Starting phenix.real_space_refine on Fri Aug 22 22:31:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w6c_37320/08_2025/8w6c_37320.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w6c_37320/08_2025/8w6c_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_37320/08_2025/8w6c_37320.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w6c_37320/08_2025/8w6c_37320.map" model { file = "/net/cci-nas-00/data/ceres_data/8w6c_37320/08_2025/8w6c_37320.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w6c_37320/08_2025/8w6c_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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8360 Number of models: 1 Model: "" Number of chains: 5 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: "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} Restraints were copied for chains: B Time building chain proxies: 2.53, per 1000 atoms: 0.30 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: 0.53 Conformation dependent library (CDL) restraints added in 344.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.17 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: 1.14 Time building geometry restraints manager: 0.70 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 - 30.64: 4989 30.64 - 61.28: 133 61.28 - 91.93: 14 91.93 - 122.57: 0 122.57 - 153.21: 2 Dihedral angle restraints: 5138 sinusoidal: 2076 harmonic: 3062 Sorted by residual: dihedral pdb=" C21 3PH A 806 " pdb=" C2 3PH A 806 " pdb=" O21 3PH A 806 " pdb=" C3 3PH A 806 " ideal model delta sinusoidal sigma weight residual 147.58 -59.21 -153.21 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C21 3PH B1101 " pdb=" C2 3PH B1101 " pdb=" O21 3PH B1101 " pdb=" C3 3PH B1101 " ideal model delta sinusoidal sigma weight residual 147.58 -64.65 -147.77 1 3.00e+01 1.11e-03 1.97e+01 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 ... (remaining 5135 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: 1.640 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.090 Find NCS groups from input model: 0.120 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:7.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 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 : 14.780 153.210 3150 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 aren 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 covalent geometry : bond 0.00669 ( 8584) covalent geometry : angle 1.04948 (11724) hydrogen bonds : bond 0.16915 ( 487) hydrogen bonds : angle 6.24429 ( 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 : 0.186 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: 0.8198 (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: 0.7077 (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: 0.4515 time to fit residues: 68.6223 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 : 0.243 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3344 r_free = 0.3344 target = 0.125777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.101456 restraints weight = 9040.832| |-----------------------------------------------------------------------------| 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: 0.2813 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8584 Z= 0.138 Angle : 0.664 7.450 11724 Z= 0.320 Chirality : 0.042 0.153 1394 Planarity : 0.007 0.057 1414 Dihedral : 10.594 153.990 1334 Min Nonbonded Distance : 2.323 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 aren not related in a simple way. whole: -0.62 (0.26), residues: 1052 helix: 0.34 (0.19), residues: 758 sheet: None (None), residues: 0 loop : -2.30 (0.36), residues: 294 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 B 497 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8584) covalent geometry : angle 0.66364 (11724) hydrogen bonds : bond 0.04978 ( 487) hydrogen bonds : angle 4.18710 ( 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 : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9121 (mtp) cc_final: 0.8855 (mtm) REVERT: A 88 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8477 (mm) REVERT: A 129 MET cc_start: 0.9147 (mtp) cc_final: 0.8692 (mtp) REVERT: A 286 GLN cc_start: 0.8537 (tt0) cc_final: 0.8237 (tt0) REVERT: A 295 ARG cc_start: 0.7618 (mtp-110) cc_final: 0.6781 (mmt180) REVERT: A 313 CYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7741 (m) REVERT: A 433 LYS cc_start: 0.8746 (tptt) cc_final: 0.8352 (tptp) REVERT: A 514 MET cc_start: 0.9010 (mtm) cc_final: 0.8731 (mtm) REVERT: B 69 MET cc_start: 0.9118 (mtp) cc_final: 0.8855 (mtm) REVERT: B 88 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8497 (mm) REVERT: B 129 MET cc_start: 0.9147 (mtp) cc_final: 0.8629 (mtp) REVERT: B 295 ARG cc_start: 0.7659 (mtp-110) cc_final: 0.6817 (mpt180) REVERT: B 313 CYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7736 (m) REVERT: B 411 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8200 (tttt) REVERT: B 433 LYS cc_start: 0.8740 (tptt) cc_final: 0.8307 (tptm) REVERT: B 446 ASN cc_start: 0.8741 (m-40) cc_final: 0.8531 (m-40) REVERT: B 514 MET cc_start: 0.9007 (mtm) cc_final: 0.8745 (mtm) outliers start: 22 outliers final: 9 residues processed: 127 average time/residue: 0.4357 time to fit residues: 59.0677 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 : 0.304 ------------------------------------------------------------------------------- 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: 6.9990 chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 0.0270 chunk 23 optimal weight: 0.1980 chunk 7 optimal weight: 3.9990 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3347 r_free = 0.3347 target = 0.125964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.101399 restraints weight = 8935.079| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.37 r_work: 0.2931 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1602 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= 0.125 Angle : 0.619 7.299 11724 Z= 0.299 Chirality : 0.041 0.156 1394 Planarity : 0.006 0.054 1414 Dihedral : 10.364 152.575 1332 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.27 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 aren not related in a simple way. whole: 0.50 (0.27), residues: 1052 helix: 1.25 (0.20), residues: 756 sheet: None (None), residues: 0 loop : -2.13 (0.37), residues: 296 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 A 351 TRP 0.019 0.001 TRP A 410 HIS 0.002 0.001 HIS B 497 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8584) covalent geometry : angle 0.61948 (11724) hydrogen bonds : bond 0.04248 ( 487) hydrogen bonds : angle 3.83767 ( 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 : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9115 (mtp) cc_final: 0.8876 (mtm) REVERT: A 129 MET cc_start: 0.9138 (mtp) cc_final: 0.8649 (mtp) REVERT: A 286 GLN cc_start: 0.8460 (tt0) cc_final: 0.8252 (tt0) REVERT: A 295 ARG cc_start: 0.7739 (mtp-110) cc_final: 0.6960 (mpt180) REVERT: A 409 ASP cc_start: 0.8684 (p0) cc_final: 0.8290 (p0) REVERT: A 411 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8180 (tttt) REVERT: A 433 LYS cc_start: 0.8753 (tptt) cc_final: 0.8346 (tptp) REVERT: A 514 MET cc_start: 0.8970 (mtm) cc_final: 0.8728 (mtm) REVERT: B 69 MET cc_start: 0.9126 (mtp) cc_final: 0.8893 (mtm) REVERT: B 129 MET cc_start: 0.9134 (mtp) cc_final: 0.8643 (mtp) REVERT: B 286 GLN cc_start: 0.8455 (tt0) cc_final: 0.8235 (tt0) REVERT: B 295 ARG cc_start: 0.7739 (mtp-110) cc_final: 0.6968 (mpt180) REVERT: B 409 ASP cc_start: 0.8669 (p0) cc_final: 0.8261 (p0) REVERT: B 411 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8170 (tttt) REVERT: B 433 LYS cc_start: 0.8788 (tptt) cc_final: 0.8336 (tptm) REVERT: B 514 MET cc_start: 0.8963 (mtm) cc_final: 0.8704 (mtm) outliers start: 24 outliers final: 16 residues processed: 123 average time/residue: 0.4251 time to fit residues: 55.8479 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 : 0.179 ------------------------------------------------------------------------------- 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: 3.9990 chunk 47 optimal weight: 0.0370 chunk 6 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3362 r_free = 0.3362 target = 0.127129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.102654 restraints weight = 9019.480| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.38 r_work: 0.2950 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1777 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 : 0.596 7.085 11724 Z= 0.287 Chirality : 0.041 0.151 1394 Planarity : 0.005 0.052 1414 Dihedral : 10.303 152.201 1332 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.63 % Allowed : 11.22 % 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 aren not related in a simple way. whole: 1.09 (0.28), residues: 1052 helix: 1.70 (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 B 108 TYR 0.004 0.001 TYR B 500 PHE 0.011 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 covalent geometry : bond 0.00267 ( 8584) covalent geometry : angle 0.59584 (11724) hydrogen bonds : bond 0.03858 ( 487) hydrogen bonds : angle 3.67735 ( 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 143 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9101 (mtp) cc_final: 0.8862 (mtm) REVERT: A 88 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8485 (mm) REVERT: A 101 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8221 (tt0) REVERT: A 129 MET cc_start: 0.9144 (mtp) cc_final: 0.8690 (mtp) REVERT: A 295 ARG cc_start: 0.7735 (mtp-110) cc_final: 0.6906 (mpt180) REVERT: A 352 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8048 (mp) REVERT: A 409 ASP cc_start: 0.8614 (p0) cc_final: 0.8306 (p0) REVERT: A 411 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8226 (tttt) REVERT: A 433 LYS cc_start: 0.8720 (tptt) cc_final: 0.8328 (tptp) REVERT: B 69 MET cc_start: 0.9106 (mtp) cc_final: 0.8864 (mtm) REVERT: B 88 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8493 (mm) REVERT: B 101 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: B 129 MET cc_start: 0.9134 (mtp) cc_final: 0.8671 (mtp) REVERT: B 295 ARG cc_start: 0.7801 (mtp-110) cc_final: 0.6964 (mpt180) REVERT: B 411 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8208 (tttt) REVERT: B 433 LYS cc_start: 0.8790 (tptt) cc_final: 0.8338 (tptm) outliers start: 32 outliers final: 13 residues processed: 130 average time/residue: 0.4665 time to fit residues: 64.5373 Evaluate side-chains 127 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 352 LEU Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 444 LEU 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: 3.9990 chunk 51 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3301 r_free = 0.3301 target = 0.122441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.097726 restraints weight = 8982.920| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.38 r_work: 0.2805 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8584 Z= 0.174 Angle : 0.689 8.525 11724 Z= 0.332 Chirality : 0.045 0.156 1394 Planarity : 0.006 0.053 1414 Dihedral : 10.528 151.434 1332 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.63 % Allowed : 11.90 % 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 aren not related in a simple way. whole: 0.94 (0.28), residues: 1052 helix: 1.46 (0.20), 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 B 108 TYR 0.009 0.002 TYR B 500 PHE 0.015 0.002 PHE A 350 TRP 0.020 0.002 TRP A 410 HIS 0.002 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 8584) covalent geometry : angle 0.68885 (11724) hydrogen bonds : bond 0.05279 ( 487) hydrogen bonds : angle 3.87037 ( 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 137 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9141 (mtp) cc_final: 0.8843 (mtm) REVERT: A 101 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8343 (tt0) REVERT: A 129 MET cc_start: 0.9138 (mtp) cc_final: 0.8656 (mtp) REVERT: A 286 GLN cc_start: 0.8507 (tt0) cc_final: 0.8054 (tt0) REVERT: A 295 ARG cc_start: 0.7782 (mtp-110) cc_final: 0.6913 (mpt180) REVERT: A 352 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8194 (mp) REVERT: A 411 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8321 (tttt) REVERT: A 433 LYS cc_start: 0.8735 (tptt) cc_final: 0.8321 (tptp) REVERT: B 69 MET cc_start: 0.9161 (mtp) cc_final: 0.8900 (mtm) REVERT: B 94 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8938 (mm) REVERT: B 101 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8367 (tt0) REVERT: B 129 MET cc_start: 0.9142 (mtp) cc_final: 0.8656 (mtp) REVERT: B 286 GLN cc_start: 0.8514 (tt0) cc_final: 0.8204 (tt0) REVERT: B 295 ARG cc_start: 0.7779 (mtp-110) cc_final: 0.6873 (mpt180) REVERT: B 352 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8173 (mp) REVERT: B 409 ASP cc_start: 0.8772 (p0) cc_final: 0.8422 (p0) REVERT: B 433 LYS cc_start: 0.8740 (tptt) cc_final: 0.8301 (tptm) outliers start: 32 outliers final: 16 residues processed: 125 average time/residue: 0.6411 time to fit residues: 85.0878 Evaluate side-chains 126 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 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 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 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 519 THR 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: 0.8980 chunk 70 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 2 optimal weight: 0.0030 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3357 r_free = 0.3357 target = 0.126485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.102181 restraints weight = 8919.923| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.35 r_work: 0.2927 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1903 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= 0.119 Angle : 0.600 7.325 11724 Z= 0.290 Chirality : 0.042 0.155 1394 Planarity : 0.005 0.052 1414 Dihedral : 10.386 152.507 1332 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.40 % Allowed : 12.81 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.28), residues: 1052 helix: 1.93 (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 0.005 0.001 TYR B 429 PHE 0.012 0.001 PHE B 351 TRP 0.018 0.001 TRP A 410 HIS 0.002 0.000 HIS A 497 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8584) covalent geometry : angle 0.60043 (11724) hydrogen bonds : bond 0.03897 ( 487) hydrogen bonds : angle 3.67971 ( 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 140 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9112 (mtp) cc_final: 0.8827 (mtm) REVERT: A 88 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8503 (mm) REVERT: A 101 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8174 (tt0) REVERT: A 129 MET cc_start: 0.9140 (mtp) cc_final: 0.8654 (mtp) REVERT: A 295 ARG cc_start: 0.7792 (mtp-110) cc_final: 0.6961 (mpt180) REVERT: A 352 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8646 (mt) REVERT: A 409 ASP cc_start: 0.8642 (p0) cc_final: 0.8262 (p0) REVERT: A 433 LYS cc_start: 0.8678 (tptt) cc_final: 0.8287 (tptp) REVERT: B 69 MET cc_start: 0.9110 (mtp) cc_final: 0.8862 (mtm) REVERT: B 88 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8479 (mm) REVERT: B 94 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8865 (mm) REVERT: B 101 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8218 (tt0) REVERT: B 129 MET cc_start: 0.9128 (mtp) cc_final: 0.8636 (mtp) REVERT: B 286 GLN cc_start: 0.8434 (tt0) cc_final: 0.8167 (tt0) REVERT: B 295 ARG cc_start: 0.7771 (mtp-110) cc_final: 0.6907 (mpt180) REVERT: B 433 LYS cc_start: 0.8759 (tptt) cc_final: 0.8316 (tptm) outliers start: 30 outliers final: 15 residues processed: 128 average time/residue: 0.6080 time to fit residues: 82.9108 Evaluate side-chains 130 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN 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 352 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 6 GLN 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 444 LEU Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 519 THR 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: 4.9990 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 88 optimal weight: 0.0870 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3343 r_free = 0.3343 target = 0.125560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.100860 restraints weight = 8987.081| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.39 r_work: 0.2863 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1947 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 : 0.612 7.375 11724 Z= 0.295 Chirality : 0.042 0.152 1394 Planarity : 0.005 0.051 1414 Dihedral : 10.356 152.312 1332 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.63 % Allowed : 12.93 % Favored : 83.45 % 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 aren not related in a simple way. whole: 1.48 (0.28), residues: 1052 helix: 2.00 (0.20), residues: 756 sheet: None (None), residues: 0 loop : -1.83 (0.37), residues: 296 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 0.017 0.001 TRP A 410 HIS 0.002 0.000 HIS A 497 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8584) covalent geometry : angle 0.61203 (11724) hydrogen bonds : bond 0.04000 ( 487) hydrogen bonds : angle 3.65970 ( 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 142 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7158 (mt-10) REVERT: A 69 MET cc_start: 0.9095 (mtp) cc_final: 0.8810 (mtm) REVERT: A 88 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8397 (mm) REVERT: A 94 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8924 (mm) REVERT: A 101 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: A 129 MET cc_start: 0.9136 (mtp) cc_final: 0.8673 (mtp) REVERT: A 295 ARG cc_start: 0.7785 (mtp-110) cc_final: 0.6910 (mpt180) REVERT: A 352 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8630 (mt) REVERT: A 409 ASP cc_start: 0.8604 (p0) cc_final: 0.8238 (p0) REVERT: A 433 LYS cc_start: 0.8671 (tptt) cc_final: 0.8271 (tptp) REVERT: B 52 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7528 (mt-10) REVERT: B 69 MET cc_start: 0.9122 (mtp) cc_final: 0.8860 (mtm) REVERT: B 88 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8412 (mm) REVERT: B 94 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8869 (mm) REVERT: B 101 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8266 (tt0) REVERT: B 129 MET cc_start: 0.9132 (mtp) cc_final: 0.8643 (mtp) REVERT: B 286 GLN cc_start: 0.8424 (tt0) cc_final: 0.8175 (tt0) REVERT: B 295 ARG cc_start: 0.7752 (mtp-110) cc_final: 0.6880 (mpt180) REVERT: B 433 LYS cc_start: 0.8746 (tptt) cc_final: 0.8291 (tptm) outliers start: 32 outliers final: 20 residues processed: 128 average time/residue: 0.6179 time to fit residues: 84.1153 Evaluate side-chains 137 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 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 444 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 56 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 66 optimal weight: 0.0870 chunk 14 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3294 r_free = 0.3294 target = 0.121759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.096899 restraints weight = 8954.419| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.38 r_work: 0.2786 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8584 Z= 0.193 Angle : 0.722 8.727 11724 Z= 0.348 Chirality : 0.046 0.156 1394 Planarity : 0.006 0.054 1414 Dihedral : 10.655 151.488 1332 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.74 % Allowed : 12.93 % Favored : 83.33 % 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 aren not related in a simple way. whole: 1.07 (0.27), residues: 1052 helix: 1.48 (0.19), residues: 782 sheet: None (None), residues: 0 loop : -1.57 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 108 TYR 0.012 0.002 TYR A 500 PHE 0.017 0.002 PHE B 350 TRP 0.021 0.002 TRP A 558 HIS 0.002 0.001 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 8584) covalent geometry : angle 0.72203 (11724) hydrogen bonds : bond 0.05647 ( 487) hydrogen bonds : angle 3.89390 ( 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 138 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 GLN cc_start: 0.7282 (OUTLIER) cc_final: 0.6881 (mp-120) REVERT: A 69 MET cc_start: 0.9148 (mtp) cc_final: 0.8866 (mtm) REVERT: A 101 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8364 (tt0) REVERT: A 129 MET cc_start: 0.9133 (mtp) cc_final: 0.8656 (mtp) REVERT: A 286 GLN cc_start: 0.8556 (tt0) cc_final: 0.8101 (tt0) REVERT: A 295 ARG cc_start: 0.7772 (mtp-110) cc_final: 0.6861 (mpt180) REVERT: A 433 LYS cc_start: 0.8732 (tptt) cc_final: 0.8299 (tptp) REVERT: A 463 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7877 (tp) REVERT: B 6 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.6894 (mp-120) REVERT: B 69 MET cc_start: 0.9164 (mtp) cc_final: 0.8868 (mtm) REVERT: B 101 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8369 (tt0) REVERT: B 129 MET cc_start: 0.9129 (mtp) cc_final: 0.8641 (mtp) REVERT: B 286 GLN cc_start: 0.8535 (tt0) cc_final: 0.8252 (tt0) REVERT: B 295 ARG cc_start: 0.7762 (mtp-110) cc_final: 0.6825 (mpt180) REVERT: B 433 LYS cc_start: 0.8737 (tptt) cc_final: 0.8304 (tptm) REVERT: B 463 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7873 (tp) outliers start: 33 outliers final: 19 residues processed: 124 average time/residue: 0.6107 time to fit residues: 80.6997 Evaluate side-chains 131 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 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 444 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 91 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3329 r_free = 0.3329 target = 0.124415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.099612 restraints weight = 8906.370| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.39 r_work: 0.2836 rms_B_bonded: 1.82 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: 0.8486 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8584 Z= 0.129 Angle : 0.627 7.911 11724 Z= 0.304 Chirality : 0.042 0.152 1394 Planarity : 0.006 0.052 1414 Dihedral : 10.528 152.909 1332 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.95 % Allowed : 13.72 % Favored : 83.33 % 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 aren not related in a simple way. whole: 1.39 (0.28), residues: 1052 helix: 1.78 (0.20), residues: 778 sheet: None (None), residues: 0 loop : -1.65 (0.39), residues: 274 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 0.012 0.001 PHE A 351 TRP 0.018 0.002 TRP A 410 HIS 0.002 0.000 HIS A 497 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8584) covalent geometry : angle 0.62697 (11724) hydrogen bonds : bond 0.04305 ( 487) hydrogen bonds : angle 3.73225 ( 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 135 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9104 (mtp) cc_final: 0.8826 (mtm) REVERT: A 88 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8434 (mm) REVERT: A 101 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8237 (tt0) REVERT: A 129 MET cc_start: 0.9137 (mtp) cc_final: 0.8642 (mtp) REVERT: A 295 ARG cc_start: 0.7761 (mtp-110) cc_final: 0.6878 (mpt180) REVERT: A 409 ASP cc_start: 0.8681 (p0) cc_final: 0.8312 (p0) REVERT: A 433 LYS cc_start: 0.8661 (tptt) cc_final: 0.8253 (tptp) REVERT: A 463 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7808 (tp) REVERT: B 69 MET cc_start: 0.9135 (mtp) cc_final: 0.8887 (mtm) REVERT: B 88 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8479 (mm) REVERT: B 101 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: B 129 MET cc_start: 0.9130 (mtp) cc_final: 0.8633 (mtp) REVERT: B 286 GLN cc_start: 0.8439 (tt0) cc_final: 0.8217 (tt0) REVERT: B 295 ARG cc_start: 0.7746 (mtp-110) cc_final: 0.6867 (mpt180) REVERT: B 409 ASP cc_start: 0.8649 (p0) cc_final: 0.8293 (p0) REVERT: B 433 LYS cc_start: 0.8744 (tptt) cc_final: 0.8301 (tptm) outliers start: 26 outliers final: 16 residues processed: 125 average time/residue: 0.6189 time to fit residues: 82.1935 Evaluate side-chains 127 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 339 LEU Chi-restraints excluded: chain A residue 444 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 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 519 THR Chi-restraints excluded: chain B residue 534 LEU 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: 0.9990 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 104 optimal weight: 0.0030 chunk 92 optimal weight: 0.6980 chunk 16 optimal weight: 0.0970 chunk 93 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3388 r_free = 0.3388 target = 0.128814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.104516 restraints weight = 8951.419| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.37 r_work: 0.2958 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2133 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= 0.107 Angle : 0.581 8.218 11724 Z= 0.280 Chirality : 0.041 0.151 1394 Planarity : 0.005 0.050 1414 Dihedral : 10.273 152.254 1332 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.15 % Allowed : 14.74 % 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 aren not related in a simple way. whole: 1.75 (0.28), residues: 1052 helix: 2.20 (0.20), residues: 752 sheet: None (None), residues: 0 loop : -1.68 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 108 TYR 0.004 0.001 TYR B 429 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 covalent geometry : bond 0.00240 ( 8584) covalent geometry : angle 0.58128 (11724) hydrogen bonds : bond 0.03250 ( 487) hydrogen bonds : angle 3.54256 ( 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 126 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.336 Fit side-chains REVERT: A 69 MET cc_start: 0.9125 (mtp) cc_final: 0.8870 (mtm) REVERT: A 88 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8436 (mm) REVERT: A 129 MET cc_start: 0.9156 (mtp) cc_final: 0.8726 (mtp) REVERT: A 295 ARG cc_start: 0.7736 (mtp-110) cc_final: 0.6888 (mpt180) REVERT: B 69 MET cc_start: 0.9139 (mtp) cc_final: 0.8896 (mtm) REVERT: B 88 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8447 (mm) REVERT: B 101 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: B 129 MET cc_start: 0.9149 (mtp) cc_final: 0.8708 (mtp) REVERT: B 286 GLN cc_start: 0.8410 (tt0) cc_final: 0.8177 (tt0) REVERT: B 295 ARG cc_start: 0.7732 (mtp-110) cc_final: 0.6870 (mpt180) REVERT: B 433 LYS cc_start: 0.8725 (tptt) cc_final: 0.8286 (tptm) outliers start: 19 outliers final: 11 residues processed: 119 average time/residue: 0.6054 time to fit residues: 76.8212 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 : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLN Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 519 THR 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 224 CYS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 519 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 0.4980 chunk 68 optimal weight: 0.0570 chunk 39 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3403 r_free = 0.3403 target = 0.129707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.105823 restraints weight = 8911.869| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.34 r_work: 0.2947 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2141 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 : 0.607 8.557 11724 Z= 0.293 Chirality : 0.042 0.151 1394 Planarity : 0.005 0.050 1414 Dihedral : 10.310 152.162 1332 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.93 % Allowed : 15.76 % 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 aren not related in a simple way. whole: 1.77 (0.28), residues: 1052 helix: 2.19 (0.20), residues: 752 sheet: None (None), residues: 0 loop : -1.61 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 108 TYR 0.006 0.001 TYR A 500 PHE 0.011 0.001 PHE B 351 TRP 0.017 0.002 TRP B 410 HIS 0.002 0.000 HIS A 497 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8584) covalent geometry : angle 0.60717 (11724) hydrogen bonds : bond 0.03730 ( 487) hydrogen bonds : angle 3.57212 ( 1455) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2968.56 seconds wall clock time: 51 minutes 20.20 seconds (3080.20 seconds total)