Starting phenix.real_space_refine on Fri Oct 23 11:08:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x0q_66439/10_2026/9x0q_66439.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x0q_66439/10_2026/9x0q_66439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x0q_66439/10_2026/9x0q_66439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x0q_66439/10_2026/9x0q_66439.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x0q_66439/10_2026/9x0q_66439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x0q_66439/10_2026/9x0q_66439.map" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 4 7.16 5 S 40 5.16 5 C 6076 2.51 5 N 1610 2.21 5 O 1804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9535 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5621 Classifications: {'peptide': 723} Link IDs: {'PCIS': 2, 'PTRANS': 44, 'TRANS': 676} Chain: "B" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2901 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 28, 'TRANS': 357} Chain breaks: 3 Chain: "C" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 97} Chain: "A" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 68 Unusual residues: {' CA': 1, 'HEC': 1, 'PQQ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'HEC': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.88, per 1000 atoms: 0.20 Number of scatterers: 9535 At special positions: 0 Unit cell: (87.618, 104.798, 109.093, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 Ca 1 19.99 S 40 16.00 O 1804 8.00 N 1610 7.00 C 6076 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 141 " - pdb=" SG CYS A 142 " distance=2.04 Simple disulfide: pdb=" SG CYS C 58 " - pdb=" SG CYS C 122 " distance=2.03 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=13, symmetry=0 Number of additional bonds: simple=13, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 380.7 milliseconds 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 14 sheets defined 31.4% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 37 through 46 removed outlier: 3.761A pdb=" N ALA A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP A 46 " --> pdb=" O ILE A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 80 Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 133 through 140 removed outlier: 3.812A pdb=" N ILE A 136 " --> pdb=" O PRO A 133 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASP A 138 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY A 140 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 302 through 308 Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 485 through 498 removed outlier: 3.514A pdb=" N VAL A 498 " --> pdb=" O ASP A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 3.730A pdb=" N GLY A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 599 removed outlier: 4.131A pdb=" N ARG A 598 " --> pdb=" O GLY A 595 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR A 599 " --> pdb=" O VAL A 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 595 through 599' Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 641 through 653 Processing helix chain 'A' and resid 653 through 658 Processing helix chain 'A' and resid 659 through 662 Processing helix chain 'A' and resid 669 through 673 Processing helix chain 'A' and resid 674 through 677 Processing helix chain 'A' and resid 678 through 687 Processing helix chain 'A' and resid 704 through 730 removed outlier: 5.067A pdb=" N ASP A 724 " --> pdb=" O ASN A 720 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ASP A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'B' and resid 43 through 54 Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 122 through 127 Processing helix chain 'B' and resid 130 through 144 Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 192 through 197 removed outlier: 3.882A pdb=" N THR B 197 " --> pdb=" O GLY B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 250 Processing helix chain 'B' and resid 258 through 268 removed outlier: 3.743A pdb=" N ASP B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 272 Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 301 through 310 Processing helix chain 'B' and resid 314 through 324 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 353 through 362 Processing helix chain 'B' and resid 386 through 398 Processing helix chain 'B' and resid 410 through 420 removed outlier: 3.589A pdb=" N THR B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 431 removed outlier: 3.640A pdb=" N TRP B 429 " --> pdb=" O THR B 426 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL B 431 " --> pdb=" O GLY B 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 60 removed outlier: 3.544A pdb=" N GLU C 60 " --> pdb=" O ASN C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 77 removed outlier: 4.090A pdb=" N GLY C 75 " --> pdb=" O PRO C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 97 removed outlier: 4.093A pdb=" N ALA C 93 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 130 Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 67 removed outlier: 4.150A pdb=" N VAL A 534 " --> pdb=" O THR A 530 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP A 548 " --> pdb=" O ASP A 554 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP A 554 " --> pdb=" O ASP A 548 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 87 removed outlier: 5.057A pdb=" N LEU A 82 " --> pdb=" O SER A 613 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N SER A 613 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 101 removed outlier: 6.270A pdb=" N ASP A 118 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU A 124 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 152 removed outlier: 5.606A pdb=" N ASP A 169 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU A 175 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 202 removed outlier: 6.084A pdb=" N ASP A 226 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A 232 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 274 through 275 removed outlier: 3.694A pdb=" N GLY A 274 " --> pdb=" O SER A 299 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 282 through 285 Processing sheet with id=AA8, first strand: chain 'A' and resid 350 through 356 removed outlier: 6.056A pdb=" N ASP A 377 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE A 383 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 395 through 398 removed outlier: 5.262A pdb=" N ASN A 406 " --> pdb=" O ASN A 396 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 420 through 422 Processing sheet with id=AB2, first strand: chain 'A' and resid 436 through 438 removed outlier: 4.396A pdb=" N GLY A 501 " --> pdb=" O HIS A 519 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE A 515 " --> pdb=" O ALA A 505 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASP A 507 " --> pdb=" O PRO A 513 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 251 through 252 removed outlier: 3.739A pdb=" N SER B 255 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 364 through 366 Processing sheet with id=AB5, first strand: chain 'C' and resid 99 through 101 317 hydrogen bonds defined for protein. 858 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: 1.83 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.36: 3173 1.36 - 1.53: 5273 1.53 - 1.69: 1303 1.69 - 1.85: 68 1.85 - 2.01: 16 Bond restraints: 9833 Sorted by residual: bond pdb=" C2D HEC A 801 " pdb=" C3D HEC A 801 " ideal model delta sigma weight residual 1.544 1.325 0.219 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C2D HEC B 503 " pdb=" C3D HEC B 503 " ideal model delta sigma weight residual 1.544 1.327 0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C2D HEC B 502 " pdb=" C3D HEC B 502 " ideal model delta sigma weight residual 1.544 1.328 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C2D HEC B 501 " pdb=" C3D HEC B 501 " ideal model delta sigma weight residual 1.544 1.331 0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" CAC HEC A 801 " pdb=" CBC HEC A 801 " ideal model delta sigma weight residual 1.544 1.362 0.182 2.00e-02 2.50e+03 8.32e+01 ... (remaining 9828 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 13303 3.02 - 6.04: 143 6.04 - 9.06: 5 9.06 - 12.08: 2 12.08 - 15.10: 1 Bond angle restraints: 13454 Sorted by residual: angle pdb=" C3D HEC B 502 " pdb=" CAD HEC B 502 " pdb=" CBD HEC B 502 " ideal model delta sigma weight residual 109.50 124.60 -15.10 3.00e+00 1.11e-01 2.53e+01 angle pdb=" C3D HEC B 503 " pdb=" CAD HEC B 503 " pdb=" CBD HEC B 503 " ideal model delta sigma weight residual 109.50 120.63 -11.13 3.00e+00 1.11e-01 1.38e+01 angle pdb=" CB GLU B 446 " pdb=" CG GLU B 446 " pdb=" CD GLU B 446 " ideal model delta sigma weight residual 112.60 118.68 -6.08 1.70e+00 3.46e-01 1.28e+01 angle pdb=" C3D HEC B 501 " pdb=" CAD HEC B 501 " pdb=" CBD HEC B 501 " ideal model delta sigma weight residual 109.50 119.29 -9.79 3.00e+00 1.11e-01 1.06e+01 angle pdb=" CB GLU A 75 " pdb=" CG GLU A 75 " pdb=" CD GLU A 75 " ideal model delta sigma weight residual 112.60 118.11 -5.51 1.70e+00 3.46e-01 1.05e+01 ... (remaining 13449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 4858 17.83 - 35.67: 555 35.67 - 53.50: 162 53.50 - 71.34: 38 71.34 - 89.17: 10 Dihedral angle restraints: 5623 sinusoidal: 2193 harmonic: 3430 Sorted by residual: dihedral pdb=" CA CYS A 141 " pdb=" C CYS A 141 " pdb=" N CYS A 142 " pdb=" CA CYS A 142 " ideal model delta harmonic sigma weight residual 180.00 -157.82 -22.18 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" C2C HEC A 801 " pdb=" C3C HEC A 801 " pdb=" CAC HEC A 801 " pdb=" CBC HEC A 801 " ideal model delta sinusoidal sigma weight residual 60.00 98.82 -38.82 2 1.00e+01 1.00e-02 1.89e+01 dihedral pdb=" CA SER C 28 " pdb=" C SER C 28 " pdb=" N PRO C 29 " pdb=" CA PRO C 29 " ideal model delta harmonic sigma weight residual 180.00 159.82 20.18 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 5620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 950 0.042 - 0.085: 304 0.085 - 0.127: 97 0.127 - 0.170: 7 0.170 - 0.212: 2 Chirality restraints: 1360 Sorted by residual: chirality pdb=" CB THR C 83 " pdb=" CA THR C 83 " pdb=" OG1 THR C 83 " pdb=" CG2 THR C 83 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CG LEU B 106 " pdb=" CB LEU B 106 " pdb=" CD1 LEU B 106 " pdb=" CD2 LEU B 106 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" CA MET B 142 " pdb=" N MET B 142 " pdb=" C MET B 142 " pdb=" CB MET B 142 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 1357 not shown) Planarity restraints: 1758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CBD HEC B 502 " -0.026 2.00e-02 2.50e+03 5.59e-02 3.12e+01 pdb=" CGD HEC B 502 " 0.097 2.00e-02 2.50e+03 pdb=" O1D HEC B 502 " -0.034 2.00e-02 2.50e+03 pdb=" O2D HEC B 502 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CBA HEC B 502 " -0.021 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" CGA HEC B 502 " 0.078 2.00e-02 2.50e+03 pdb=" O1A HEC B 502 " -0.029 2.00e-02 2.50e+03 pdb=" O2A HEC B 502 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CBD HEC B 503 " -0.019 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" CGD HEC B 503 " 0.072 2.00e-02 2.50e+03 pdb=" O1D HEC B 503 " -0.026 2.00e-02 2.50e+03 pdb=" O2D HEC B 503 " -0.027 2.00e-02 2.50e+03 ... (remaining 1755 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 28 2.63 - 3.19: 8759 3.19 - 3.76: 16101 3.76 - 4.33: 23817 4.33 - 4.90: 37362 Nonbonded interactions: 86067 Sorted by model distance: nonbonded pdb=" OD1 ASN A 297 " pdb=" O7A PQQ A 802 " model vdw 2.057 3.040 nonbonded pdb=" ND2 ASN A 297 " pdb="CA CA A 803 " model vdw 2.252 2.590 nonbonded pdb=" N6 PQQ A 802 " pdb="CA CA A 803 " model vdw 2.253 2.590 nonbonded pdb=" OE2 GLU A 215 " pdb="CA CA A 803 " model vdw 2.260 2.510 nonbonded pdb=" OD2 ASP A 342 " pdb="CA CA A 803 " model vdw 2.307 2.510 ... (remaining 86062 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.100 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.600 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:8.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9176 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 : 0.010 0.577 9848 Z= 0.681 Angle : 0.700 15.103 13458 Z= 0.329 Chirality : 0.045 0.212 1360 Planarity : 0.005 0.056 1758 Dihedral : 16.932 89.172 3457 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.07 % Allowed : 25.10 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: -0.43 (0.25), residues: 1204 helix: 0.43 (0.32), residues: 293 sheet: -1.12 (0.40), residues: 157 loop : -0.32 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 135 TYR 0.027 0.001 TYR B 118 PHE 0.011 0.001 PHE B 140 TRP 0.011 0.001 TRP A 331 HIS 0.004 0.001 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00785 / 0.35 ( 9833) covalent geometry : angle 0.69940 / 0.33 (13454) SS BOND : bond 0.00576 / 0.30 ( 2) SS BOND : angle 1.51439 / 0.86 ( 4) hydrogen bonds : bond 0.11466 / 7.78 ( 317) hydrogen bonds : angle 7.92302 / 5.38 ( 858) Misc. bond : bond 0.17992 / 9.69 ( 13) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8275 (mtm180) cc_final: 0.7578 (mpt90) REVERT: A 266 ASN cc_start: 0.8903 (OUTLIER) cc_final: 0.8703 (p0) REVERT: B 66 GLN cc_start: 0.6838 (OUTLIER) cc_final: 0.6600 (pp30) REVERT: B 121 MET cc_start: 0.7176 (mmm) cc_final: 0.6930 (mmt) REVERT: B 137 MET cc_start: 0.8156 (mmp) cc_final: 0.7710 (mmt) REVERT: B 166 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.5102 (pp-130) REVERT: B 261 MET cc_start: 0.9326 (tpt) cc_final: 0.8167 (tpt) REVERT: C 78 GLU cc_start: 0.8816 (pt0) cc_final: 0.8382 (pp20) REVERT: C 81 LYS cc_start: 0.9256 (mttp) cc_final: 0.8925 (mmpt) REVERT: C 127 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8314 (mptt) outliers start: 20 outliers final: 14 residues processed: 95 average time/residue: 0.5224 time to fit residues: 53.8160 Evaluate side-chains 98 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain B residue 66 GLN Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain C residue 127 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [108, 49, 97, 113, 53, 5, 33, 65, 62, 51, 117] chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.0770 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 92 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.081814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.057398 restraints weight = 18911.801| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.33 r_work: 0.2689 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9133 moved from start: 0.0403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.212 9848 Z= 0.127 Angle : 0.567 6.774 13458 Z= 0.276 Chirality : 0.044 0.152 1360 Planarity : 0.004 0.038 1758 Dihedral : 8.895 87.265 1381 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.41 % Allowed : 22.52 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: -0.36 (0.26), residues: 1204 helix: 0.45 (0.32), residues: 302 sheet: -1.11 (0.40), residues: 159 loop : -0.24 (0.25), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 135 TYR 0.022 0.001 TYR B 118 PHE 0.008 0.001 PHE C 100 TRP 0.011 0.001 TRP A 331 HIS 0.003 0.000 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 ( 9833) covalent geometry : angle 0.56644 / 0.28 (13454) SS BOND : bond 0.00577 / 0.30 ( 2) SS BOND : angle 1.49091 / 0.85 ( 4) hydrogen bonds : bond 0.03358 / 2.29 ( 317) hydrogen bonds : angle 6.30811 / 4.39 ( 858) Misc. bond : bond 0.07333 / 4.52 ( 13) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 84 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8551 (t0) cc_final: 0.8351 (p0) REVERT: A 139 ARG cc_start: 0.8241 (mtm180) cc_final: 0.7492 (mpt90) REVERT: A 359 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7211 (pp20) REVERT: B 137 MET cc_start: 0.8177 (mmp) cc_final: 0.7776 (mmt) REVERT: B 166 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.5137 (pp-130) REVERT: B 206 THR cc_start: 0.5243 (OUTLIER) cc_final: 0.4982 (t) REVERT: B 261 MET cc_start: 0.9281 (tpt) cc_final: 0.8044 (tpt) REVERT: B 378 MET cc_start: 0.9107 (ttt) cc_final: 0.8513 (ttt) REVERT: C 78 GLU cc_start: 0.8867 (pt0) cc_final: 0.8391 (pp20) REVERT: C 81 LYS cc_start: 0.9246 (mttp) cc_final: 0.8892 (mmpt) outliers start: 33 outliers final: 10 residues processed: 109 average time/residue: 0.4807 time to fit residues: 57.0731 Evaluate side-chains 90 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain C residue 28 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [17, 10, 34, 57, 60, 44, 83, 1, 18, 25, 89] chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 89 optimal weight: 0.6980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 92 HIS ** B 143 HIS ** 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 = 0.3211 r_free = 0.3211 target = 0.079886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.055900 restraints weight = 19219.731| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 2.27 r_work: 0.2657 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9170 moved from start: 0.0528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.263 9848 Z= 0.180 Angle : 0.594 8.078 13458 Z= 0.290 Chirality : 0.045 0.143 1360 Planarity : 0.004 0.040 1758 Dihedral : 8.447 86.381 1359 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.93 % Allowed : 22.52 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: -0.29 (0.25), residues: 1204 helix: 0.53 (0.32), residues: 299 sheet: -0.85 (0.42), residues: 140 loop : -0.29 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 418 TYR 0.014 0.001 TYR A 329 PHE 0.010 0.001 PHE B 140 TRP 0.010 0.001 TRP A 331 HIS 0.004 0.001 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.18 ( 9833) covalent geometry : angle 0.59314 / 0.29 (13454) SS BOND : bond 0.00480 / 0.25 ( 2) SS BOND : angle 1.48329 / 0.85 ( 4) hydrogen bonds : bond 0.03502 / 2.42 ( 317) hydrogen bonds : angle 6.16377 / 4.28 ( 858) Misc. bond : bond 0.09218 / 5.67 ( 13) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 76 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8301 (mtm180) cc_final: 0.7522 (mpt90) REVERT: A 340 GLU cc_start: 0.9311 (OUTLIER) cc_final: 0.8842 (pt0) REVERT: A 359 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7227 (pp20) REVERT: B 137 MET cc_start: 0.8259 (mmp) cc_final: 0.7831 (mmt) REVERT: B 166 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.5279 (pp-130) REVERT: B 206 THR cc_start: 0.5240 (OUTLIER) cc_final: 0.5005 (t) REVERT: B 261 MET cc_start: 0.9283 (tpt) cc_final: 0.8084 (tpt) REVERT: B 378 MET cc_start: 0.9264 (ttt) cc_final: 0.8845 (ttt) REVERT: C 27 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7223 (pp30) REVERT: C 78 GLU cc_start: 0.8879 (pt0) cc_final: 0.8431 (pp20) REVERT: C 81 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.8976 (mmpt) REVERT: C 127 LYS cc_start: 0.8607 (mptt) cc_final: 0.8396 (mptt) outliers start: 38 outliers final: 16 residues processed: 105 average time/residue: 0.5276 time to fit residues: 59.8243 Evaluate side-chains 95 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 81 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [108, 64, 101, 81, 97, 106, 42, 111, 77, 104, 7] chunk 108 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 97 optimal weight: 0.2980 chunk 106 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 92 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.080454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.055990 restraints weight = 19111.103| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.27 r_work: 0.2656 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9173 moved from start: 0.0626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.220 9848 Z= 0.140 Angle : 0.569 6.796 13458 Z= 0.279 Chirality : 0.044 0.142 1360 Planarity : 0.004 0.041 1758 Dihedral : 8.389 86.964 1359 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.93 % Allowed : 22.11 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: -0.29 (0.25), residues: 1204 helix: 0.49 (0.31), residues: 302 sheet: -0.86 (0.42), residues: 140 loop : -0.28 (0.25), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 418 TYR 0.024 0.001 TYR B 118 PHE 0.008 0.001 PHE A 515 TRP 0.011 0.001 TRP A 331 HIS 0.003 0.000 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 ( 9833) covalent geometry : angle 0.56825 / 0.28 (13454) SS BOND : bond 0.00548 / 0.29 ( 2) SS BOND : angle 1.47395 / 0.84 ( 4) hydrogen bonds : bond 0.03213 / 2.22 ( 317) hydrogen bonds : angle 5.99193 / 4.17 ( 858) Misc. bond : bond 0.08002 / 4.93 ( 13) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 78 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8273 (mtm180) cc_final: 0.7538 (mpt90) REVERT: A 340 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.8926 (pt0) REVERT: A 359 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7200 (pp20) REVERT: B 137 MET cc_start: 0.8193 (mmp) cc_final: 0.7893 (mmt) REVERT: B 166 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.5305 (pp-130) REVERT: B 206 THR cc_start: 0.5011 (OUTLIER) cc_final: 0.4781 (t) REVERT: B 378 MET cc_start: 0.9209 (ttt) cc_final: 0.8850 (ttt) REVERT: C 27 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7271 (pp30) REVERT: C 78 GLU cc_start: 0.8842 (pt0) cc_final: 0.8394 (pp20) REVERT: C 81 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8950 (mmpt) outliers start: 38 outliers final: 16 residues processed: 107 average time/residue: 0.4948 time to fit residues: 57.3821 Evaluate side-chains 95 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 81 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [41, 110, 7, 27, 77, 58, 30, 79, 72, 42, 34] chunk 41 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 92 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.080292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.055900 restraints weight = 18988.524| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 2.26 r_work: 0.2654 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9176 moved from start: 0.0647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.231 9848 Z= 0.148 Angle : 0.577 6.767 13458 Z= 0.283 Chirality : 0.044 0.143 1360 Planarity : 0.004 0.041 1758 Dihedral : 8.361 87.421 1359 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.03 % Allowed : 22.52 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: -0.28 (0.25), residues: 1204 helix: 0.56 (0.31), residues: 299 sheet: -0.85 (0.42), residues: 140 loop : -0.29 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 135 TYR 0.011 0.001 TYR A 329 PHE 0.012 0.001 PHE B 140 TRP 0.011 0.001 TRP A 331 HIS 0.003 0.000 HIS A 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 9833) covalent geometry : angle 0.57689 / 0.28 (13454) SS BOND : bond 0.00546 / 0.29 ( 2) SS BOND : angle 1.48799 / 0.85 ( 4) hydrogen bonds : bond 0.03228 / 2.23 ( 317) hydrogen bonds : angle 5.97192 / 4.16 ( 858) Misc. bond : bond 0.08346 / 5.06 ( 13) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 73 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8290 (mtm180) cc_final: 0.7554 (mpt90) REVERT: A 201 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.7427 (mpt180) REVERT: A 340 GLU cc_start: 0.9258 (OUTLIER) cc_final: 0.8997 (pt0) REVERT: A 359 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7192 (pp20) REVERT: B 137 MET cc_start: 0.8155 (mmp) cc_final: 0.7835 (mmt) REVERT: B 166 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.5415 (pp-130) REVERT: B 206 THR cc_start: 0.4957 (OUTLIER) cc_final: 0.4728 (t) REVERT: C 27 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7316 (pp30) REVERT: C 78 GLU cc_start: 0.8863 (pt0) cc_final: 0.8412 (pp20) REVERT: C 81 LYS cc_start: 0.9298 (mttp) cc_final: 0.8954 (mmpt) REVERT: C 127 LYS cc_start: 0.8539 (mptt) cc_final: 0.8274 (mptt) outliers start: 39 outliers final: 17 residues processed: 104 average time/residue: 0.5023 time to fit residues: 56.8644 Evaluate side-chains 94 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 28 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [21, 78, 51, 15, 7, 18, 32, 0, 72, 17, 95] chunk 21 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.078408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.053616 restraints weight = 19091.002| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 2.27 r_work: 0.2605 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9209 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.312 9848 Z= 0.245 Angle : 0.640 9.077 13458 Z= 0.312 Chirality : 0.047 0.164 1360 Planarity : 0.004 0.042 1758 Dihedral : 8.488 88.418 1359 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.34 % Allowed : 22.00 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: -0.35 (0.25), residues: 1204 helix: 0.49 (0.31), residues: 301 sheet: -1.07 (0.38), residues: 154 loop : -0.28 (0.25), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 106 TYR 0.024 0.001 TYR B 118 PHE 0.008 0.001 PHE B 140 TRP 0.013 0.002 TRP A 585 HIS 0.003 0.001 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.24 ( 9833) covalent geometry : angle 0.63921 / 0.31 (13454) SS BOND : bond 0.00374 / 0.19 ( 2) SS BOND : angle 1.46872 / 0.85 ( 4) hydrogen bonds : bond 0.03635 / 2.52 ( 317) hydrogen bonds : angle 6.08352 / 4.23 ( 858) Misc. bond : bond 0.11607 / 7.08 ( 13) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 73 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8318 (mtm180) cc_final: 0.7476 (mpt90) REVERT: A 201 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.8820 (mmt-90) REVERT: A 340 GLU cc_start: 0.9305 (OUTLIER) cc_final: 0.8971 (pt0) REVERT: A 359 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7165 (pp20) REVERT: B 137 MET cc_start: 0.8238 (mmp) cc_final: 0.7829 (mmt) REVERT: B 166 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.5453 (pp-130) REVERT: B 206 THR cc_start: 0.4941 (OUTLIER) cc_final: 0.4727 (t) REVERT: B 261 MET cc_start: 0.9297 (tpt) cc_final: 0.8025 (tpt) REVERT: B 378 MET cc_start: 0.9208 (ttt) cc_final: 0.8486 (ttt) REVERT: C 27 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.7329 (pp30) REVERT: C 78 GLU cc_start: 0.8881 (pt0) cc_final: 0.8467 (pp20) REVERT: C 81 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.9005 (mmpt) REVERT: C 127 LYS cc_start: 0.8642 (mptt) cc_final: 0.8381 (mptt) outliers start: 42 outliers final: 20 residues processed: 105 average time/residue: 0.5552 time to fit residues: 62.9601 Evaluate side-chains 98 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 81 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [28, 18, 115, 83, 61, 39, 8, 51, 50, 65, 82] chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 39 optimal weight: 0.0570 chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 92 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.080220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.055774 restraints weight = 18948.529| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 2.27 r_work: 0.2654 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9174 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.199 9848 Z= 0.134 Angle : 0.593 8.619 13458 Z= 0.290 Chirality : 0.044 0.149 1360 Planarity : 0.004 0.042 1758 Dihedral : 8.383 88.316 1359 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.41 % Allowed : 23.24 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: -0.36 (0.25), residues: 1204 helix: 0.53 (0.31), residues: 299 sheet: -1.07 (0.39), residues: 157 loop : -0.30 (0.25), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 135 TYR 0.011 0.001 TYR B 123 PHE 0.010 0.001 PHE B 140 TRP 0.012 0.001 TRP A 331 HIS 0.006 0.001 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.13 ( 9833) covalent geometry : angle 0.59225 / 0.29 (13454) SS BOND : bond 0.00562 / 0.30 ( 2) SS BOND : angle 1.46993 / 0.84 ( 4) hydrogen bonds : bond 0.03191 / 2.21 ( 317) hydrogen bonds : angle 5.92571 / 4.13 ( 858) Misc. bond : bond 0.08669 / 5.56 ( 13) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 76 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8301 (mtm180) cc_final: 0.7568 (mpt90) REVERT: A 201 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.7609 (mpt180) REVERT: A 359 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7142 (pp20) REVERT: B 137 MET cc_start: 0.8140 (mmp) cc_final: 0.7806 (mmt) REVERT: B 166 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.5549 (pp-130) REVERT: B 206 THR cc_start: 0.4736 (OUTLIER) cc_final: 0.4514 (t) REVERT: B 378 MET cc_start: 0.9116 (ttt) cc_final: 0.8531 (ttt) REVERT: C 27 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.7160 (pp30) REVERT: C 78 GLU cc_start: 0.8864 (pt0) cc_final: 0.8438 (pp20) REVERT: C 81 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.8938 (mmpt) REVERT: C 127 LYS cc_start: 0.8664 (mptt) cc_final: 0.8411 (mptt) outliers start: 33 outliers final: 16 residues processed: 103 average time/residue: 0.5311 time to fit residues: 59.1896 Evaluate side-chains 94 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 81 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [86, 7, 65, 97, 15, 107, 53, 66, 26, 68, 78] chunk 86 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 78 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 92 HIS ** B 143 HIS ** 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 = 0.3193 r_free = 0.3193 target = 0.079935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.055452 restraints weight = 18973.955| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.27 r_work: 0.2647 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9180 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.238 9848 Z= 0.153 Angle : 0.602 6.964 13458 Z= 0.295 Chirality : 0.045 0.166 1360 Planarity : 0.004 0.041 1758 Dihedral : 8.357 88.182 1359 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.31 % Allowed : 23.55 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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 (0.25), residues: 1204 helix: 0.57 (0.31), residues: 299 sheet: -0.93 (0.40), residues: 151 loop : -0.33 (0.25), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 135 TYR 0.022 0.001 TYR B 118 PHE 0.009 0.001 PHE A 216 TRP 0.011 0.001 TRP A 331 HIS 0.009 0.001 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.15 ( 9833) covalent geometry : angle 0.60200 / 0.30 (13454) SS BOND : bond 0.00501 / 0.26 ( 2) SS BOND : angle 1.43136 / 0.82 ( 4) hydrogen bonds : bond 0.03226 / 2.23 ( 317) hydrogen bonds : angle 5.91376 / 4.13 ( 858) Misc. bond : bond 0.09261 / 5.74 ( 13) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 74 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8295 (mtm180) cc_final: 0.7561 (mpt90) REVERT: A 201 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.7466 (mpt180) REVERT: A 359 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7161 (pp20) REVERT: B 137 MET cc_start: 0.8170 (mmp) cc_final: 0.7837 (mmt) REVERT: B 166 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.5683 (pp-130) REVERT: B 378 MET cc_start: 0.9125 (ttt) cc_final: 0.8572 (ttt) REVERT: B 447 ASP cc_start: 0.8746 (p0) cc_final: 0.8363 (p0) REVERT: C 27 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.7179 (pp30) REVERT: C 78 GLU cc_start: 0.8882 (pt0) cc_final: 0.8459 (pp20) REVERT: C 81 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8946 (mmpt) REVERT: C 127 LYS cc_start: 0.8685 (mptt) cc_final: 0.8407 (mptt) outliers start: 32 outliers final: 19 residues processed: 99 average time/residue: 0.5234 time to fit residues: 56.1728 Evaluate side-chains 96 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 81 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [83, 84, 69, 70, 102, 1, 65, 30, 24, 101, 61] chunk 83 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 70 optimal weight: 0.1980 chunk 102 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 92 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.080563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.056252 restraints weight = 18974.785| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 2.27 r_work: 0.2662 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9170 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.218 9848 Z= 0.137 Angle : 0.612 9.611 13458 Z= 0.299 Chirality : 0.045 0.172 1360 Planarity : 0.004 0.045 1758 Dihedral : 8.311 87.732 1359 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.00 % Allowed : 23.86 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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 (0.25), residues: 1204 helix: 0.59 (0.31), residues: 299 sheet: -1.08 (0.39), residues: 158 loop : -0.29 (0.25), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 135 TYR 0.012 0.001 TYR B 123 PHE 0.009 0.001 PHE B 140 TRP 0.011 0.001 TRP A 331 HIS 0.013 0.001 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 9833) covalent geometry : angle 0.61112 / 0.30 (13454) SS BOND : bond 0.00565 / 0.30 ( 2) SS BOND : angle 1.45735 / 0.83 ( 4) hydrogen bonds : bond 0.03097 / 2.13 ( 317) hydrogen bonds : angle 5.86640 / 4.10 ( 858) Misc. bond : bond 0.08556 / 5.31 ( 13) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8272 (mtm180) cc_final: 0.7535 (mpt90) REVERT: A 201 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.7598 (mpt180) REVERT: A 359 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7143 (pp20) REVERT: B 125 GLU cc_start: 0.6945 (tm-30) cc_final: 0.6614 (tm-30) REVERT: B 137 MET cc_start: 0.8204 (mmp) cc_final: 0.7866 (mmt) REVERT: B 166 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.5693 (pp-130) REVERT: B 378 MET cc_start: 0.9109 (ttt) cc_final: 0.8584 (ttt) REVERT: C 27 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.7153 (pp30) REVERT: C 78 GLU cc_start: 0.8871 (pt0) cc_final: 0.8452 (pp20) REVERT: C 81 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8900 (mmpt) REVERT: C 127 LYS cc_start: 0.8706 (mptt) cc_final: 0.8416 (mptt) outliers start: 29 outliers final: 19 residues processed: 97 average time/residue: 0.5480 time to fit residues: 57.1567 Evaluate side-chains 98 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 81 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [67, 110, 6, 27, 63, 73, 0, 53, 74, 112, 39] chunk 67 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 6 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 73 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 92 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.080447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.056058 restraints weight = 18948.948| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 2.27 r_work: 0.2662 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9171 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.246 9848 Z= 0.144 Angle : 0.616 8.159 13458 Z= 0.301 Chirality : 0.045 0.195 1360 Planarity : 0.004 0.042 1758 Dihedral : 8.303 87.476 1359 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.89 % Allowed : 24.07 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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 (0.25), residues: 1204 helix: 0.56 (0.31), residues: 300 sheet: -1.09 (0.39), residues: 158 loop : -0.28 (0.25), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 135 TYR 0.022 0.001 TYR B 118 PHE 0.008 0.001 PHE A 515 TRP 0.011 0.001 TRP A 331 HIS 0.004 0.001 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.14 ( 9833) covalent geometry : angle 0.61513 / 0.30 (13454) SS BOND : bond 0.00551 / 0.29 ( 2) SS BOND : angle 1.45264 / 0.83 ( 4) hydrogen bonds : bond 0.03113 / 2.15 ( 317) hydrogen bonds : angle 5.83843 / 4.08 ( 858) Misc. bond : bond 0.09368 / 5.55 ( 13) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8278 (mtm180) cc_final: 0.7541 (mpt90) REVERT: A 201 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.7608 (mpt180) REVERT: A 359 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7148 (pp20) REVERT: B 121 MET cc_start: 0.6990 (mmm) cc_final: 0.6686 (mmt) REVERT: B 125 GLU cc_start: 0.6860 (tm-30) cc_final: 0.6539 (tm-30) REVERT: B 137 MET cc_start: 0.8181 (mmp) cc_final: 0.7870 (mmt) REVERT: B 143 HIS cc_start: 0.8259 (m90) cc_final: 0.7983 (m90) REVERT: B 166 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.6911 (pmm) REVERT: B 378 MET cc_start: 0.9115 (ttt) cc_final: 0.8566 (ttt) REVERT: B 447 ASP cc_start: 0.8735 (p0) cc_final: 0.8304 (p0) REVERT: C 27 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.7154 (pp30) REVERT: C 78 GLU cc_start: 0.8886 (pt0) cc_final: 0.8469 (pp20) REVERT: C 81 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8890 (mmpt) REVERT: C 127 LYS cc_start: 0.8701 (mptt) cc_final: 0.8413 (mptt) outliers start: 28 outliers final: 19 residues processed: 96 average time/residue: 0.5347 time to fit residues: 55.5451 Evaluate side-chains 98 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 653 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 81 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: [22, 66, 59, 71, 96, 6, 8, 56, 76, 116, 32] chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 116 optimal weight: 0.0070 chunk 32 optimal weight: 0.0970 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 92 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.080072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.055675 restraints weight = 18935.607| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 2.26 r_work: 0.2649 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9176 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.267 9848 Z= 0.158 Angle : 0.632 10.673 13458 Z= 0.306 Chirality : 0.045 0.201 1360 Planarity : 0.004 0.042 1758 Dihedral : 8.318 87.529 1359 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.00 % Allowed : 23.97 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: -0.34 (0.25), residues: 1204 helix: 0.56 (0.31), residues: 300 sheet: -1.08 (0.39), residues: 157 loop : -0.29 (0.25), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 135 TYR 0.013 0.001 TYR B 123 PHE 0.010 0.001 PHE B 140 TRP 0.010 0.001 TRP A 177 HIS 0.004 0.001 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 ( 9833) covalent geometry : angle 0.63123 / 0.31 (13454) SS BOND : bond 0.00518 / 0.27 ( 2) SS BOND : angle 1.46001 / 0.83 ( 4) hydrogen bonds : bond 0.03164 / 2.20 ( 317) hydrogen bonds : angle 5.86041 / 4.09 ( 858) Misc. bond : bond 0.09808 / 5.76 ( 13) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3274.10 seconds wall clock time: 56 minutes 32.52 seconds (3392.52 seconds total)