Starting phenix.real_space_refine on Thu Jul 2 10:28:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w6c_37320/07_2026/8w6c_37320.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w6c_37320/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8w6c_37320/07_2026/8w6c_37320.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w6c_37320/07_2026/8w6c_37320.map" model { file = "/net/cci-nas-00/data/ceres_data/8w6c_37320/07_2026/8w6c_37320.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w6c_37320/07_2026/8w6c_37320.cif" } 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-dev-6108/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, 131 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'3PH': 1, 'CIT': 1, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 2 Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'3PH': 1, 'CIT': 1} Classifications: {'undetermined': 2} Chain breaks: 2 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: 1.96, 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: 0.71 Conformation dependent library (CDL) restraints added in 397.8 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: 0.15 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: 1.18 Time building geometry restraints manager: 0.96 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: 1.620 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.770 Find NCS groups from input model: 0.090 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:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.370 ------------------------------------------------------------------------------- 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 : 0.246 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: 0.4464 time to fit residues: 68.0337 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 : 0.308 ------------------------------------------------------------------------------- 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 = 0.3346 r_free = 0.3346 target = 0.125858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.101613 restraints weight = 9047.854| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.36 r_work: 0.2928 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 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 0.037 8584 Z= 0.140 Angle : 0.667 7.674 11724 Z= 0.323 Chirality : 0.042 0.153 1394 Planarity : 0.007 0.058 1414 Dihedral : 8.374 59.318 1316 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.49 % Allowed : 8.96 % Favored : 88.55 % 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: -0.62 (0.26), residues: 1052 helix: 0.36 (0.19), residues: 758 sheet: None (None), residues: 0 loop : -2.35 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 120 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 0.003 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 8584) covalent geometry : angle 0.66701 / 0.32 (11724) hydrogen bonds : bond 0.04837 / 3.13 ( 487) hydrogen bonds : angle 4.21547 / 3.05 ( 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 : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9133 (mtp) cc_final: 0.8863 (mtm) REVERT: A 88 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8438 (mm) REVERT: A 129 MET cc_start: 0.9153 (mtp) cc_final: 0.8686 (mtp) REVERT: A 286 GLN cc_start: 0.8550 (tt0) cc_final: 0.8265 (tt0) REVERT: A 295 ARG cc_start: 0.7644 (mtp-110) cc_final: 0.6842 (mpt180) REVERT: A 313 CYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7678 (m) REVERT: A 433 LYS cc_start: 0.8747 (tptt) cc_final: 0.8356 (tptp) REVERT: A 514 MET cc_start: 0.9004 (mtm) cc_final: 0.8741 (mtm) REVERT: B 69 MET cc_start: 0.9139 (mtp) cc_final: 0.8869 (mtm) REVERT: B 88 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8523 (mm) REVERT: B 129 MET cc_start: 0.9153 (mtp) cc_final: 0.8678 (mtp) REVERT: B 286 GLN cc_start: 0.8468 (tt0) cc_final: 0.8108 (tt0) REVERT: B 295 ARG cc_start: 0.7666 (mtp-110) cc_final: 0.6816 (mmt180) REVERT: B 313 CYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7722 (m) REVERT: B 411 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8141 (mppt) REVERT: B 433 LYS cc_start: 0.8746 (tptt) cc_final: 0.8324 (tptm) REVERT: B 446 ASN cc_start: 0.8747 (m-40) cc_final: 0.8545 (m-40) REVERT: B 514 MET cc_start: 0.9008 (mtm) cc_final: 0.8748 (mtm) outliers start: 22 outliers final: 9 residues processed: 127 average time/residue: 0.4541 time to fit residues: 61.6395 Evaluate side-chains 124 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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: 5.9990 chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3320 r_free = 0.3320 target = 0.123710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.099136 restraints weight = 8946.418| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.37 r_work: 0.2831 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8584 Z= 0.165 Angle : 0.686 8.238 11724 Z= 0.331 Chirality : 0.044 0.157 1394 Planarity : 0.006 0.053 1414 Dihedral : 8.404 58.617 1314 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.06 % Allowed : 10.54 % Favored : 86.39 % 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: 0.19 (0.27), residues: 1052 helix: 0.90 (0.19), residues: 772 sheet: None (None), residues: 0 loop : -1.99 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 112 TYR 0.009 0.002 TYR B 500 PHE 0.015 0.002 PHE A 350 TRP 0.021 0.002 TRP A 410 HIS 0.003 0.001 HIS B 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 8584) covalent geometry : angle 0.68637 / 0.33 (11724) hydrogen bonds : bond 0.05284 / 3.41 ( 487) hydrogen bonds : angle 4.04845 / 2.91 ( 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 136 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9145 (mtp) cc_final: 0.8881 (mtm) REVERT: A 101 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8349 (tt0) REVERT: A 129 MET cc_start: 0.9153 (mtp) cc_final: 0.8644 (mtp) REVERT: A 295 ARG cc_start: 0.7763 (mtp-110) cc_final: 0.6937 (mpt180) REVERT: A 411 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8290 (tttt) REVERT: A 433 LYS cc_start: 0.8738 (tptt) cc_final: 0.8294 (tptm) REVERT: A 514 MET cc_start: 0.8995 (mtm) cc_final: 0.8755 (mtm) REVERT: B 69 MET cc_start: 0.9134 (mtp) cc_final: 0.8877 (mtm) REVERT: B 101 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8380 (tt0) REVERT: B 129 MET cc_start: 0.9151 (mtp) cc_final: 0.8636 (mtp) REVERT: B 286 GLN cc_start: 0.8441 (tt0) cc_final: 0.8050 (tt0) REVERT: B 295 ARG cc_start: 0.7746 (mtp-110) cc_final: 0.6925 (mpt180) REVERT: B 411 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8284 (tttt) REVERT: B 433 LYS cc_start: 0.8743 (tptt) cc_final: 0.8320 (tptm) REVERT: B 514 MET cc_start: 0.8992 (mtm) cc_final: 0.8761 (mtm) outliers start: 27 outliers final: 14 residues processed: 125 average time/residue: 0.4275 time to fit residues: 57.0221 Evaluate side-chains 124 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 161 SER Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 411 LYS 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 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 411 LYS 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: 0.9990 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN A 286 GLN B 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.125297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.100577 restraints weight = 9060.653| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.39 r_work: 0.2857 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1733 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= 0.124 Angle : 0.619 7.599 11724 Z= 0.298 Chirality : 0.041 0.154 1394 Planarity : 0.006 0.053 1414 Dihedral : 8.196 58.935 1314 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.40 % Allowed : 11.90 % Favored : 84.69 % 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: 0.79 (0.28), residues: 1052 helix: 1.50 (0.20), residues: 756 sheet: None (None), residues: 0 loop : -2.10 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 108 TYR 0.004 0.001 TYR A 429 PHE 0.012 0.001 PHE B 351 TRP 0.019 0.001 TRP B 410 HIS 0.002 0.000 HIS B 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 8584) covalent geometry : angle 0.61894 / 0.30 (11724) hydrogen bonds : bond 0.04130 / 2.66 ( 487) hydrogen bonds : angle 3.84802 / 2.76 ( 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 144 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7540 (mt-10) REVERT: A 69 MET cc_start: 0.9110 (mtp) cc_final: 0.8850 (mtm) REVERT: A 88 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8470 (mm) REVERT: A 129 MET cc_start: 0.9132 (mtp) cc_final: 0.8661 (mtp) REVERT: A 295 ARG cc_start: 0.7726 (mtp-110) cc_final: 0.6928 (mpt180) REVERT: A 409 ASP cc_start: 0.8660 (p0) cc_final: 0.8278 (p0) REVERT: A 433 LYS cc_start: 0.8666 (tptt) cc_final: 0.8266 (tptp) REVERT: B 6 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.6711 (mp-120) REVERT: B 69 MET cc_start: 0.9110 (mtp) cc_final: 0.8851 (mtm) REVERT: B 129 MET cc_start: 0.9126 (mtp) cc_final: 0.8648 (mtp) REVERT: B 295 ARG cc_start: 0.7743 (mtp-110) cc_final: 0.6926 (mpt180) REVERT: B 409 ASP cc_start: 0.8660 (p0) cc_final: 0.8284 (p0) REVERT: B 433 LYS cc_start: 0.8751 (tptt) cc_final: 0.8291 (tptm) outliers start: 30 outliers final: 15 residues processed: 130 average time/residue: 0.3979 time to fit residues: 55.2140 Evaluate side-chains 125 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 161 SER Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 534 LEU 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 147 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 534 LEU 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: 0.6980 chunk 44 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 35 optimal weight: 0.0370 chunk 84 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 overall best weight: 1.1464 ------------------------------------------------------------------------------- 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 = 0.3330 r_free = 0.3330 target = 0.124480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.099863 restraints weight = 8991.952| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.38 r_work: 0.2840 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1801 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= 0.143 Angle : 0.643 8.060 11724 Z= 0.310 Chirality : 0.043 0.156 1394 Planarity : 0.006 0.051 1414 Dihedral : 8.222 58.485 1314 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % 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: 0.96 (0.28), residues: 1052 helix: 1.62 (0.20), residues: 756 sheet: None (None), residues: 0 loop : -2.02 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 108 TYR 0.006 0.001 TYR B 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 0.00338 / 0.14 ( 8584) covalent geometry : angle 0.64257 / 0.31 (11724) hydrogen bonds : bond 0.04531 / 2.90 ( 487) hydrogen bonds : angle 3.85528 / 2.77 ( 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 141 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9130 (mtp) cc_final: 0.8857 (mtm) REVERT: A 94 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8906 (mm) REVERT: A 101 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8285 (tt0) REVERT: A 129 MET cc_start: 0.9134 (mtp) cc_final: 0.8667 (mtp) REVERT: A 286 GLN cc_start: 0.8415 (tt0) cc_final: 0.8146 (tt0) REVERT: A 295 ARG cc_start: 0.7785 (mtp-110) cc_final: 0.6925 (mpt180) REVERT: A 352 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8116 (mp) REVERT: A 409 ASP cc_start: 0.8695 (p0) cc_final: 0.8329 (p0) REVERT: A 433 LYS cc_start: 0.8716 (tptt) cc_final: 0.8306 (tptp) REVERT: B 69 MET cc_start: 0.9115 (mtp) cc_final: 0.8853 (mtm) REVERT: B 94 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8863 (mm) REVERT: B 101 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8303 (tt0) REVERT: B 129 MET cc_start: 0.9133 (mtp) cc_final: 0.8660 (mtp) REVERT: B 286 GLN cc_start: 0.8486 (tt0) cc_final: 0.8259 (tt0) REVERT: B 295 ARG cc_start: 0.7737 (mtp-110) cc_final: 0.6916 (mpt180) REVERT: B 352 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8109 (mp) REVERT: B 409 ASP cc_start: 0.8692 (p0) cc_final: 0.8327 (p0) REVERT: B 433 LYS cc_start: 0.8743 (tptt) cc_final: 0.8309 (tptm) outliers start: 31 outliers final: 21 residues processed: 128 average time/residue: 0.4462 time to fit residues: 60.7197 Evaluate side-chains 136 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 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 94 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 463 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 534 LEU 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 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 215 LEU Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 352 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 2 optimal weight: 0.0570 overall best weight: 1.1102 ------------------------------------------------------------------------------- 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 = 0.3335 r_free = 0.3335 target = 0.124767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.100226 restraints weight = 8947.942| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.37 r_work: 0.2848 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1889 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= 0.139 Angle : 0.633 7.647 11724 Z= 0.307 Chirality : 0.043 0.154 1394 Planarity : 0.006 0.051 1414 Dihedral : 8.235 59.509 1314 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.97 % Allowed : 13.04 % 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: 1.19 (0.28), residues: 1052 helix: 1.77 (0.20), residues: 754 sheet: None (None), residues: 0 loop : -1.86 (0.39), 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 429 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 0.00330 / 0.14 ( 8584) covalent geometry : angle 0.63271 / 0.31 (11724) hydrogen bonds : bond 0.04477 / 2.87 ( 487) hydrogen bonds : angle 3.79330 / 2.73 ( 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 147 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9116 (mtp) cc_final: 0.8832 (mtm) REVERT: A 88 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8471 (mm) REVERT: A 94 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8869 (mm) REVERT: A 101 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: A 129 MET cc_start: 0.9137 (mtp) cc_final: 0.8661 (mtp) REVERT: A 295 ARG cc_start: 0.7778 (mtp-110) cc_final: 0.6848 (mpt180) REVERT: A 352 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8626 (mt) REVERT: A 409 ASP cc_start: 0.8675 (p0) cc_final: 0.8325 (p0) REVERT: A 433 LYS cc_start: 0.8710 (tptt) cc_final: 0.8298 (tptp) REVERT: B 69 MET cc_start: 0.9127 (mtp) cc_final: 0.8840 (mtm) REVERT: B 88 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8476 (mm) REVERT: B 94 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8860 (mm) REVERT: B 101 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8287 (tt0) REVERT: B 129 MET cc_start: 0.9131 (mtp) cc_final: 0.8654 (mtp) REVERT: B 286 GLN cc_start: 0.8412 (tt0) cc_final: 0.8189 (tt0) REVERT: B 295 ARG cc_start: 0.7764 (mtp-110) cc_final: 0.6868 (mpt180) REVERT: B 352 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8631 (mt) REVERT: B 409 ASP cc_start: 0.8673 (p0) cc_final: 0.8320 (p0) REVERT: B 433 LYS cc_start: 0.8736 (tptt) cc_final: 0.8299 (tptm) outliers start: 35 outliers final: 17 residues processed: 130 average time/residue: 0.4434 time to fit residues: 61.4710 Evaluate side-chains 134 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN 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 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 339 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 534 LEU 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 161 SER Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 534 LEU 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: 0.0000 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 88 optimal weight: 0.0370 overall best weight: 0.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 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 = 0.3399 r_free = 0.3399 target = 0.129458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.105678 restraints weight = 9011.772| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.35 r_work: 0.2888 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1968 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= 0.115 Angle : 0.593 7.152 11724 Z= 0.288 Chirality : 0.041 0.152 1394 Planarity : 0.005 0.050 1414 Dihedral : 8.114 58.068 1314 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.95 % Allowed : 14.51 % Favored : 82.54 % 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: 1.43 (0.28), residues: 1052 helix: 1.96 (0.20), residues: 754 sheet: None (None), residues: 0 loop : -1.79 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 108 TYR 0.004 0.001 TYR B 40 PHE 0.012 0.001 PHE A 351 TRP 0.018 0.001 TRP B 410 HIS 0.003 0.000 HIS B 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 8584) covalent geometry : angle 0.59340 / 0.29 (11724) hydrogen bonds : bond 0.03778 / 2.42 ( 487) hydrogen bonds : angle 3.69933 / 2.66 ( 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 138 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9098 (mtp) cc_final: 0.8857 (mtm) REVERT: A 88 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8416 (mm) REVERT: A 94 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8863 (mm) REVERT: A 129 MET cc_start: 0.9138 (mtp) cc_final: 0.8653 (mtp) REVERT: A 286 GLN cc_start: 0.8378 (tt0) cc_final: 0.8163 (tt0) REVERT: A 295 ARG cc_start: 0.7780 (mtp-110) cc_final: 0.6883 (mpt180) REVERT: A 352 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8626 (mt) REVERT: A 433 LYS cc_start: 0.8675 (tptt) cc_final: 0.8288 (tptp) REVERT: B 52 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: B 69 MET cc_start: 0.9096 (mtp) cc_final: 0.8848 (mtm) REVERT: B 88 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8427 (mm) REVERT: B 94 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8856 (mm) REVERT: B 101 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8287 (tt0) REVERT: B 129 MET cc_start: 0.9133 (mtp) cc_final: 0.8640 (mtp) REVERT: B 295 ARG cc_start: 0.7796 (mtp-110) cc_final: 0.6932 (mpt180) REVERT: B 352 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8614 (mt) REVERT: B 433 LYS cc_start: 0.8757 (tptt) cc_final: 0.8319 (tptm) outliers start: 26 outliers final: 12 residues processed: 129 average time/residue: 0.4205 time to fit residues: 57.9767 Evaluate side-chains 133 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 94 LEU 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 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 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 352 LEU Chi-restraints excluded: chain B residue 519 THR 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: 6.9990 chunk 29 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 66 optimal weight: 0.0470 chunk 14 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 104 optimal weight: 0.2980 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN B 6 GLN B 286 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.126584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.102218 restraints weight = 8972.513| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.37 r_work: 0.2871 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2007 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= 0.123 Angle : 0.605 7.391 11724 Z= 0.292 Chirality : 0.042 0.153 1394 Planarity : 0.005 0.050 1414 Dihedral : 8.093 58.483 1314 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.40 % Allowed : 14.29 % Favored : 82.31 % 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: 1.49 (0.28), residues: 1052 helix: 1.98 (0.20), residues: 754 sheet: None (None), residues: 0 loop : -1.72 (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 0.011 0.001 PHE A 351 TRP 0.017 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 0.60469 / 0.29 (11724) hydrogen bonds : bond 0.03976 / 2.55 ( 487) hydrogen bonds : angle 3.67907 / 2.65 ( 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 143 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.6773 (mp-120) REVERT: A 69 MET cc_start: 0.9124 (mtp) cc_final: 0.8857 (mtm) REVERT: A 88 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8432 (mm) REVERT: A 94 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8892 (mm) REVERT: A 101 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8278 (tt0) REVERT: A 129 MET cc_start: 0.9146 (mtp) cc_final: 0.8660 (mtp) REVERT: A 286 GLN cc_start: 0.8405 (tt0) cc_final: 0.8164 (tt0) REVERT: A 295 ARG cc_start: 0.7789 (mtp-110) cc_final: 0.7579 (mmm-85) REVERT: A 352 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8647 (mt) REVERT: A 433 LYS cc_start: 0.8681 (tptt) cc_final: 0.8292 (tptp) REVERT: B 52 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7575 (mt-10) REVERT: B 69 MET cc_start: 0.9132 (mtp) cc_final: 0.8858 (mtm) REVERT: B 88 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8435 (mm) REVERT: B 94 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8886 (mm) REVERT: B 101 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8313 (tt0) REVERT: B 129 MET cc_start: 0.9138 (mtp) cc_final: 0.8647 (mtp) REVERT: B 286 GLN cc_start: 0.8437 (tt0) cc_final: 0.8186 (tt0) REVERT: B 352 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8635 (mt) REVERT: B 433 LYS cc_start: 0.8754 (tptt) cc_final: 0.8312 (tptm) outliers start: 30 outliers final: 15 residues processed: 131 average time/residue: 0.4114 time to fit residues: 57.6301 Evaluate side-chains 136 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 352 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 534 LEU 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 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 352 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 534 LEU 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: 3.9990 chunk 9 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3333 r_free = 0.3333 target = 0.124668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.100225 restraints weight = 8941.205| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.37 r_work: 0.2842 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8584 Z= 0.158 Angle : 0.656 8.128 11724 Z= 0.318 Chirality : 0.044 0.155 1394 Planarity : 0.006 0.052 1414 Dihedral : 8.188 58.458 1314 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.40 % Allowed : 14.29 % Favored : 82.31 % 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: 1.33 (0.28), residues: 1052 helix: 1.85 (0.20), residues: 754 sheet: None (None), residues: 0 loop : -1.73 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 295 TYR 0.009 0.001 TYR A 500 PHE 0.014 0.002 PHE B 350 TRP 0.018 0.002 TRP A 410 HIS 0.002 0.000 HIS A 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 ( 8584) covalent geometry : angle 0.65558 / 0.32 (11724) hydrogen bonds : bond 0.04712 / 3.01 ( 487) hydrogen bonds : angle 3.76704 / 2.71 ( 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 141 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9134 (mtp) cc_final: 0.8863 (mtm) REVERT: A 88 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8479 (mm) REVERT: A 94 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8937 (mm) REVERT: A 101 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8284 (tt0) REVERT: A 129 MET cc_start: 0.9152 (mtp) cc_final: 0.8696 (mtp) REVERT: A 286 GLN cc_start: 0.8447 (tt0) cc_final: 0.8229 (tt0) REVERT: A 295 ARG cc_start: 0.7799 (mtp-110) cc_final: 0.7586 (mmm-85) REVERT: A 409 ASP cc_start: 0.8639 (p0) cc_final: 0.8295 (p0) REVERT: A 433 LYS cc_start: 0.8685 (tptt) cc_final: 0.8289 (tptp) REVERT: B 69 MET cc_start: 0.9143 (mtp) cc_final: 0.8867 (mtm) REVERT: B 94 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8939 (mm) REVERT: B 101 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8311 (tt0) REVERT: B 129 MET cc_start: 0.9150 (mtp) cc_final: 0.8686 (mtp) REVERT: B 286 GLN cc_start: 0.8485 (tt0) cc_final: 0.8191 (tt0) REVERT: B 409 ASP cc_start: 0.8639 (p0) cc_final: 0.8292 (p0) REVERT: B 433 LYS cc_start: 0.8747 (tptt) cc_final: 0.8312 (tptm) outliers start: 30 outliers final: 20 residues processed: 131 average time/residue: 0.4383 time to fit residues: 61.3436 Evaluate side-chains 133 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 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 339 LEU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 562 LEU 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 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 519 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 562 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 75 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 104 optimal weight: 0.3980 chunk 92 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 93 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3376 r_free = 0.3376 target = 0.127941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.103655 restraints weight = 8927.752| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.37 r_work: 0.2936 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2097 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= 0.117 Angle : 0.599 8.156 11724 Z= 0.290 Chirality : 0.041 0.152 1394 Planarity : 0.005 0.050 1414 Dihedral : 8.053 59.167 1314 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.29 % Allowed : 14.51 % Favored : 82.20 % 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: 1.58 (0.28), residues: 1052 helix: 2.08 (0.20), residues: 752 sheet: None (None), residues: 0 loop : -1.73 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 295 TYR 0.005 0.001 TYR A 500 PHE 0.012 0.001 PHE B 351 TRP 0.017 0.001 TRP A 410 HIS 0.003 0.000 HIS A 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 8584) covalent geometry : angle 0.59887 / 0.29 (11724) hydrogen bonds : bond 0.03702 / 2.37 ( 487) hydrogen bonds : angle 3.64167 / 2.61 ( 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: 29 poor density : 111 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9143 (mtp) cc_final: 0.8881 (mtm) REVERT: A 88 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8469 (mm) REVERT: A 94 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8886 (mm) REVERT: A 101 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: A 129 MET cc_start: 0.9151 (mtp) cc_final: 0.8677 (mtp) REVERT: A 286 GLN cc_start: 0.8394 (tt0) cc_final: 0.8162 (tt0) REVERT: B 69 MET cc_start: 0.9127 (mtp) cc_final: 0.8870 (mtm) REVERT: B 88 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8468 (mm) REVERT: B 94 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8880 (mm) REVERT: B 101 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8263 (tt0) REVERT: B 129 MET cc_start: 0.9146 (mtp) cc_final: 0.8666 (mtp) REVERT: B 286 GLN cc_start: 0.8439 (tt0) cc_final: 0.8194 (tt0) REVERT: B 433 LYS cc_start: 0.8778 (tptt) cc_final: 0.8348 (tptm) outliers start: 29 outliers final: 22 residues processed: 131 average time/residue: 0.4548 time to fit residues: 63.9350 Evaluate side-chains 137 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 339 LEU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 562 LEU 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 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 519 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 562 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.129873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.106013 restraints weight = 8918.057| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.35 r_work: 0.2877 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2112 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= 0.122 Angle : 0.605 8.693 11724 Z= 0.292 Chirality : 0.041 0.152 1394 Planarity : 0.005 0.050 1414 Dihedral : 8.050 59.697 1314 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.63 % Allowed : 14.17 % Favored : 82.20 % 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: 1.60 (0.28), residues: 1052 helix: 2.07 (0.20), residues: 752 sheet: None (None), residues: 0 loop : -1.67 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 295 TYR 0.006 0.001 TYR A 500 PHE 0.012 0.001 PHE B 351 TRP 0.017 0.001 TRP A 410 HIS 0.002 0.000 HIS A 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 8584) covalent geometry : angle 0.60496 / 0.29 (11724) hydrogen bonds : bond 0.03866 / 2.47 ( 487) hydrogen bonds : angle 3.64054 / 2.61 ( 1455) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2412.09 seconds wall clock time: 41 minutes 43.80 seconds (2503.80 seconds total)