r_work: 0.2955 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8584 Z= 0.108 Angle : 0.577 6.935 11724 Z= 0.278 Chirality : 0.040 0.151 1394 Planarity : 0.005 0.051 1414 Dihedral : 7.771 55.477 1314 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.51 % Allowed : 11.34 % Favored : 85.15 % 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: 1.13 (0.28), residues: 1052 helix: 1.73 (0.20), residues: 756 sheet: None (None), residues: 0 loop : -1.93 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 346 TYR 0.004 0.001 TYR A 40 PHE 0.011 0.001 PHE B 351 TRP 0.017 0.001 TRP A 410 HIS 0.002 0.000 HIS B 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 8584) covalent geometry : angle 0.57747 / 0.28 (11724) hydrogen bonds : bond 0.03464 / 2.23 ( 487) hydrogen bonds : angle 3.62705 / 2.61 ( 1455) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9088 (mtp) cc_final: 0.8858 (mtm) REVERT: A 88 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8440 (mm) REVERT: A 101 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8160 (tt0) REVERT: A 129 MET cc_start: 0.9142 (mtp) cc_final: 0.8652 (mtp) REVERT: A 295 ARG cc_start: 0.7749 (mtp-110) cc_final: 0.6961 (mpt180) REVERT: A 411 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8170 (tttt) REVERT: A 433 LYS cc_start: 0.8693 (tptt) cc_final: 0.8300 (tptp) REVERT: B 52 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7367 (mt-10) REVERT: B 69 MET cc_start: 0.9081 (mtp) cc_final: 0.8848 (mtm) REVERT: B 88 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8446 (mm) REVERT: B 101 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8208 (tt0) REVERT: B 129 MET cc_start: 0.9132 (mtp) cc_final: 0.8633 (mtp) REVERT: B 295 ARG cc_start: 0.7781 (mtp-110) cc_final: 0.6970 (mpt180) REVERT: B 409 ASP cc_start: 0.8463 (p0) cc_final: 0.8211 (p0) REVERT: B 411 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8137 (tttt) REVERT: B 433 LYS cc_start: 0.8782 (tptt) cc_final: 0.8315 (tptm) outliers start: 31 outliers final: 10 residues processed: 133 average time/residue: 0.4207 time to fit residues: 59.8047 Evaluate side-chains 130 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 411 LYS Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 519 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 29 optimal weight: 4.9990 chunk 51 optimal weight: 0.0980 chunk 44 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.121937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.097202 restraints weight = 8984.051| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.38 r_work: 0.2799 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8584 Z= 0.198 Angle : 0.721 8.891 11724 Z= 0.348 Chirality : 0.047 0.157 1394 Planarity : 0.006 0.053 1414 Dihedral : 8.286 57.788 1314 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.74 % Allowed : 11.79 % Favored : 84.47 % 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: 0.87 (0.28), residues: 1052 helix: 1.40 (0.19), residues: 772 sheet: None (None), residues: 0 loop : -1.78 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 538 TYR 0.011 0.002 TYR B 500 PHE 0.017 0.002 PHE B 350 TRP 0.021 0.002 TRP B 410 HIS 0.002 0.001 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.20 ( 8584) covalent geometry : angle 0.72128 / 0.35 (11724) hydrogen bonds : bond 0.05609 / 3.60 ( 487) hydrogen bonds : angle 3.94126 / 2.83 ( 1455) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9144 (mtp) cc_final: 0.8884 (mtm) REVERT: A 101 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8357 (tt0) REVERT: A 129 MET cc_start: 0.9143 (mtp) cc_final: 0.8655 (mtp) REVERT: A 286 GLN cc_start: 0.8540 (tt0) cc_final: 0.8241 (tt0) REVERT: A 295 ARG cc_start: 0.7776 (mtp-110) cc_final: 0.6896 (mpt180) REVERT: A 352 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8173 (mp) REVERT: A 411 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8326 (tttt) REVERT: A 433 LYS cc_start: 0.8726 (tptt) cc_final: 0.8319 (tptp) REVERT: B 6 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6744 (mp-120) REVERT: B 69 MET cc_start: 0.9154 (mtp) cc_final: 0.8898 (mtm) REVERT: B 101 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8368 (tt0) REVERT: B 129 MET cc_start: 0.9140 (mtp) cc_final: 0.8643 (mtp) REVERT: B 286 GLN cc_start: 0.8514 (tt0) cc_final: 0.8292 (tt0) REVERT: B 295 ARG cc_start: 0.7798 (mtp-110) cc_final: 0.6896 (mpt180) REVERT: B 352 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8166 (mp) REVERT: B 411 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8316 (tttt) REVERT: B 433 LYS cc_start: 0.8743 (tptt) cc_final: 0.8321 (tptm) outliers start: 33 outliers final: 20 residues processed: 126 average time/residue: 0.4529 time to fit residues: 60.7008 Evaluate side-chains 134 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 411 LYS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 538 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 2 optimal weight: 0.0370 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.124521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.099836 restraints weight = 8950.928| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.37 r_work: 0.2850 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8584 Z= 0.128 Angle : 0.623 7.768 11724 Z= 0.301 Chirality : 0.042 0.154 1394 Planarity : 0.006 0.051 1414 Dihedral : 8.108 56.876 1314 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.74 % Allowed : 12.59 % Favored : 83.67 % 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: 1.26 (0.28), residues: 1052 helix: 1.86 (0.20), residues: 754 sheet: None (None), residues: 0 loop : -1.95 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 108 TYR 0.005 0.001 TYR A 500 PHE 0.012 0.001 PHE A 351 TRP 0.019 0.002 TRP B 410 HIS 0.002 0.000 HIS B 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 8584) covalent geometry : angle 0.62272 / 0.30 (11724) hydrogen bonds : bond 0.04308 / 2.76 ( 487) hydrogen bonds : angle 3.80000 / 2.74 ( 1455) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9112 (mtp) cc_final: 0.8854 (mtm) REVERT: A 88 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8475 (mm) REVERT: A 101 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8234 (tt0) REVERT: A 129 MET cc_start: 0.9138 (mtp) cc_final: 0.8651 (mtp) REVERT: A 286 GLN cc_start: 0.8410 (tt0) cc_final: 0.8199 (tt0) REVERT: A 295 ARG cc_start: 0.7753 (mtp-110) cc_final: 0.6845 (mpt180) REVERT: A 352 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8165 (mp) REVERT: A 409 ASP cc_start: 0.8702 (p0) cc_final: 0.8336 (p0) REVERT: A 433 LYS cc_start: 0.8714 (tptt) cc_final: 0.8309 (tptp) REVERT: B 69 MET cc_start: 0.9119 (mtp) cc_final: 0.8854 (mtm) REVERT: B 88 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8484 (mm) REVERT: B 101 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8237 (tt0) REVERT: B 129 MET cc_start: 0.9133 (mtp) cc_final: 0.8639 (mtp) REVERT: B 286 GLN cc_start: 0.8374 (tt0) cc_final: 0.8171 (tt0) REVERT: B 295 ARG cc_start: 0.7766 (mtp-110) cc_final: 0.6872 (mpt180) REVERT: B 352 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8164 (mp) REVERT: B 409 ASP cc_start: 0.8703 (p0) cc_final: 0.8338 (p0) REVERT: B 433 LYS cc_start: 0.8752 (tptt) cc_final: 0.8320 (tptm) outliers start: 33 outliers final: 18 residues processed: 128 average time/residue: 0.4280 time to fit residues: 58.4801 Evaluate side-chains 133 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 538 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.125930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.101464 restraints weight = 8966.365| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.37 r_work: 0.2864 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8584 Z= 0.123 Angle : 0.613 7.573 11724 Z= 0.296 Chirality : 0.042 0.152 1394 Planarity : 0.005 0.050 1414 Dihedral : 8.043 56.226 1314 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.85 % Allowed : 13.04 % Favored : 83.11 % 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: 1.41 (0.28), residues: 1052 helix: 1.97 (0.20), residues: 754 sheet: None (None), residues: 0 loop : -1.90 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 108 TYR 0.006 0.001 TYR A 500 PHE 0.012 0.001 PHE B 351 TRP 0.018 0.001 TRP B 410 HIS 0.002 0.000 HIS A 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 8584) covalent geometry : angle 0.61326 / 0.30 (11724) hydrogen bonds : bond 0.04100 / 2.62 ( 487) hydrogen bonds : angle 3.73803 / 2.69 ( 1455) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9109 (mtp) cc_final: 0.8862 (mtm) REVERT: A 88 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8438 (mm) REVERT: A 101 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8277 (tt0) REVERT: A 129 MET cc_start: 0.9144 (mtp) cc_final: 0.8684 (mtp) REVERT: A 286 GLN cc_start: 0.8404 (tt0) cc_final: 0.8177 (tt0) REVERT: A 295 ARG cc_start: 0.7804 (mtp-110) cc_final: 0.6926 (mpt180) REVERT: A 352 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8636 (mt) REVERT: A 409 ASP cc_start: 0.8641 (p0) cc_final: 0.8275 (p0) REVERT: A 433 LYS cc_start: 0.8687 (tptt) cc_final: 0.8294 (tptp) REVERT: B 6 GLN cc_start: 0.7150 (OUTLIER) cc_final: 0.6740 (mp-120) REVERT: B 52 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7571 (mt-10) REVERT: B 69 MET cc_start: 0.9104 (mtp) cc_final: 0.8849 (mtm) REVERT: B 88 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8445 (mm) REVERT: B 101 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: B 129 MET cc_start: 0.9141 (mtp) cc_final: 0.8655 (mtp) REVERT: B 295 ARG cc_start: 0.7805 (mtp-110) cc_final: 0.6899 (mpt180) REVERT: B 409 ASP cc_start: 0.8638 (p0) cc_final: 0.8269 (p0) REVERT: B 433 LYS cc_start: 0.8768 (tptt) cc_final: 0.8325 (tptm) outliers start: 34 outliers final: 19 residues processed: 132 average time/residue: 0.4186 time to fit residues: 59.2719 Evaluate side-chains 139 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 538 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN B 286 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.125433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.100998 restraints weight = 8942.474| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.36 r_work: 0.2835 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8584 Z= 0.133 Angle : 0.627 7.717 11724 Z= 0.302 Chirality : 0.042 0.153 1394 Planarity : 0.006 0.051 1414 Dihedral : 8.064 57.389 1314 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.74 % Allowed : 13.38 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.28), residues: 1052 helix: 1.97 (0.20), residues: 754 sheet: None (None), residues: 0 loop : -1.88 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 108 TYR 0.007 0.001 TYR A 500 PHE 0.012 0.001 PHE A 351 TRP 0.017 0.002 TRP A 410 HIS 0.001 0.000 HIS B 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 8584) covalent geometry : angle 0.62679 / 0.30 (11724) hydrogen bonds : bond 0.04309 / 2.76 ( 487) hydrogen bonds : angle 3.73884 / 2.69 ( 1455) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.6711 (mp-120) REVERT: A 69 MET cc_start: 0.9114 (mtp) cc_final: 0.8834 (mtm) REVERT: A 88 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8445 (mm) REVERT: A 101 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: A 129 MET cc_start: 0.9149 (mtp) cc_final: 0.8683 (mtp) REVERT: A 286 GLN cc_start: 0.8408 (tt0) cc_final: 0.8185 (tt0) REVERT: A 295 ARG cc_start: 0.7797 (mtp-110) cc_final: 0.6924 (mpt180) REVERT: A 352 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8657 (mt) REVERT: A 409 ASP cc_start: 0.8652 (p0) cc_final: 0.8292 (p0) REVERT: A 433 LYS cc_start: 0.8689 (tptt) cc_final: 0.8293 (tptp) REVERT: B 52 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7553 (mt-10) REVERT: B 69 MET cc_start: 0.9138 (mtp) cc_final: 0.8883 (mtm) REVERT: B 88 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8453 (mm) REVERT: B 101 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: B 129 MET cc_start: 0.9142 (mtp) cc_final: 0.8659 (mtp) REVERT: B 286 GLN cc_start: 0.8460 (tt0) cc_final: 0.8206 (tt0) REVERT: B 295 ARG cc_start: 0.7793 (mtp-110) cc_final: 0.6870 (mpt180) REVERT: B 409 ASP cc_start: 0.8648 (p0) cc_final: 0.8282 (p0) REVERT: B 433 LYS cc_start: 0.8770 (tptt) cc_final: 0.8324 (tptm) outliers start: 33 outliers final: 22 residues processed: 128 average time/residue: 0.4251 time to fit residues: 58.0737 Evaluate side-chains 139 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 411 LYS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 538 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 91 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.129058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.105132 restraints weight = 8827.001| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.35 r_work: 0.2835 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8584 Z= 0.138 Angle : 0.636 7.850 11724 Z= 0.307 Chirality : 0.043 0.153 1394 Planarity : 0.006 0.051 1414 Dihedral : 8.086 58.679 1314 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.85 % Allowed : 13.15 % Favored : 82.99 % 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: 1.40 (0.28), residues: 1052 helix: 1.96 (0.20), residues: 754 sheet: None (None), residues: 0 loop : -1.88 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 108 TYR 0.007 0.001 TYR A 500 PHE 0.013 0.001 PHE B 351 TRP 0.018 0.002 TRP B 410 HIS 0.001 0.000 HIS B 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 8584) covalent geometry : angle 0.63618 / 0.31 (11724) hydrogen bonds : bond 0.04430 / 2.83 ( 487) hydrogen bonds : angle 3.74783 / 2.70 ( 1455) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9115 (mtp) cc_final: 0.8834 (mtm) REVERT: A 88 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8473 (mm) REVERT: A 101 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8238 (tt0) REVERT: A 129 MET cc_start: 0.9149 (mtp) cc_final: 0.8664 (mtp) REVERT: A 286 GLN cc_start: 0.8425 (tt0) cc_final: 0.8223 (tt0) REVERT: A 295 ARG cc_start: 0.7804 (mtp-110) cc_final: 0.6884 (mpt180) REVERT: A 409 ASP cc_start: 0.8665 (p0) cc_final: 0.8320 (p0) REVERT: A 433 LYS cc_start: 0.8685 (tptt) cc_final: 0.8284 (tptp) REVERT: B 69 MET cc_start: 0.9136 (mtp) cc_final: 0.8847 (mtm) REVERT: B 88 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8476 (mm) REVERT: B 101 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8252 (tt0) REVERT: B 129 MET cc_start: 0.9145 (mtp) cc_final: 0.8643 (mtp) REVERT: B 286 GLN cc_start: 0.8464 (tt0) cc_final: 0.8192 (tt0) REVERT: B 295 ARG cc_start: 0.7781 (mtp-110) cc_final: 0.6893 (mpt180) REVERT: B 409 ASP cc_start: 0.8661 (p0) cc_final: 0.8296 (p0) REVERT: B 433 LYS cc_start: 0.8765 (tptt) cc_final: 0.8328 (tptm) outliers start: 34 outliers final: 22 residues processed: 128 average time/residue: 0.4351 time to fit residues: 59.5185 Evaluate side-chains 135 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 538 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 75 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 104 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.126148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.101653 restraints weight = 8905.798| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.37 r_work: 0.2941 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8584 Z= 0.120 Angle : 0.610 8.024 11724 Z= 0.295 Chirality : 0.042 0.151 1394 Planarity : 0.005 0.050 1414 Dihedral : 8.009 59.340 1314 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.51 % Allowed : 13.49 % Favored : 82.99 % 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: 1.56 (0.28), residues: 1052 helix: 2.07 (0.20), residues: 754 sheet: None (None), residues: 0 loop : -1.81 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 108 TYR 0.006 0.001 TYR A 500 PHE 0.012 0.001 PHE B 351 TRP 0.018 0.001 TRP B 410 HIS 0.002 0.000 HIS B 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 8584) covalent geometry : angle 0.61008 / 0.29 (11724) hydrogen bonds : bond 0.03975 / 2.54 ( 487) hydrogen bonds : angle 3.68960 / 2.65 ( 1455) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9134 (mtp) cc_final: 0.8864 (mtm) REVERT: A 88 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8461 (mm) REVERT: A 94 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8954 (mm) REVERT: A 101 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8214 (tt0) REVERT: A 129 MET cc_start: 0.9158 (mtp) cc_final: 0.8707 (mtp) REVERT: A 295 ARG cc_start: 0.7787 (mtp-110) cc_final: 0.6960 (mpt180) REVERT: A 433 LYS cc_start: 0.8697 (tptt) cc_final: 0.8308 (tptp) REVERT: B 69 MET cc_start: 0.9150 (mtp) cc_final: 0.8910 (mtm) REVERT: B 88 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8465 (mm) REVERT: B 94 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8949 (mm) REVERT: B 101 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: B 129 MET cc_start: 0.9149 (mtp) cc_final: 0.8674 (mtp) REVERT: B 286 GLN cc_start: 0.8470 (tt0) cc_final: 0.8196 (tt0) REVERT: B 295 ARG cc_start: 0.7780 (mtp-110) cc_final: 0.6948 (mpt180) REVERT: B 433 LYS cc_start: 0.8788 (tptt) cc_final: 0.8349 (tptm) outliers start: 31 outliers final: 24 residues processed: 127 average time/residue: 0.4177 time to fit residues: 56.6978 Evaluate side-chains 139 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 538 ARG Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 411 LYS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 538 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 0.0070 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 96 optimal weight: 0.4980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN A 286 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.127097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.102613 restraints weight = 8903.170| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.36 r_work: 0.2930 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8584 Z= 0.113 Angle : 0.596 8.361 11724 Z= 0.288 Chirality : 0.041 0.150 1394 Planarity : 0.005 0.050 1414 Dihedral : 7.926 59.834 1314 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.51 % Allowed : 13.27 % Favored : 83.22 % 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: 1.71 (0.28), residues: 1052 helix: 2.18 (0.20), residues: 752 sheet: None (None), residues: 0 loop : -1.72 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 12 TYR 0.005 0.001 TYR A 500 PHE 0.011 0.001 PHE A 351 TRP 0.018 0.001 TRP A 410 HIS 0.002 0.000 HIS A 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 8584) covalent geometry : angle 0.59585 / 0.29 (11724) hydrogen bonds : bond 0.03693 / 2.36 ( 487) hydrogen bonds : angle 3.64248 / 2.62 ( 1455) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2414.41 seconds wall clock time: 41 minutes 41.12 seconds (2501.12 seconds total)