Starting phenix.real_space_refine on Tue Aug 4 17:56:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tzv_41770/08_2026/8tzv_41770.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tzv_41770/08_2026/8tzv_41770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tzv_41770/08_2026/8tzv_41770.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tzv_41770/08_2026/8tzv_41770.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tzv_41770/08_2026/8tzv_41770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tzv_41770/08_2026/8tzv_41770.map" } resolution = 2.8 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= 0.002 sd= 0.030 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 44 5.16 5 C 3634 2.51 5 N 948 2.21 5 O 1052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5680 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2839 Classifications: {'peptide': 348} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 322} Chain breaks: 1 Chain: "B" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2839 Classifications: {'peptide': 348} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 322} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 138 SG CYS A 23 22.992 26.367 78.483 1.00205.25 S ATOM 160 SG CYS A 26 20.287 26.051 79.798 1.00196.05 S ATOM 528 SG CYS A 71 19.264 28.175 79.875 1.00207.19 S ATOM 534 SG CYS A 72 23.034 28.417 80.130 1.00186.79 S ATOM 2977 SG CYS B 23 23.388 44.045 32.883 1.00220.55 S ATOM 2999 SG CYS B 26 21.848 44.317 31.167 1.00214.45 S ATOM 3367 SG CYS B 71 20.232 42.218 31.374 1.00209.17 S ATOM 3373 SG CYS B 72 23.292 42.074 29.559 1.00201.96 S Time building chain proxies: 1.42, per 1000 atoms: 0.25 Number of scatterers: 5680 At special positions: 0 Unit cell: (75.04, 69.68, 111.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 44 16.00 O 1052 8.00 N 948 7.00 C 3634 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: 0.44 Conformation dependent library (CDL) restraints added in 202.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 600 " pdb="ZN ZN A 600 " - pdb=" SG CYS A 23 " pdb="ZN ZN A 600 " - pdb=" SG CYS A 71 " pdb="ZN ZN A 600 " - pdb=" SG CYS A 26 " pdb="ZN ZN A 600 " - pdb=" SG CYS A 72 " pdb=" ZN B 600 " pdb="ZN ZN B 600 " - pdb=" SG CYS B 26 " pdb="ZN ZN B 600 " - pdb=" SG CYS B 72 " pdb="ZN ZN B 600 " - pdb=" SG CYS B 71 " pdb="ZN ZN B 600 " - pdb=" SG CYS B 23 " Number of angles added : 12 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1320 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 6 sheets defined 39.8% alpha, 18.7% 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 43 through 52 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 281 through 287 Processing helix chain 'A' and resid 287 through 302 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 311 through 320 Processing helix chain 'A' and resid 372 through 375 Processing helix chain 'A' and resid 378 through 396 removed outlier: 3.853A pdb=" N ALA A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 448 Proline residue: A 443 - end of helix Processing helix chain 'A' and resid 467 through 470 Processing helix chain 'A' and resid 482 through 487 removed outlier: 4.110A pdb=" N LYS A 487 " --> pdb=" O GLY A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 511 removed outlier: 3.793A pdb=" N GLU A 495 " --> pdb=" O ASP A 491 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLN A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 9.708A pdb=" N LYS A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N CYS A 509 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 511 " --> pdb=" O GLN A 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 53 removed outlier: 3.911A pdb=" N ASP B 49 " --> pdb=" O GLN B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 84 removed outlier: 3.652A pdb=" N PHE B 84 " --> pdb=" O PRO B 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 81 through 84' Processing helix chain 'B' and resid 87 through 104 Processing helix chain 'B' and resid 281 through 287 Processing helix chain 'B' and resid 287 through 302 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 311 through 320 Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.646A pdb=" N PHE B 376 " --> pdb=" O ASP B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 398 removed outlier: 3.716A pdb=" N TYR B 382 " --> pdb=" O SER B 378 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS B 397 " --> pdb=" O GLN B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 441 through 446 removed outlier: 3.624A pdb=" N LEU B 445 " --> pdb=" O CYS B 441 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 441 through 446' Processing helix chain 'B' and resid 467 through 470 Processing helix chain 'B' and resid 482 through 489 Processing helix chain 'B' and resid 494 through 512 removed outlier: 3.901A pdb=" N VAL B 498 " --> pdb=" O GLU B 494 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLN B 507 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N LYS B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N CYS B 509 " --> pdb=" O VAL B 505 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG B 512 " --> pdb=" O LYS B 508 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 removed outlier: 3.600A pdb=" N GLY A 36 " --> pdb=" O PHE A 15 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 11 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N SER A 10 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 404 through 405 Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 276 removed outlier: 6.674A pdb=" N GLY A 338 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASP A 357 " --> pdb=" O GLY A 338 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE A 340 " --> pdb=" O VAL A 355 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL A 355 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLN A 342 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL A 353 " --> pdb=" O GLN A 342 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR A 344 " --> pdb=" O ILE A 351 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TYR A 367 " --> pdb=" O VAL A 355 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASP A 357 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N SER A 365 " --> pdb=" O ASP A 357 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 472 through 474 Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 57 removed outlier: 5.262A pdb=" N MET B 37 " --> pdb=" O PHE B 15 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE B 15 " --> pdb=" O MET B 37 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ALA B 39 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASP B 13 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLN B 472 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 270 through 276 removed outlier: 4.043A pdb=" N ALA B 352 " --> pdb=" O TYR B 344 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU B 346 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASP B 357 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N SER B 365 " --> pdb=" O ASP B 357 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL B 363 " --> pdb=" O TYR B 405 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY B 407 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N SER B 365 " --> pdb=" O GLY B 407 " (cutoff:3.500A) removed outlier: 9.833A pdb=" N TYR B 409 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 15.313A pdb=" N TYR B 367 " --> pdb=" O TYR B 409 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ILE B 77 " --> pdb=" O MET B 406 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N PHE B 408 " --> pdb=" O TYR B 75 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N TYR B 75 " --> pdb=" O PHE B 408 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N THR B 76 " --> pdb=" O LEU B 428 " (cutoff:3.500A) 221 hydrogen bonds defined for protein. 600 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: 0.62 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1794 1.34 - 1.46: 1391 1.46 - 1.58: 2597 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 5842 Sorted by residual: bond pdb=" CA VAL A 66 " pdb=" CB VAL A 66 " ideal model delta sigma weight residual 1.530 1.539 -0.010 1.11e-02 8.12e+03 7.34e-01 bond pdb=" CA VAL B 277 " pdb=" CB VAL B 277 " ideal model delta sigma weight residual 1.528 1.539 -0.011 1.34e-02 5.57e+03 6.65e-01 bond pdb=" CA GLY A 59 " pdb=" C GLY A 59 " ideal model delta sigma weight residual 1.514 1.523 -0.008 1.41e-02 5.03e+03 3.44e-01 bond pdb=" CA PRO B 443 " pdb=" C PRO B 443 " ideal model delta sigma weight residual 1.528 1.521 0.007 1.20e-02 6.94e+03 3.24e-01 bond pdb=" CA LEU A 442 " pdb=" C LEU A 442 " ideal model delta sigma weight residual 1.520 1.526 -0.006 1.23e-02 6.61e+03 2.46e-01 ... (remaining 5837 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 7699 0.95 - 1.89: 137 1.89 - 2.84: 38 2.84 - 3.79: 26 3.79 - 4.74: 2 Bond angle restraints: 7902 Sorted by residual: angle pdb=" C LEU B 442 " pdb=" N PRO B 443 " pdb=" CA PRO B 443 " ideal model delta sigma weight residual 121.91 118.95 2.96 1.35e+00 5.49e-01 4.79e+00 angle pdb=" N VAL B 277 " pdb=" CA VAL B 277 " pdb=" C VAL B 277 " ideal model delta sigma weight residual 106.32 109.71 -3.39 1.61e+00 3.86e-01 4.43e+00 angle pdb=" C ILE A 479 " pdb=" N MET A 480 " pdb=" CA MET A 480 " ideal model delta sigma weight residual 122.74 119.25 3.49 2.44e+00 1.68e-01 2.05e+00 angle pdb=" CA PRO A 9 " pdb=" C PRO A 9 " pdb=" N SER A 10 " ideal model delta sigma weight residual 114.75 116.68 -1.93 1.45e+00 4.76e-01 1.78e+00 angle pdb=" C ARG A 423 " pdb=" CA ARG A 423 " pdb=" CB ARG A 423 " ideal model delta sigma weight residual 108.91 111.01 -2.10 1.65e+00 3.67e-01 1.62e+00 ... (remaining 7897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.83: 3279 10.83 - 21.66: 186 21.66 - 32.49: 51 32.49 - 43.32: 13 43.32 - 54.15: 3 Dihedral angle restraints: 3532 sinusoidal: 1466 harmonic: 2066 Sorted by residual: dihedral pdb=" N TYR A 485 " pdb=" CA TYR A 485 " pdb=" CB TYR A 485 " pdb=" CG TYR A 485 " ideal model delta sinusoidal sigma weight residual 60.00 114.15 -54.15 3 1.50e+01 4.44e-03 9.26e+00 dihedral pdb=" N ARG A 33 " pdb=" CA ARG A 33 " pdb=" CB ARG A 33 " pdb=" CG ARG A 33 " ideal model delta sinusoidal sigma weight residual -180.00 -127.29 -52.71 3 1.50e+01 4.44e-03 9.14e+00 dihedral pdb=" CA ARG A 33 " pdb=" CB ARG A 33 " pdb=" CG ARG A 33 " pdb=" CD ARG A 33 " ideal model delta sinusoidal sigma weight residual -180.00 -134.43 -45.57 3 1.50e+01 4.44e-03 8.19e+00 ... (remaining 3529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 434 0.025 - 0.050: 233 0.050 - 0.074: 73 0.074 - 0.099: 39 0.099 - 0.124: 23 Chirality restraints: 802 Sorted by residual: chirality pdb=" CA ILE A 479 " pdb=" N ILE A 479 " pdb=" C ILE A 479 " pdb=" CB ILE A 479 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CA ILE B 479 " pdb=" N ILE B 479 " pdb=" C ILE B 479 " pdb=" CB ILE B 479 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.69e-01 chirality pdb=" CA VAL A 62 " pdb=" N VAL A 62 " pdb=" C VAL A 62 " pdb=" CB VAL A 62 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.53e-01 ... (remaining 799 not shown) Planarity restraints: 1024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 442 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO B 443 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 443 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 443 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 456 " -0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO A 457 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 457 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 457 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 491 " -0.016 5.00e-02 4.00e+02 2.42e-02 9.36e-01 pdb=" N PRO B 492 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO B 492 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 492 " -0.013 5.00e-02 4.00e+02 ... (remaining 1021 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 350 2.74 - 3.28: 5618 3.28 - 3.82: 9529 3.82 - 4.36: 11107 4.36 - 4.90: 19281 Nonbonded interactions: 45885 Sorted by model distance: nonbonded pdb=" OE1 GLU A 387 " pdb=" OH TYR A 404 " model vdw 2.199 3.040 nonbonded pdb=" OE1 GLU B 387 " pdb=" OH TYR B 404 " model vdw 2.216 3.040 nonbonded pdb=" OD2 ASP B 491 " pdb=" OG SER B 493 " model vdw 2.224 3.040 nonbonded pdb=" OD1 ASP A 52 " pdb=" OH TYR A 405 " model vdw 2.250 3.040 nonbonded pdb=" OD1 ASP B 52 " pdb=" OH TYR B 405 " model vdw 2.254 3.040 ... (remaining 45880 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 7.220 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 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 : 0.002 0.037 5850 Z= 0.079 Angle : 1.218 49.160 7914 Z= 0.295 Chirality : 0.039 0.124 802 Planarity : 0.003 0.032 1024 Dihedral : 7.771 54.148 2212 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.47 % Allowed : 2.04 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.07 (0.32), residues: 688 helix: 0.69 (0.37), residues: 236 sheet: -0.23 (0.51), residues: 110 loop : -0.19 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 517 TYR 0.007 0.001 TYR B 369 PHE 0.006 0.001 PHE B 390 TRP 0.005 0.001 TRP A 345 HIS 0.003 0.000 HIS B 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00136 / 0.07 ( 5842) covalent geometry : angle 0.40051 / 0.21 ( 7902) hydrogen bonds : bond 0.17600 / 11.11 ( 221) hydrogen bonds : angle 7.07185 / 4.75 ( 600) metal coordination : bond 0.02023 / 1.56 ( 8) metal coordination : angle 29.55387 / 18.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 201 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.7276 (m110) cc_final: 0.5984 (m-40) REVERT: A 50 LEU cc_start: 0.8162 (mt) cc_final: 0.7945 (mp) REVERT: A 60 LYS cc_start: 0.8420 (mttm) cc_final: 0.7948 (mtpp) REVERT: A 69 GLN cc_start: 0.8706 (mt0) cc_final: 0.8367 (tp40) REVERT: A 92 LYS cc_start: 0.8121 (mttm) cc_final: 0.7884 (ptmt) REVERT: A 281 ASP cc_start: 0.7399 (t0) cc_final: 0.7177 (t70) REVERT: A 466 THR cc_start: 0.9333 (p) cc_final: 0.8980 (t) REVERT: A 467 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8506 (mm-30) REVERT: A 470 ARG cc_start: 0.8806 (mmt180) cc_final: 0.8210 (mmm-85) REVERT: A 495 GLU cc_start: 0.8969 (tt0) cc_final: 0.8721 (tm-30) REVERT: A 513 MET cc_start: 0.7586 (mtm) cc_final: 0.7374 (mtm) REVERT: B 13 ASP cc_start: 0.8350 (t0) cc_final: 0.7746 (t0) REVERT: B 74 GLN cc_start: 0.8789 (mt0) cc_final: 0.8548 (mt0) REVERT: B 92 LYS cc_start: 0.9135 (tttt) cc_final: 0.8370 (ttpp) REVERT: B 99 LYS cc_start: 0.9073 (tppt) cc_final: 0.8810 (tptp) REVERT: B 103 LYS cc_start: 0.8860 (mttm) cc_final: 0.8570 (tmmt) REVERT: B 270 LEU cc_start: 0.8563 (tp) cc_final: 0.8298 (tm) REVERT: B 271 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7680 (mm-30) REVERT: B 317 ARG cc_start: 0.8165 (mtp-110) cc_final: 0.7130 (tmt-80) REVERT: B 325 GLU cc_start: 0.8328 (tt0) cc_final: 0.8099 (mm-30) REVERT: B 416 MET cc_start: 0.8711 (mmt) cc_final: 0.8293 (mmp) outliers start: 3 outliers final: 1 residues processed: 203 average time/residue: 0.5045 time to fit residues: 106.9770 Evaluate side-chains 111 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.0030 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 ASN A 40 HIS ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 GLN A 489 GLN B 304 GLN ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 GLN B 472 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.100664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.086258 restraints weight = 12939.537| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 4.08 r_work: 0.3641 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5850 Z= 0.179 Angle : 1.078 43.128 7914 Z= 0.370 Chirality : 0.046 0.150 802 Planarity : 0.005 0.043 1024 Dihedral : 4.199 59.075 784 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.99 % Allowed : 14.15 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.06 (0.32), residues: 688 helix: 0.49 (0.35), residues: 232 sheet: -0.06 (0.52), residues: 106 loop : -0.30 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 477 TYR 0.018 0.002 TYR A 404 PHE 0.020 0.002 PHE B 292 TRP 0.008 0.001 TRP B 55 HIS 0.007 0.001 HIS B 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 5842) covalent geometry : angle 0.68581 / 0.34 ( 7902) hydrogen bonds : bond 0.04004 / 2.45 ( 221) hydrogen bonds : angle 4.99664 / 3.50 ( 600) metal coordination : bond 0.01178 / 0.99 ( 8) metal coordination : angle 21.38275 / 13.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8224 (mt) cc_final: 0.7919 (mp) REVERT: A 60 LYS cc_start: 0.8657 (mttm) cc_final: 0.8215 (mtpt) REVERT: A 92 LYS cc_start: 0.8293 (mttm) cc_final: 0.7887 (ttpp) REVERT: A 99 LYS cc_start: 0.8629 (tptp) cc_final: 0.8261 (mmmm) REVERT: A 400 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8592 (tp-100) REVERT: A 418 TYR cc_start: 0.7986 (p90) cc_final: 0.7695 (p90) REVERT: A 419 LYS cc_start: 0.8567 (mttt) cc_final: 0.8138 (ptpp) REVERT: A 466 THR cc_start: 0.9375 (p) cc_final: 0.9166 (t) REVERT: A 467 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8585 (mm-30) REVERT: A 470 ARG cc_start: 0.8862 (mmt180) cc_final: 0.8494 (mmm-85) REVERT: A 513 MET cc_start: 0.7381 (mtm) cc_final: 0.7113 (mtm) REVERT: B 13 ASP cc_start: 0.8477 (t0) cc_final: 0.8153 (t0) REVERT: B 60 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8161 (mmmm) REVERT: B 92 LYS cc_start: 0.8952 (tttt) cc_final: 0.8392 (ttpp) REVERT: B 99 LYS cc_start: 0.9008 (tppt) cc_final: 0.8795 (tptp) REVERT: B 103 LYS cc_start: 0.8972 (mttm) cc_final: 0.8651 (tptp) REVERT: B 270 LEU cc_start: 0.8594 (tp) cc_final: 0.8285 (tm) REVERT: B 271 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7845 (mm-30) REVERT: B 325 GLU cc_start: 0.8623 (tt0) cc_final: 0.8230 (mm-30) REVERT: B 416 MET cc_start: 0.8652 (mmt) cc_final: 0.8195 (mmp) REVERT: B 477 ARG cc_start: 0.7812 (mtm110) cc_final: 0.7072 (ttp-110) REVERT: B 480 MET cc_start: 0.7435 (ptp) cc_final: 0.7194 (ptp) outliers start: 19 outliers final: 7 residues processed: 115 average time/residue: 0.5915 time to fit residues: 71.0101 Evaluate side-chains 91 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 400 GLN Chi-restraints excluded: chain A residue 485 TYR Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 460 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 0.0170 chunk 59 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.098375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.083360 restraints weight = 13170.160| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 4.20 r_work: 0.3599 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5850 Z= 0.154 Angle : 1.000 42.619 7914 Z= 0.343 Chirality : 0.047 0.387 802 Planarity : 0.004 0.037 1024 Dihedral : 4.045 50.378 784 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.93 % Allowed : 13.05 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.32), residues: 688 helix: 0.32 (0.35), residues: 236 sheet: -0.42 (0.49), residues: 118 loop : -0.30 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 517 TYR 0.015 0.001 TYR A 404 PHE 0.015 0.002 PHE B 15 TRP 0.009 0.002 TRP B 38 HIS 0.007 0.001 HIS B 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 5842) covalent geometry : angle 0.62576 / 0.31 ( 7902) hydrogen bonds : bond 0.03697 / 2.21 ( 221) hydrogen bonds : angle 4.87280 / 3.46 ( 600) metal coordination : bond 0.00913 / 0.67 ( 8) metal coordination : angle 20.05355 / 12.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8134 (mt) cc_final: 0.7815 (mp) REVERT: A 60 LYS cc_start: 0.8714 (mttm) cc_final: 0.8368 (mtpp) REVERT: A 64 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.6832 (tptm) REVERT: A 92 LYS cc_start: 0.8014 (mttm) cc_final: 0.7748 (ttpp) REVERT: A 99 LYS cc_start: 0.8430 (tptp) cc_final: 0.8188 (mmmm) REVERT: A 400 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8630 (tp-100) REVERT: A 416 MET cc_start: 0.8810 (ppp) cc_final: 0.8545 (ppp) REVERT: A 464 ARG cc_start: 0.8632 (ttp80) cc_final: 0.8423 (ptm-80) REVERT: A 466 THR cc_start: 0.9397 (p) cc_final: 0.9136 (t) REVERT: A 467 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8725 (mm-30) REVERT: A 495 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8421 (tm-30) REVERT: A 499 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8708 (mp) REVERT: B 13 ASP cc_start: 0.8413 (t0) cc_final: 0.8203 (t0) REVERT: B 60 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8223 (mmmm) REVERT: B 92 LYS cc_start: 0.9104 (tttt) cc_final: 0.8791 (ptmm) REVERT: B 99 LYS cc_start: 0.9011 (tppt) cc_final: 0.8742 (tptp) REVERT: B 103 LYS cc_start: 0.8910 (mttm) cc_final: 0.8685 (tptp) REVERT: B 270 LEU cc_start: 0.8436 (tp) cc_final: 0.8131 (tt) REVERT: B 271 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7895 (mm-30) REVERT: B 273 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6960 (mpt-90) REVERT: B 325 GLU cc_start: 0.8690 (tt0) cc_final: 0.8273 (mm-30) REVERT: B 416 MET cc_start: 0.8770 (mmt) cc_final: 0.8343 (mmp) REVERT: B 477 ARG cc_start: 0.7898 (mtm110) cc_final: 0.7264 (ttt-90) REVERT: B 480 MET cc_start: 0.7428 (ptp) cc_final: 0.7201 (ptp) outliers start: 25 outliers final: 10 residues processed: 106 average time/residue: 0.5532 time to fit residues: 61.5650 Evaluate side-chains 96 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 400 GLN Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 518 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 10 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN B 303 HIS B 331 ASN ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.096262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.081259 restraints weight = 13382.968| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 4.20 r_work: 0.3560 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5850 Z= 0.167 Angle : 0.972 41.702 7914 Z= 0.337 Chirality : 0.046 0.224 802 Planarity : 0.004 0.041 1024 Dihedral : 3.652 14.297 782 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.09 % Allowed : 13.99 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.32), residues: 688 helix: 0.34 (0.35), residues: 234 sheet: -0.53 (0.49), residues: 118 loop : -0.27 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 22 TYR 0.020 0.002 TYR A 422 PHE 0.020 0.002 PHE B 15 TRP 0.012 0.002 TRP B 38 HIS 0.006 0.001 HIS B 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 ( 5842) covalent geometry : angle 0.62344 / 0.31 ( 7902) hydrogen bonds : bond 0.03537 / 2.10 ( 221) hydrogen bonds : angle 4.93074 / 3.51 ( 600) metal coordination : bond 0.01034 / 0.74 ( 8) metal coordination : angle 19.14802 / 11.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7677 (OUTLIER) cc_final: 0.7288 (t-100) REVERT: A 50 LEU cc_start: 0.8204 (mt) cc_final: 0.7877 (mp) REVERT: A 60 LYS cc_start: 0.8734 (mttm) cc_final: 0.8372 (mtpt) REVERT: A 67 MET cc_start: 0.8787 (mmt) cc_final: 0.8351 (mmt) REVERT: A 99 LYS cc_start: 0.8549 (tptp) cc_final: 0.8317 (mmmm) REVERT: A 419 LYS cc_start: 0.8513 (mttt) cc_final: 0.8123 (mtmm) REVERT: A 466 THR cc_start: 0.9438 (p) cc_final: 0.9180 (t) REVERT: A 467 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8738 (mm-30) REVERT: A 495 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8389 (tm-30) REVERT: A 499 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8710 (mp) REVERT: B 13 ASP cc_start: 0.8289 (t0) cc_final: 0.8049 (t0) REVERT: B 60 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8233 (mmmm) REVERT: B 92 LYS cc_start: 0.9079 (tttt) cc_final: 0.8618 (ptmm) REVERT: B 99 LYS cc_start: 0.9041 (tppt) cc_final: 0.8755 (tptp) REVERT: B 103 LYS cc_start: 0.9054 (mttm) cc_final: 0.8745 (tptp) REVERT: B 271 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7809 (mm-30) REVERT: B 273 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7007 (mpt-90) REVERT: B 325 GLU cc_start: 0.8744 (tt0) cc_final: 0.8359 (mp0) REVERT: B 392 ARG cc_start: 0.7815 (ttm170) cc_final: 0.7228 (mtt-85) REVERT: B 416 MET cc_start: 0.8808 (mmt) cc_final: 0.8338 (mmp) REVERT: B 477 ARG cc_start: 0.7885 (mtm110) cc_final: 0.7281 (ttp-170) REVERT: B 480 MET cc_start: 0.7513 (ptp) cc_final: 0.7246 (ptp) outliers start: 26 outliers final: 11 residues processed: 102 average time/residue: 0.5307 time to fit residues: 56.8512 Evaluate side-chains 92 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 38 TRP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 460 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 60 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.093929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.078963 restraints weight = 13774.242| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 4.20 r_work: 0.3517 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5850 Z= 0.184 Angle : 0.888 35.743 7914 Z= 0.339 Chirality : 0.047 0.297 802 Planarity : 0.004 0.043 1024 Dihedral : 3.814 14.723 782 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.93 % Allowed : 15.57 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.33 (0.32), residues: 688 helix: 0.42 (0.36), residues: 228 sheet: -0.90 (0.46), residues: 120 loop : -0.26 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 464 TYR 0.015 0.001 TYR B 404 PHE 0.016 0.002 PHE A 408 TRP 0.013 0.002 TRP A 55 HIS 0.006 0.001 HIS B 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 5842) covalent geometry : angle 0.65209 / 0.32 ( 7902) hydrogen bonds : bond 0.03634 / 2.21 ( 221) hydrogen bonds : angle 5.08242 / 3.60 ( 600) metal coordination : bond 0.01375 / 0.91 ( 8) metal coordination : angle 15.48986 / 10.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7792 (OUTLIER) cc_final: 0.7138 (t-100) REVERT: A 50 LEU cc_start: 0.8287 (mt) cc_final: 0.7971 (mp) REVERT: A 60 LYS cc_start: 0.8693 (mttm) cc_final: 0.8344 (mtpt) REVERT: A 99 LYS cc_start: 0.8649 (tptp) cc_final: 0.8402 (tptp) REVERT: A 353 VAL cc_start: 0.8645 (t) cc_final: 0.8340 (t) REVERT: A 419 LYS cc_start: 0.8516 (mttt) cc_final: 0.8102 (mtmm) REVERT: A 466 THR cc_start: 0.9377 (p) cc_final: 0.9172 (t) REVERT: A 467 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8893 (mm-30) REVERT: A 480 MET cc_start: 0.7495 (ppp) cc_final: 0.6751 (pp-130) REVERT: A 495 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8441 (tm-30) REVERT: A 499 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8718 (mp) REVERT: B 13 ASP cc_start: 0.8404 (t0) cc_final: 0.8133 (t0) REVERT: B 60 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8108 (mmmm) REVERT: B 92 LYS cc_start: 0.9100 (tttt) cc_final: 0.8730 (ptmm) REVERT: B 97 MET cc_start: 0.8734 (tmm) cc_final: 0.8523 (tmm) REVERT: B 99 LYS cc_start: 0.9056 (tppt) cc_final: 0.8794 (tptp) REVERT: B 103 LYS cc_start: 0.9064 (mttm) cc_final: 0.8801 (tptp) REVERT: B 271 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7798 (mm-30) REVERT: B 273 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7045 (mpt-90) REVERT: B 325 GLU cc_start: 0.8773 (tt0) cc_final: 0.8330 (mp0) REVERT: B 392 ARG cc_start: 0.7822 (ttm170) cc_final: 0.7283 (mtt-85) REVERT: B 406 MET cc_start: 0.7951 (mmm) cc_final: 0.7640 (mmm) REVERT: B 416 MET cc_start: 0.8836 (mmt) cc_final: 0.8382 (mmp) outliers start: 25 outliers final: 11 residues processed: 101 average time/residue: 0.4670 time to fit residues: 49.5962 Evaluate side-chains 90 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 38 TRP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 460 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 GLN B 400 GLN ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.093236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.078757 restraints weight = 13682.008| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 4.03 r_work: 0.3521 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5850 Z= 0.181 Angle : 0.715 17.922 7914 Z= 0.328 Chirality : 0.049 0.307 802 Planarity : 0.004 0.046 1024 Dihedral : 3.903 18.821 782 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.62 % Allowed : 15.88 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.40 (0.32), residues: 688 helix: 0.47 (0.36), residues: 228 sheet: -1.02 (0.46), residues: 120 loop : -0.36 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 464 TYR 0.014 0.001 TYR B 404 PHE 0.016 0.002 PHE A 408 TRP 0.013 0.002 TRP B 38 HIS 0.006 0.001 HIS B 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 ( 5842) covalent geometry : angle 0.65654 / 0.32 ( 7902) hydrogen bonds : bond 0.03601 / 2.18 ( 221) hydrogen bonds : angle 5.09990 / 3.64 ( 600) metal coordination : bond 0.00981 / 0.60 ( 8) metal coordination : angle 7.31380 / 4.87 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7790 (OUTLIER) cc_final: 0.7240 (t-100) REVERT: A 50 LEU cc_start: 0.8345 (mt) cc_final: 0.7978 (mt) REVERT: A 55 TRP cc_start: 0.8186 (m100) cc_final: 0.7973 (m100) REVERT: A 60 LYS cc_start: 0.8669 (mttm) cc_final: 0.8300 (mtpp) REVERT: A 99 LYS cc_start: 0.8789 (tptp) cc_final: 0.8541 (tptp) REVERT: A 419 LYS cc_start: 0.8530 (mttt) cc_final: 0.8159 (mtmm) REVERT: A 433 TYR cc_start: 0.7968 (m-80) cc_final: 0.7489 (m-80) REVERT: A 466 THR cc_start: 0.9428 (p) cc_final: 0.9216 (t) REVERT: A 467 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8857 (mm-30) REVERT: A 480 MET cc_start: 0.7453 (ppp) cc_final: 0.7170 (pp-130) REVERT: A 495 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8410 (tm-30) REVERT: A 499 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8740 (mp) REVERT: B 13 ASP cc_start: 0.8453 (t0) cc_final: 0.8215 (t0) REVERT: B 60 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8134 (mmmm) REVERT: B 92 LYS cc_start: 0.9176 (tttt) cc_final: 0.8852 (ptmm) REVERT: B 99 LYS cc_start: 0.9150 (tppt) cc_final: 0.8807 (tptp) REVERT: B 103 LYS cc_start: 0.9082 (mttm) cc_final: 0.8826 (tptp) REVERT: B 271 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7863 (mm-30) REVERT: B 273 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.6952 (mpt-90) REVERT: B 325 GLU cc_start: 0.8872 (tt0) cc_final: 0.8564 (mt-10) REVERT: B 406 MET cc_start: 0.7641 (mmm) cc_final: 0.7331 (mmm) REVERT: B 416 MET cc_start: 0.8841 (mmt) cc_final: 0.8411 (mmp) outliers start: 23 outliers final: 11 residues processed: 86 average time/residue: 0.5186 time to fit residues: 46.9776 Evaluate side-chains 88 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 38 TRP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 460 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 23 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 0.0470 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.094935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.080540 restraints weight = 13789.373| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 4.09 r_work: 0.3552 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5850 Z= 0.120 Angle : 0.676 14.388 7914 Z= 0.315 Chirality : 0.047 0.292 802 Planarity : 0.004 0.045 1024 Dihedral : 3.845 21.150 782 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.46 % Allowed : 16.04 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.32), residues: 688 helix: 0.57 (0.36), residues: 226 sheet: -1.07 (0.45), residues: 128 loop : -0.26 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 464 TYR 0.024 0.001 TYR A 422 PHE 0.019 0.001 PHE B 516 TRP 0.016 0.001 TRP B 38 HIS 0.005 0.001 HIS B 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 5842) covalent geometry : angle 0.64139 / 0.31 ( 7902) hydrogen bonds : bond 0.03426 / 2.09 ( 221) hydrogen bonds : angle 5.10589 / 3.66 ( 600) metal coordination : bond 0.00786 / 0.47 ( 8) metal coordination : angle 5.52197 / 3.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8307 (mt) cc_final: 0.7957 (mt) REVERT: A 60 LYS cc_start: 0.8583 (mttm) cc_final: 0.8308 (mtpp) REVERT: A 99 LYS cc_start: 0.8773 (tptp) cc_final: 0.8392 (tptp) REVERT: A 318 PHE cc_start: 0.7043 (OUTLIER) cc_final: 0.6329 (m-10) REVERT: A 401 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8235 (tm) REVERT: A 419 LYS cc_start: 0.8475 (mttt) cc_final: 0.8122 (mtmm) REVERT: A 433 TYR cc_start: 0.7910 (m-80) cc_final: 0.7433 (m-80) REVERT: A 466 THR cc_start: 0.9432 (p) cc_final: 0.9197 (t) REVERT: A 467 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8803 (mm-30) REVERT: A 480 MET cc_start: 0.7346 (ppp) cc_final: 0.6162 (pp-130) REVERT: A 495 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8436 (tm-30) REVERT: A 499 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8717 (mp) REVERT: B 92 LYS cc_start: 0.9180 (tttt) cc_final: 0.8800 (ptmm) REVERT: B 99 LYS cc_start: 0.9158 (tppt) cc_final: 0.8796 (tptp) REVERT: B 271 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7818 (mm-30) REVERT: B 273 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6951 (mpt-90) REVERT: B 325 GLU cc_start: 0.8855 (tt0) cc_final: 0.8453 (mp0) REVERT: B 392 ARG cc_start: 0.7850 (ttm170) cc_final: 0.7530 (mtt-85) REVERT: B 406 MET cc_start: 0.7682 (mmm) cc_final: 0.7436 (mmm) REVERT: B 416 MET cc_start: 0.8845 (mmt) cc_final: 0.8448 (mmp) REVERT: B 477 ARG cc_start: 0.7769 (mtm110) cc_final: 0.7098 (ttt-90) outliers start: 22 outliers final: 9 residues processed: 95 average time/residue: 0.4712 time to fit residues: 47.2173 Evaluate side-chains 88 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 460 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 0.0030 chunk 39 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 4 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.0264 > 50:) chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.095018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.081190 restraints weight = 13491.181| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 3.96 r_work: 0.3562 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5850 Z= 0.125 Angle : 0.667 10.618 7914 Z= 0.318 Chirality : 0.047 0.277 802 Planarity : 0.004 0.044 1024 Dihedral : 3.873 21.185 782 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.83 % Allowed : 17.14 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.20 (0.32), residues: 688 helix: 0.61 (0.36), residues: 226 sheet: -0.69 (0.52), residues: 100 loop : -0.35 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 464 TYR 0.031 0.001 TYR A 485 PHE 0.020 0.001 PHE B 516 TRP 0.017 0.002 TRP B 38 HIS 0.004 0.001 HIS B 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 5842) covalent geometry : angle 0.64540 / 0.32 ( 7902) hydrogen bonds : bond 0.03360 / 2.06 ( 221) hydrogen bonds : angle 5.08696 / 3.66 ( 600) metal coordination : bond 0.00609 / 0.37 ( 8) metal coordination : angle 4.38963 / 2.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7290 (OUTLIER) cc_final: 0.6929 (m-90) REVERT: A 50 LEU cc_start: 0.8302 (mt) cc_final: 0.7840 (mt) REVERT: A 60 LYS cc_start: 0.8535 (mttm) cc_final: 0.7949 (tttp) REVERT: A 99 LYS cc_start: 0.8833 (tptp) cc_final: 0.8505 (tptp) REVERT: A 325 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8198 (mp0) REVERT: A 401 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8142 (tm) REVERT: A 406 MET cc_start: 0.7965 (mmm) cc_final: 0.7706 (mmm) REVERT: A 419 LYS cc_start: 0.8437 (mttt) cc_final: 0.8090 (mtmm) REVERT: A 433 TYR cc_start: 0.7902 (m-80) cc_final: 0.7441 (m-80) REVERT: A 466 THR cc_start: 0.9410 (p) cc_final: 0.9136 (t) REVERT: A 467 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8783 (mm-30) REVERT: A 480 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6109 (pp-130) REVERT: A 495 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8427 (tm-30) REVERT: A 499 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8734 (mp) REVERT: B 92 LYS cc_start: 0.9201 (tttt) cc_final: 0.8846 (ptmm) REVERT: B 99 LYS cc_start: 0.9181 (tppt) cc_final: 0.8837 (tptp) REVERT: B 271 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7805 (mm-30) REVERT: B 273 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.6988 (mpt-90) REVERT: B 325 GLU cc_start: 0.8826 (tt0) cc_final: 0.8421 (mp0) REVERT: B 406 MET cc_start: 0.7636 (mmm) cc_final: 0.7256 (mmm) REVERT: B 416 MET cc_start: 0.8793 (mmt) cc_final: 0.8384 (mmp) outliers start: 18 outliers final: 9 residues processed: 88 average time/residue: 0.4962 time to fit residues: 46.0332 Evaluate side-chains 86 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TRP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 460 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 16 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.094469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.080461 restraints weight = 13598.437| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 4.02 r_work: 0.3550 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5850 Z= 0.135 Angle : 0.681 11.954 7914 Z= 0.323 Chirality : 0.048 0.339 802 Planarity : 0.004 0.042 1024 Dihedral : 3.834 22.630 782 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.83 % Allowed : 17.45 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 (0.32), residues: 688 helix: 0.64 (0.36), residues: 226 sheet: -0.70 (0.52), residues: 100 loop : -0.36 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 464 TYR 0.025 0.001 TYR A 485 PHE 0.017 0.001 PHE B 516 TRP 0.016 0.002 TRP B 38 HIS 0.003 0.001 HIS B 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 5842) covalent geometry : angle 0.66343 / 0.32 ( 7902) hydrogen bonds : bond 0.03417 / 2.08 ( 221) hydrogen bonds : angle 5.10103 / 3.64 ( 600) metal coordination : bond 0.00616 / 0.38 ( 8) metal coordination : angle 3.99460 / 2.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7324 (OUTLIER) cc_final: 0.6925 (m-90) REVERT: A 50 LEU cc_start: 0.8287 (mt) cc_final: 0.7814 (mt) REVERT: A 60 LYS cc_start: 0.8508 (mttm) cc_final: 0.7936 (tttp) REVERT: A 99 LYS cc_start: 0.8834 (tptp) cc_final: 0.8530 (tptp) REVERT: A 318 PHE cc_start: 0.7060 (OUTLIER) cc_final: 0.6450 (m-10) REVERT: A 325 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8167 (mp0) REVERT: A 401 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8169 (tm) REVERT: A 406 MET cc_start: 0.8188 (mmm) cc_final: 0.7965 (mmm) REVERT: A 419 LYS cc_start: 0.8457 (mttt) cc_final: 0.8055 (mtmm) REVERT: A 433 TYR cc_start: 0.7925 (m-80) cc_final: 0.7487 (m-80) REVERT: A 466 THR cc_start: 0.9400 (p) cc_final: 0.9099 (t) REVERT: A 467 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8788 (mm-30) REVERT: A 480 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6148 (pp-130) REVERT: A 495 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8436 (tm-30) REVERT: A 499 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8729 (mp) REVERT: B 92 LYS cc_start: 0.9219 (tttt) cc_final: 0.8867 (ptmm) REVERT: B 99 LYS cc_start: 0.9151 (tppt) cc_final: 0.8799 (tptp) REVERT: B 271 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7823 (mm-30) REVERT: B 273 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7014 (mpt-90) REVERT: B 406 MET cc_start: 0.7714 (mmm) cc_final: 0.7369 (mmm) REVERT: B 416 MET cc_start: 0.8802 (mmt) cc_final: 0.8354 (mmp) REVERT: B 477 ARG cc_start: 0.7767 (mtm110) cc_final: 0.7090 (ttt-90) REVERT: B 480 MET cc_start: 0.7635 (ptp) cc_final: 0.7156 (pmm) outliers start: 18 outliers final: 8 residues processed: 85 average time/residue: 0.5225 time to fit residues: 46.7398 Evaluate side-chains 89 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TRP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 21 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.094238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.080403 restraints weight = 13749.428| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 3.97 r_work: 0.3544 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5850 Z= 0.138 Angle : 0.697 12.048 7914 Z= 0.330 Chirality : 0.048 0.315 802 Planarity : 0.004 0.046 1024 Dihedral : 3.855 21.925 782 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.20 % Allowed : 18.24 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.08 (0.32), residues: 688 helix: 0.77 (0.37), residues: 214 sheet: -0.72 (0.52), residues: 100 loop : -0.25 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 78 TYR 0.023 0.001 TYR A 485 PHE 0.017 0.001 PHE B 516 TRP 0.017 0.002 TRP B 38 HIS 0.003 0.001 HIS B 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 5842) covalent geometry : angle 0.68231 / 0.33 ( 7902) hydrogen bonds : bond 0.03520 / 2.17 ( 221) hydrogen bonds : angle 5.14677 / 3.68 ( 600) metal coordination : bond 0.00581 / 0.37 ( 8) metal coordination : angle 3.72448 / 2.56 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASN cc_start: 0.8132 (t0) cc_final: 0.7855 (t0) REVERT: A 38 TRP cc_start: 0.7257 (OUTLIER) cc_final: 0.6962 (m-90) REVERT: A 50 LEU cc_start: 0.8267 (mt) cc_final: 0.7808 (mt) REVERT: A 60 LYS cc_start: 0.8537 (mttm) cc_final: 0.7979 (tttp) REVERT: A 99 LYS cc_start: 0.8943 (tptp) cc_final: 0.8672 (tptp) REVERT: A 318 PHE cc_start: 0.7127 (OUTLIER) cc_final: 0.6686 (m-10) REVERT: A 325 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8148 (mp0) REVERT: A 401 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8231 (tm) REVERT: A 419 LYS cc_start: 0.8480 (mttt) cc_final: 0.8038 (mtmm) REVERT: A 433 TYR cc_start: 0.7906 (m-80) cc_final: 0.7467 (m-80) REVERT: A 480 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6118 (pp-130) REVERT: A 495 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8455 (tm-30) REVERT: A 499 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8721 (mp) REVERT: B 92 LYS cc_start: 0.9242 (tttt) cc_final: 0.8890 (ptmm) REVERT: B 99 LYS cc_start: 0.9223 (tppt) cc_final: 0.8820 (tptp) REVERT: B 271 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7904 (mm-30) REVERT: B 273 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7014 (mpt-90) REVERT: B 406 MET cc_start: 0.7748 (mmm) cc_final: 0.7413 (mmm) REVERT: B 416 MET cc_start: 0.8820 (mmt) cc_final: 0.8371 (mmp) REVERT: B 477 ARG cc_start: 0.7772 (mtm110) cc_final: 0.7094 (ttt-90) outliers start: 14 outliers final: 8 residues processed: 85 average time/residue: 0.4890 time to fit residues: 43.9410 Evaluate side-chains 88 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TRP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 49 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 26 optimal weight: 0.0870 chunk 23 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.096007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.081764 restraints weight = 13441.216| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 4.02 r_work: 0.3579 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5850 Z= 0.121 Angle : 0.703 11.793 7914 Z= 0.332 Chirality : 0.048 0.306 802 Planarity : 0.004 0.048 1024 Dihedral : 3.850 20.298 782 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.36 % Allowed : 18.55 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.12 (0.32), residues: 688 helix: 0.66 (0.36), residues: 226 sheet: -0.71 (0.52), residues: 100 loop : -0.27 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 78 TYR 0.023 0.001 TYR A 485 PHE 0.013 0.001 PHE A 408 TRP 0.018 0.002 TRP B 55 HIS 0.003 0.001 HIS B 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 5842) covalent geometry : angle 0.69252 / 0.33 ( 7902) hydrogen bonds : bond 0.03449 / 2.08 ( 221) hydrogen bonds : angle 5.17878 / 3.69 ( 600) metal coordination : bond 0.00415 / 0.27 ( 8) metal coordination : angle 3.13810 / 2.09 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1946.41 seconds wall clock time: 34 minutes 0.54 seconds (2040.54 seconds total)