Starting phenix.real_space_refine on Thu Jun 5 08:42:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tzv_41770/06_2025/8tzv_41770.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tzv_41770/06_2025/8tzv_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tzv_41770/06_2025/8tzv_41770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tzv_41770/06_2025/8tzv_41770.map" model { file = "/net/cci-nas-00/data/ceres_data/8tzv_41770/06_2025/8tzv_41770.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tzv_41770/06_2025/8tzv_41770.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 3.70, per 1000 atoms: 0.65 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: 1.29 Conformation dependent library (CDL) restraints added in 748.3 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: 0.67 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: 1.87 Time building geometry restraints manager: 1.56 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: 0.04 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: 0.550 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.440 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.001 TRP A 345 HIS 0.003 0.000 HIS B 395 PHE 0.006 0.001 PHE B 390 TYR 0.007 0.001 TYR B 369 ARG 0.001 0.000 ARG B 517 Details of bonding type rmsd hydrogen bonds : bond 0.17600 ( 221) hydrogen bonds : angle 7.07185 ( 600) metal coordination : bond 0.02023 ( 8) metal coordination : angle 29.55387 ( 12) covalent geometry : bond 0.00136 ( 5842) covalent geometry : angle 0.40051 ( 7902) *********************** 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 : 0.687 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: 0.7941 (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: 0.8979 (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: 0.7373 (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: 0.8574 (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: 0.8299 (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: 0.7114 (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: 0.8296 (mmp) REVERT: B 500 GLN cc_start: 0.8638 (mt0) cc_final: 0.8287 (tp-100) outliers start: 3 outliers final: 1 residues processed: 203 average time/residue: 1.1164 time to fit residues: 236.5577 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 : 0.694 ------------------------------------------------------------------------------- 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 57 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 40 HIS A 83 GLN ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 GLN A 489 GLN B 35 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.102977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.089227 restraints weight = 12573.456| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 3.85 r_work: 0.3697 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3180 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= 0.155 Angle : 1.070 42.953 7914 Z= 0.358 Chirality : 0.045 0.161 802 Planarity : 0.005 0.050 1024 Dihedral : 4.016 57.192 784 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.83 % Allowed : 14.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.32), residues: 688 helix: 0.55 (0.35), residues: 232 sheet: -0.07 (0.53), residues: 108 loop : -0.24 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 55 HIS 0.007 0.001 HIS B 395 PHE 0.016 0.002 PHE B 292 TYR 0.018 0.001 TYR A 404 ARG 0.007 0.001 ARG B 477 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 221) hydrogen bonds : angle 4.98334 ( 600) metal coordination : bond 0.01233 ( 8) metal coordination : angle 21.66020 ( 12) covalent geometry : bond 0.00335 ( 5842) covalent geometry : angle 0.65849 ( 7902) *********************** 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 128 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.700 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: 0.8258 (mt) cc_final: 0.8001 (mp) REVERT: A 60 LYS cc_start: 0.8650 (mttm) cc_final: 0.8222 (mtpp) REVERT: A 92 LYS cc_start: 0.8279 (mttm) cc_final: 0.7774 (ptmt) REVERT: A 99 LYS cc_start: 0.8595 (tptp) cc_final: 0.8242 (mmmm) REVERT: A 400 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8549 (tp-100) REVERT: A 416 MET cc_start: 0.8628 (ppp) cc_final: 0.8219 (ppp) REVERT: A 418 TYR cc_start: 0.7945 (p90) cc_final: 0.7672 (p90) REVERT: A 419 LYS cc_start: 0.8568 (mttt) cc_final: 0.8137 (ptpp) REVERT: A 466 THR cc_start: 0.9324 (p) cc_final: 0.8864 (t) REVERT: A 467 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8403 (mm-30) REVERT: A 470 ARG cc_start: 0.8884 (mmt180) cc_final: 0.8540 (mmm-85) REVERT: B 13 ASP cc_start: 0.8476 (t0) cc_final: 0.8206 (t0) REVERT: B 60 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8129 (mmmm) REVERT: B 92 LYS cc_start: 0.8931 (tttt) cc_final: 0.8349 (ttpp) REVERT: B 99 LYS cc_start: 0.8986 (tppt) cc_final: 0.8754 (tptp) REVERT: B 270 LEU cc_start: 0.8613 (tp) cc_final: 0.8280 (tm) REVERT: B 271 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7656 (mm-30) REVERT: B 317 ARG cc_start: 0.7385 (mtp-110) cc_final: 0.7154 (tpt90) REVERT: B 325 GLU cc_start: 0.8638 (tt0) cc_final: 0.8262 (mm-30) REVERT: B 416 MET cc_start: 0.8591 (mmt) cc_final: 0.8120 (mmp) REVERT: B 480 MET cc_start: 0.7605 (ptp) cc_final: 0.7384 (ptp) outliers start: 18 outliers final: 6 residues processed: 119 average time/residue: 1.2621 time to fit residues: 156.9157 Evaluate side-chains 92 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 77 ILE 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 342 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 44 optimal weight: 2.9990 chunk 58 optimal weight: 0.0170 chunk 5 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 65 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 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 = 0.4071 r_free = 0.4071 target = 0.102625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.087426 restraints weight = 12872.417| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 4.22 r_work: 0.3677 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5850 Z= 0.119 Angle : 0.993 42.512 7914 Z= 0.333 Chirality : 0.047 0.402 802 Planarity : 0.004 0.034 1024 Dihedral : 4.026 56.264 784 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.46 % Allowed : 13.99 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.32), residues: 688 helix: 0.48 (0.36), residues: 234 sheet: -0.22 (0.49), residues: 118 loop : -0.31 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 55 HIS 0.007 0.001 HIS B 341 PHE 0.014 0.001 PHE A 408 TYR 0.014 0.001 TYR A 404 ARG 0.004 0.000 ARG B 477 Details of bonding type rmsd hydrogen bonds : bond 0.03458 ( 221) hydrogen bonds : angle 4.76970 ( 600) metal coordination : bond 0.00880 ( 8) metal coordination : angle 20.04152 ( 12) covalent geometry : bond 0.00277 ( 5842) covalent geometry : angle 0.61396 ( 7902) *********************** 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 116 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.710 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 28 ASN cc_start: 0.8460 (t0) cc_final: 0.8209 (t0) REVERT: A 38 TRP cc_start: 0.7769 (OUTLIER) cc_final: 0.7370 (t-100) REVERT: A 50 LEU cc_start: 0.8103 (mt) cc_final: 0.7875 (mp) REVERT: A 60 LYS cc_start: 0.8700 (mttm) cc_final: 0.8265 (mtpp) REVERT: A 92 LYS cc_start: 0.8135 (mttm) cc_final: 0.7592 (ttpp) REVERT: A 99 LYS cc_start: 0.8381 (tptp) cc_final: 0.8141 (mmmm) REVERT: A 400 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8617 (tp-100) REVERT: A 464 ARG cc_start: 0.8509 (ttp80) cc_final: 0.8304 (ptm-80) REVERT: A 466 THR cc_start: 0.9367 (p) cc_final: 0.8910 (t) REVERT: A 467 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8463 (mm-30) REVERT: A 470 ARG cc_start: 0.8833 (mmt180) cc_final: 0.8432 (mmm-85) REVERT: A 495 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8367 (tm-30) REVERT: A 499 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8673 (mp) REVERT: B 11 VAL cc_start: 0.8855 (t) cc_final: 0.8551 (p) REVERT: B 13 ASP cc_start: 0.8411 (t0) cc_final: 0.8175 (t0) REVERT: B 60 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8206 (mmmm) REVERT: B 92 LYS cc_start: 0.9024 (tttt) cc_final: 0.8713 (ptmm) REVERT: B 99 LYS cc_start: 0.9055 (tppt) cc_final: 0.8739 (tptp) REVERT: B 270 LEU cc_start: 0.8586 (tp) cc_final: 0.8290 (tm) REVERT: B 271 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7614 (mm-30) REVERT: B 317 ARG cc_start: 0.7705 (mtp-110) cc_final: 0.7175 (tmt-80) REVERT: B 325 GLU cc_start: 0.8697 (tt0) cc_final: 0.8291 (mm-30) REVERT: B 416 MET cc_start: 0.8626 (mmt) cc_final: 0.8173 (mmp) REVERT: B 433 TYR cc_start: 0.8153 (m-80) cc_final: 0.7777 (m-80) outliers start: 22 outliers final: 7 residues processed: 105 average time/residue: 1.0937 time to fit residues: 121.0518 Evaluate side-chains 97 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TRP Chi-restraints excluded: chain A residue 77 ILE 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 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 460 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 42 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 63 optimal weight: 0.1980 chunk 38 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 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** B 500 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.100880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.085460 restraints weight = 13390.360| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 4.34 r_work: 0.3632 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5850 Z= 0.117 Angle : 0.922 41.548 7914 Z= 0.313 Chirality : 0.045 0.258 802 Planarity : 0.004 0.044 1024 Dihedral : 3.473 12.007 782 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.46 % Allowed : 13.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.32), residues: 688 helix: 0.50 (0.36), residues: 234 sheet: -0.24 (0.49), residues: 118 loop : -0.29 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 55 HIS 0.006 0.001 HIS B 341 PHE 0.016 0.001 PHE A 408 TYR 0.014 0.001 TYR A 382 ARG 0.002 0.000 ARG B 477 Details of bonding type rmsd hydrogen bonds : bond 0.03245 ( 221) hydrogen bonds : angle 4.59946 ( 600) metal coordination : bond 0.00875 ( 8) metal coordination : angle 18.45328 ( 12) covalent geometry : bond 0.00266 ( 5842) covalent geometry : angle 0.57850 ( 7902) *********************** 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 111 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7630 (OUTLIER) cc_final: 0.7211 (t-100) REVERT: A 50 LEU cc_start: 0.8174 (mt) cc_final: 0.7913 (mp) REVERT: A 60 LYS cc_start: 0.8668 (mttm) cc_final: 0.8295 (mtpt) REVERT: A 64 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7317 (ttpp) REVERT: A 67 MET cc_start: 0.8675 (mmt) cc_final: 0.8302 (mmt) REVERT: A 92 LYS cc_start: 0.8098 (mttm) cc_final: 0.7778 (ptmt) REVERT: A 99 LYS cc_start: 0.8624 (tptp) cc_final: 0.8401 (mmmm) REVERT: A 400 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8644 (tp-100) REVERT: A 464 ARG cc_start: 0.8593 (ttp80) cc_final: 0.8385 (ptm-80) REVERT: A 466 THR cc_start: 0.9388 (p) cc_final: 0.8933 (t) REVERT: A 467 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8590 (mm-30) REVERT: A 480 MET cc_start: 0.7514 (ptp) cc_final: 0.7177 (ptt) REVERT: A 495 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8353 (tm-30) REVERT: A 499 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8654 (mp) REVERT: B 11 VAL cc_start: 0.8823 (t) cc_final: 0.8529 (p) REVERT: B 60 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8191 (mmmm) REVERT: B 92 LYS cc_start: 0.9032 (tttt) cc_final: 0.8533 (ptmm) REVERT: B 99 LYS cc_start: 0.9073 (tppt) cc_final: 0.8765 (tptp) REVERT: B 270 LEU cc_start: 0.8554 (tp) cc_final: 0.8323 (tm) REVERT: B 271 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7835 (mm-30) REVERT: B 273 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.6912 (mpt-90) REVERT: B 317 ARG cc_start: 0.7477 (mtp-110) cc_final: 0.7026 (tpt90) REVERT: B 325 GLU cc_start: 0.8668 (tt0) cc_final: 0.8281 (mm-30) REVERT: B 396 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8143 (mm-30) REVERT: B 406 MET cc_start: 0.7483 (mmm) cc_final: 0.7185 (mmm) REVERT: B 416 MET cc_start: 0.8715 (mmt) cc_final: 0.8303 (mmp) REVERT: B 477 ARG cc_start: 0.8003 (mtm110) cc_final: 0.7338 (ttp-170) outliers start: 22 outliers final: 8 residues processed: 102 average time/residue: 1.1045 time to fit residues: 118.8253 Evaluate side-chains 93 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TRP Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 400 GLN Chi-restraints excluded: chain A residue 401 LEU 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 24 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 66 optimal weight: 0.0000 chunk 53 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.098299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.083262 restraints weight = 13107.115| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 4.14 r_work: 0.3596 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5850 Z= 0.150 Angle : 0.856 37.403 7914 Z= 0.316 Chirality : 0.046 0.202 802 Planarity : 0.004 0.047 1024 Dihedral : 3.571 15.423 782 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.83 % Allowed : 15.41 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.32), residues: 688 helix: 0.51 (0.36), residues: 228 sheet: -0.45 (0.50), residues: 118 loop : -0.20 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 38 HIS 0.005 0.001 HIS B 341 PHE 0.023 0.002 PHE B 15 TYR 0.027 0.001 TYR A 485 ARG 0.010 0.001 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.03295 ( 221) hydrogen bonds : angle 4.68413 ( 600) metal coordination : bond 0.01246 ( 8) metal coordination : angle 15.62098 ( 12) covalent geometry : bond 0.00345 ( 5842) covalent geometry : angle 0.60213 ( 7902) *********************** 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 99 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7785 (OUTLIER) cc_final: 0.7110 (t-100) REVERT: A 50 LEU cc_start: 0.8204 (mt) cc_final: 0.7920 (mp) REVERT: A 60 LYS cc_start: 0.8607 (mttm) cc_final: 0.8269 (mtpt) REVERT: A 64 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7335 (ttpp) REVERT: A 92 LYS cc_start: 0.7953 (mttm) cc_final: 0.7714 (ttpp) REVERT: A 466 THR cc_start: 0.9403 (p) cc_final: 0.9112 (t) REVERT: A 467 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8640 (mm-30) REVERT: A 495 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8378 (tm-30) REVERT: A 499 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8637 (mp) REVERT: B 60 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8242 (mmmm) REVERT: B 92 LYS cc_start: 0.9044 (tttt) cc_final: 0.8703 (ptmm) REVERT: B 99 LYS cc_start: 0.9062 (tppt) cc_final: 0.8738 (tptp) REVERT: B 271 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7796 (mm-30) REVERT: B 273 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.6951 (mpt-90) REVERT: B 317 ARG cc_start: 0.7784 (mtp-110) cc_final: 0.7160 (tpt90) REVERT: B 325 GLU cc_start: 0.8699 (tt0) cc_final: 0.8269 (mm-30) REVERT: B 396 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8212 (mm-30) REVERT: B 406 MET cc_start: 0.7473 (mmm) cc_final: 0.7142 (mmm) REVERT: B 416 MET cc_start: 0.8746 (mmt) cc_final: 0.8271 (mmp) REVERT: B 477 ARG cc_start: 0.7958 (mtm110) cc_final: 0.7280 (ttt-90) outliers start: 18 outliers final: 9 residues processed: 93 average time/residue: 1.8185 time to fit residues: 177.9719 Evaluate side-chains 90 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TRP Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 77 ILE 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 65 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3977 r_free = 0.3977 target = 0.097043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.082553 restraints weight = 13364.351| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 4.08 r_work: 0.3588 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.4569 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= 0.148 Angle : 0.696 23.381 7914 Z= 0.312 Chirality : 0.046 0.196 802 Planarity : 0.004 0.049 1024 Dihedral : 3.618 17.878 782 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.99 % Allowed : 16.19 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.32), residues: 688 helix: 0.39 (0.35), residues: 234 sheet: -0.54 (0.49), residues: 118 loop : -0.27 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 55 HIS 0.005 0.001 HIS B 341 PHE 0.014 0.001 PHE A 408 TYR 0.017 0.001 TYR A 485 ARG 0.009 0.001 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.03300 ( 221) hydrogen bonds : angle 4.69204 ( 600) metal coordination : bond 0.01021 ( 8) metal coordination : angle 8.31555 ( 12) covalent geometry : bond 0.00338 ( 5842) covalent geometry : angle 0.61697 ( 7902) *********************** 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 101 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7692 (OUTLIER) cc_final: 0.7120 (t-100) REVERT: A 50 LEU cc_start: 0.8231 (mt) cc_final: 0.7883 (mp) REVERT: A 60 LYS cc_start: 0.8678 (mttm) cc_final: 0.8346 (mtpm) REVERT: A 67 MET cc_start: 0.8613 (mmt) cc_final: 0.8367 (mmt) REVERT: A 92 LYS cc_start: 0.8022 (mttm) cc_final: 0.7767 (ttpp) REVERT: A 99 LYS cc_start: 0.8894 (mmmm) cc_final: 0.8570 (mmtp) REVERT: A 466 THR cc_start: 0.9407 (p) cc_final: 0.9136 (t) REVERT: A 467 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8639 (mm-30) REVERT: A 495 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8395 (tm-30) REVERT: A 499 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8645 (mp) REVERT: B 60 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8216 (mmmm) REVERT: B 92 LYS cc_start: 0.9092 (tttt) cc_final: 0.8749 (ptmm) REVERT: B 99 LYS cc_start: 0.9045 (tppt) cc_final: 0.8722 (tptp) REVERT: B 271 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7767 (mm-30) REVERT: B 273 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.6924 (mpt-90) REVERT: B 281 ASP cc_start: 0.7848 (t70) cc_final: 0.7556 (t70) REVERT: B 317 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7313 (tmt-80) REVERT: B 325 GLU cc_start: 0.8729 (tt0) cc_final: 0.8390 (mp0) REVERT: B 396 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8247 (mm-30) REVERT: B 406 MET cc_start: 0.7602 (mmm) cc_final: 0.7335 (mmm) REVERT: B 416 MET cc_start: 0.8776 (mmt) cc_final: 0.8324 (mmp) REVERT: B 477 ARG cc_start: 0.7895 (mtm110) cc_final: 0.7219 (ttt-90) outliers start: 19 outliers final: 9 residues processed: 93 average time/residue: 1.1161 time to fit residues: 109.1751 Evaluate side-chains 92 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TRP Chi-restraints excluded: chain A residue 77 ILE 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 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 97 MET Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 317 ARG 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 6 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 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 = 0.3990 r_free = 0.3990 target = 0.097724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.083491 restraints weight = 13220.656| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 4.03 r_work: 0.3605 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4730 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= 0.117 Angle : 0.643 17.667 7914 Z= 0.297 Chirality : 0.045 0.177 802 Planarity : 0.004 0.050 1024 Dihedral : 3.601 18.862 782 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.20 % Allowed : 16.98 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.32), residues: 688 helix: 0.44 (0.35), residues: 234 sheet: -0.60 (0.48), residues: 118 loop : -0.28 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 38 HIS 0.004 0.001 HIS B 341 PHE 0.012 0.001 PHE A 408 TYR 0.013 0.001 TYR A 370 ARG 0.007 0.001 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.03112 ( 221) hydrogen bonds : angle 4.64499 ( 600) metal coordination : bond 0.00868 ( 8) metal coordination : angle 6.24838 ( 12) covalent geometry : bond 0.00272 ( 5842) covalent geometry : angle 0.59552 ( 7902) *********************** 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 98 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7753 (OUTLIER) cc_final: 0.7355 (t-100) REVERT: A 60 LYS cc_start: 0.8628 (mttm) cc_final: 0.8272 (mtpp) REVERT: A 92 LYS cc_start: 0.8021 (mttm) cc_final: 0.7739 (ttpp) REVERT: A 318 PHE cc_start: 0.6929 (OUTLIER) cc_final: 0.6667 (m-10) REVERT: A 466 THR cc_start: 0.9437 (p) cc_final: 0.9069 (t) REVERT: A 467 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8558 (mm-30) REVERT: A 495 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8389 (tm-30) REVERT: A 499 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8652 (mp) REVERT: B 60 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8124 (mmmm) REVERT: B 92 LYS cc_start: 0.9115 (tttt) cc_final: 0.8802 (ptmm) REVERT: B 99 LYS cc_start: 0.9052 (tppt) cc_final: 0.8735 (tptp) REVERT: B 271 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7825 (mm-30) REVERT: B 273 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6895 (mpt-90) REVERT: B 317 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7272 (tmt-80) REVERT: B 325 GLU cc_start: 0.8713 (tt0) cc_final: 0.8350 (mm-30) REVERT: B 396 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8254 (mm-30) REVERT: B 406 MET cc_start: 0.7437 (mmm) cc_final: 0.7081 (mmm) REVERT: B 410 ILE cc_start: 0.8014 (mm) cc_final: 0.7808 (mm) REVERT: B 416 MET cc_start: 0.8758 (mmt) cc_final: 0.8337 (mmp) REVERT: B 477 ARG cc_start: 0.7653 (mtm110) cc_final: 0.7238 (ttm-80) outliers start: 14 outliers final: 6 residues processed: 90 average time/residue: 1.1488 time to fit residues: 108.7600 Evaluate side-chains 91 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TRP Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 484 VAL 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 97 MET Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 317 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 18 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 28 optimal weight: 0.0010 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.097043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.082719 restraints weight = 13191.251| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 4.04 r_work: 0.3593 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5850 Z= 0.128 Angle : 0.651 13.454 7914 Z= 0.303 Chirality : 0.045 0.176 802 Planarity : 0.004 0.050 1024 Dihedral : 3.658 20.336 782 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.14 % Allowed : 16.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.32), residues: 688 helix: 0.44 (0.35), residues: 234 sheet: -0.15 (0.52), residues: 102 loop : -0.35 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 55 HIS 0.003 0.001 HIS B 341 PHE 0.014 0.001 PHE A 408 TYR 0.014 0.001 TYR B 404 ARG 0.006 0.001 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.03161 ( 221) hydrogen bonds : angle 4.67513 ( 600) metal coordination : bond 0.00815 ( 8) metal coordination : angle 5.08398 ( 12) covalent geometry : bond 0.00298 ( 5842) covalent geometry : angle 0.62022 ( 7902) *********************** 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 97 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7692 (OUTLIER) cc_final: 0.7203 (t-100) REVERT: A 60 LYS cc_start: 0.8637 (mttm) cc_final: 0.8299 (mtpp) REVERT: A 67 MET cc_start: 0.8527 (mmt) cc_final: 0.8309 (mmt) REVERT: A 92 LYS cc_start: 0.7995 (mttm) cc_final: 0.7719 (ptmt) REVERT: A 325 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8304 (mp0) REVERT: A 466 THR cc_start: 0.9426 (p) cc_final: 0.9138 (t) REVERT: A 467 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8682 (mm-30) REVERT: A 495 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8359 (tm-30) REVERT: A 499 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8633 (mp) REVERT: B 60 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8079 (mmmm) REVERT: B 92 LYS cc_start: 0.9160 (tttt) cc_final: 0.8877 (ptmm) REVERT: B 99 LYS cc_start: 0.9052 (tppt) cc_final: 0.8748 (tptp) REVERT: B 271 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7813 (mm-30) REVERT: B 273 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.6876 (mpt-90) REVERT: B 281 ASP cc_start: 0.7939 (t70) cc_final: 0.7615 (t70) REVERT: B 317 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7335 (tmt-80) REVERT: B 325 GLU cc_start: 0.8774 (tt0) cc_final: 0.8419 (mp0) REVERT: B 396 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8188 (mm-30) REVERT: B 406 MET cc_start: 0.7539 (mmm) cc_final: 0.7218 (mmm) REVERT: B 410 ILE cc_start: 0.8053 (mm) cc_final: 0.7842 (mm) REVERT: B 416 MET cc_start: 0.8769 (mmt) cc_final: 0.8352 (mmp) outliers start: 20 outliers final: 8 residues processed: 87 average time/residue: 1.2231 time to fit residues: 111.8512 Evaluate side-chains 90 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TRP Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 77 ILE 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 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 97 MET Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 317 ARG 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 52 optimal weight: 0.9980 chunk 58 optimal weight: 0.0000 chunk 64 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 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 = 0.3997 r_free = 0.3997 target = 0.097974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.083182 restraints weight = 13403.735| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 4.12 r_work: 0.3603 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5850 Z= 0.119 Angle : 0.646 10.296 7914 Z= 0.306 Chirality : 0.045 0.173 802 Planarity : 0.004 0.050 1024 Dihedral : 3.697 21.482 782 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.36 % Allowed : 17.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.32), residues: 688 helix: 0.42 (0.35), residues: 234 sheet: 0.21 (0.56), residues: 88 loop : -0.36 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 55 HIS 0.004 0.001 HIS B 341 PHE 0.012 0.001 PHE A 408 TYR 0.014 0.001 TYR A 370 ARG 0.005 0.000 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.03185 ( 221) hydrogen bonds : angle 4.69170 ( 600) metal coordination : bond 0.00651 ( 8) metal coordination : angle 3.99073 ( 12) covalent geometry : bond 0.00281 ( 5842) covalent geometry : angle 0.62760 ( 7902) *********************** 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 95 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7598 (OUTLIER) cc_final: 0.7113 (t-100) REVERT: A 60 LYS cc_start: 0.8617 (mttm) cc_final: 0.8264 (mtpp) REVERT: A 67 MET cc_start: 0.8482 (mmt) cc_final: 0.8278 (mmt) REVERT: A 92 LYS cc_start: 0.8232 (mttm) cc_final: 0.7863 (ptmt) REVERT: A 99 LYS cc_start: 0.8921 (mmmm) cc_final: 0.8604 (mmtm) REVERT: A 318 PHE cc_start: 0.6996 (OUTLIER) cc_final: 0.6661 (m-10) REVERT: A 325 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8136 (mp0) REVERT: A 401 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8223 (tm) REVERT: A 466 THR cc_start: 0.9428 (p) cc_final: 0.9042 (t) REVERT: A 467 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8620 (mm-30) REVERT: A 495 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8315 (tm-30) REVERT: A 499 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8694 (mp) REVERT: B 60 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8194 (mmmm) REVERT: B 92 LYS cc_start: 0.9182 (tttt) cc_final: 0.8894 (ptmm) REVERT: B 99 LYS cc_start: 0.9073 (tppt) cc_final: 0.8757 (tptp) REVERT: B 271 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7887 (mm-30) REVERT: B 273 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.6842 (mpt-90) REVERT: B 317 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7383 (tmt-80) REVERT: B 325 GLU cc_start: 0.8781 (tt0) cc_final: 0.8402 (mp0) REVERT: B 396 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8188 (mm-30) REVERT: B 406 MET cc_start: 0.7699 (mmm) cc_final: 0.7402 (mmm) REVERT: B 416 MET cc_start: 0.8750 (mmt) cc_final: 0.8322 (mmp) REVERT: B 477 ARG cc_start: 0.7594 (mtm110) cc_final: 0.6906 (ttt-90) outliers start: 15 outliers final: 6 residues processed: 87 average time/residue: 1.3010 time to fit residues: 118.4314 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 : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TRP Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 484 VAL 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 97 MET Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 317 ARG 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 42 optimal weight: 0.9980 chunk 29 optimal weight: 0.0040 chunk 48 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 0.0000 chunk 65 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 0.4980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 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 = 0.4010 r_free = 0.4010 target = 0.098435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.083728 restraints weight = 13418.846| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 4.14 r_work: 0.3633 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5850 Z= 0.116 Angle : 0.658 10.798 7914 Z= 0.316 Chirality : 0.045 0.167 802 Planarity : 0.004 0.057 1024 Dihedral : 3.730 21.553 782 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.20 % Allowed : 18.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.32), residues: 688 helix: 0.32 (0.35), residues: 234 sheet: -0.02 (0.52), residues: 100 loop : -0.35 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 55 HIS 0.001 0.000 HIS B 395 PHE 0.017 0.001 PHE B 516 TYR 0.010 0.001 TYR B 404 ARG 0.005 0.000 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.03188 ( 221) hydrogen bonds : angle 4.76268 ( 600) metal coordination : bond 0.00537 ( 8) metal coordination : angle 3.67038 ( 12) covalent geometry : bond 0.00276 ( 5842) covalent geometry : angle 0.64289 ( 7902) ********************** 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 : 0.672 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: 0.7490 (OUTLIER) cc_final: 0.6980 (t-100) REVERT: A 92 LYS cc_start: 0.8059 (mttm) cc_final: 0.7710 (ptmt) REVERT: A 325 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8189 (mp0) REVERT: A 401 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8206 (tm) REVERT: A 466 THR cc_start: 0.9439 (p) cc_final: 0.9004 (t) REVERT: A 467 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8577 (mm-30) REVERT: A 495 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8305 (tm-30) REVERT: A 499 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8675 (mp) REVERT: B 60 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8211 (mmmm) REVERT: B 92 LYS cc_start: 0.9185 (tttt) cc_final: 0.8907 (ptmm) REVERT: B 99 LYS cc_start: 0.9068 (tppt) cc_final: 0.8781 (tptp) REVERT: B 271 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7861 (mm-30) REVERT: B 273 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6747 (mpt-90) REVERT: B 281 ASP cc_start: 0.7954 (t70) cc_final: 0.7628 (t70) REVERT: B 317 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7357 (tmt-80) REVERT: B 325 GLU cc_start: 0.8766 (tt0) cc_final: 0.8372 (mm-30) REVERT: B 396 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8172 (mm-30) REVERT: B 406 MET cc_start: 0.7672 (mmm) cc_final: 0.7372 (mmm) REVERT: B 416 MET cc_start: 0.8737 (mmt) cc_final: 0.8312 (mmp) outliers start: 14 outliers final: 5 residues processed: 84 average time/residue: 1.0985 time to fit residues: 96.9686 Evaluate side-chains 86 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TRP Chi-restraints excluded: chain A residue 77 ILE 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 495 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 317 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 17 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 30 optimal weight: 0.0970 chunk 67 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 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 = 0.3998 r_free = 0.3998 target = 0.097929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.083049 restraints weight = 13476.574| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 4.16 r_work: 0.3606 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 5850 Z= 0.127 Angle : 0.657 11.369 7914 Z= 0.314 Chirality : 0.046 0.190 802 Planarity : 0.004 0.057 1024 Dihedral : 3.729 21.331 782 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.52 % Allowed : 18.24 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.32), residues: 688 helix: 0.39 (0.35), residues: 234 sheet: 0.13 (0.56), residues: 88 loop : -0.29 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 55 HIS 0.005 0.001 HIS B 341 PHE 0.019 0.001 PHE B 516 TYR 0.032 0.001 TYR A 485 ARG 0.005 0.000 ARG A 464 Details of bonding type rmsd hydrogen bonds : bond 0.03233 ( 221) hydrogen bonds : angle 4.76215 ( 600) metal coordination : bond 0.00589 ( 8) metal coordination : angle 3.58038 ( 12) covalent geometry : bond 0.00301 ( 5842) covalent geometry : angle 0.64233 ( 7902) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4727.85 seconds wall clock time: 85 minutes 0.92 seconds (5100.92 seconds total)