Starting phenix.real_space_refine on Tue Aug 4 11:46:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11zv_76232/08_2026/11zv_76232.cif Found real_map, /net/cci-nas-00/data/ceres_data/11zv_76232/08_2026/11zv_76232.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11zv_76232/08_2026/11zv_76232.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11zv_76232/08_2026/11zv_76232.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11zv_76232/08_2026/11zv_76232.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11zv_76232/08_2026/11zv_76232.map" } resolution = 2.84 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= 0.018 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: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 1253 2.51 5 N 311 2.21 5 O 422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2002 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 876 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 111} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 991 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 3, 'TRANS': 123} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Time building chain proxies: 0.94, per 1000 atoms: 0.47 Number of scatterers: 2002 At special positions: 0 Unit cell: (79.237, 68.204, 54.162, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 422 8.00 N 311 7.00 C 1253 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 378 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS A 386 " 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=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 311 " " NAG D 1 " - " ASN A 331 " Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 87.4 milliseconds 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 456 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 2 sheets defined 47.1% alpha, 48.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.199A pdb=" N ASN A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 371 " --> pdb=" O VAL A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 15 removed outlier: 3.811A pdb=" N HIS B 15 " --> pdb=" O ILE B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 31 removed outlier: 3.526A pdb=" N PHE B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 51 Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 58 through 81 removed outlier: 3.795A pdb=" N GLN B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 107 removed outlier: 3.587A pdb=" N SER B 105 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE B 106 " --> pdb=" O TRP B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 126 Processing sheet with id=AA1, first strand: chain 'A' and resid 320 through 328 removed outlier: 6.687A pdb=" N SER A 313 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL A 326 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASN A 311 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE A 328 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLN A 309 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLU A 306 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N GLU A 344 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL A 308 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASN A 346 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU A 310 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N MET A 348 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE A 312 " --> pdb=" O MET A 348 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N THR A 350 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ALA A 314 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 10.690A pdb=" N ALA A 408 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 11.975A pdb=" N SER A 380 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 11.387A pdb=" N GLU A 410 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 11.004A pdb=" N CYS A 378 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 9.022A pdb=" N GLN A 412 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N GLN A 376 " --> pdb=" O GLN A 412 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 320 through 328 removed outlier: 6.687A pdb=" N SER A 313 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL A 326 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASN A 311 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE A 328 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLN A 309 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLU A 306 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N GLU A 344 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL A 308 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASN A 346 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU A 310 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N MET A 348 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE A 312 " --> pdb=" O MET A 348 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N THR A 350 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ALA A 314 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE A 390 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N GLN A 402 " --> pdb=" O MET A 388 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N MET A 388 " --> pdb=" O GLN A 402 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU A 404 " --> pdb=" O CYS A 386 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N CYS A 386 " --> pdb=" O LEU A 404 " (cutoff:3.500A) 100 hydrogen bonds defined for protein. 282 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.35 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 315 1.32 - 1.44: 531 1.44 - 1.57: 1117 1.57 - 1.69: 0 1.69 - 1.82: 26 Bond restraints: 1989 Sorted by residual: bond pdb=" C ASN A 311 " pdb=" O ASN A 311 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.14e-02 7.69e+03 1.55e+01 bond pdb=" N GLU A 320 " pdb=" CA GLU A 320 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.54e+00 bond pdb=" N ARG B 58 " pdb=" CA ARG B 58 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.32e-02 5.74e+03 4.70e+00 bond pdb=" N GLU B 44 " pdb=" CA GLU B 44 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.23e-02 6.61e+03 4.07e+00 bond pdb=" N LEU A 305 " pdb=" CA LEU A 305 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 ... (remaining 1984 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 2570 1.56 - 3.12: 89 3.12 - 4.68: 29 4.68 - 6.24: 3 6.24 - 7.81: 1 Bond angle restraints: 2692 Sorted by residual: angle pdb=" C ASN A 311 " pdb=" CA ASN A 311 " pdb=" CB ASN A 311 " ideal model delta sigma weight residual 111.23 103.42 7.81 1.68e+00 3.54e-01 2.16e+01 angle pdb=" CA ASN A 311 " pdb=" C ASN A 311 " pdb=" O ASN A 311 " ideal model delta sigma weight residual 120.57 117.08 3.49 1.26e+00 6.30e-01 7.67e+00 angle pdb=" C GLU A 320 " pdb=" CA GLU A 320 " pdb=" CB GLU A 320 " ideal model delta sigma weight residual 110.16 106.17 3.99 1.66e+00 3.63e-01 5.78e+00 angle pdb=" N GLU B 44 " pdb=" CA GLU B 44 " pdb=" C GLU B 44 " ideal model delta sigma weight residual 111.36 108.81 2.55 1.09e+00 8.42e-01 5.49e+00 angle pdb=" CA CYS A 349 " pdb=" CB CYS A 349 " pdb=" SG CYS A 349 " ideal model delta sigma weight residual 114.40 119.75 -5.35 2.30e+00 1.89e-01 5.41e+00 ... (remaining 2687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.88: 1211 20.88 - 41.76: 48 41.76 - 62.64: 12 62.64 - 83.52: 9 83.52 - 104.40: 4 Dihedral angle restraints: 1284 sinusoidal: 581 harmonic: 703 Sorted by residual: dihedral pdb=" CB CYS A 349 " pdb=" SG CYS A 349 " pdb=" SG CYS A 352 " pdb=" CB CYS A 352 " ideal model delta sinusoidal sigma weight residual -86.00 -167.66 81.66 1 1.00e+01 1.00e-02 8.21e+01 dihedral pdb=" CA MET A 348 " pdb=" C MET A 348 " pdb=" N CYS A 349 " pdb=" CA CYS A 349 " ideal model delta harmonic sigma weight residual 180.00 157.13 22.87 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA GLU A 387 " pdb=" C GLU A 387 " pdb=" N MET A 388 " pdb=" CA MET A 388 " ideal model delta harmonic sigma weight residual 180.00 158.96 21.04 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 1281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 323 0.119 - 0.238: 6 0.238 - 0.357: 4 0.357 - 0.476: 1 0.476 - 0.595: 1 Chirality restraints: 335 Sorted by residual: chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 3.05e+01 chirality pdb=" C1 MAN C 5 " pdb=" O6 BMA C 3 " pdb=" C2 MAN C 5 " pdb=" O5 MAN C 5 " both_signs ideal model delta sigma weight residual False 2.40 2.33 0.07 2.00e-02 2.50e+03 1.37e+01 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 311 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.85e+00 ... (remaining 332 not shown) Planarity restraints: 329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 58 " -0.522 9.50e-02 1.11e+02 2.34e-01 3.35e+01 pdb=" NE ARG B 58 " 0.031 2.00e-02 2.50e+03 pdb=" CZ ARG B 58 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 58 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 58 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.028 2.00e-02 2.50e+03 2.27e-02 6.46e+00 pdb=" C7 NAG C 1 " 0.009 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.022 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.035 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 398 " -0.007 2.00e-02 2.50e+03 1.70e-02 5.78e+00 pdb=" CG TYR A 398 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR A 398 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 398 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 398 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR A 398 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 398 " 0.021 2.00e-02 2.50e+03 pdb=" OH TYR A 398 " -0.031 2.00e-02 2.50e+03 ... (remaining 326 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 675 2.86 - 3.37: 1831 3.37 - 3.88: 3396 3.88 - 4.39: 3950 4.39 - 4.90: 6739 Nonbonded interactions: 16591 Sorted by model distance: nonbonded pdb=" OH TYR B 92 " pdb=" OD1 ASP B 122 " model vdw 2.347 3.040 nonbonded pdb=" O VAL A 326 " pdb=" O HOH A 501 " model vdw 2.372 3.040 nonbonded pdb=" OD2 ASP A 324 " pdb=" O HOH A 502 " model vdw 2.382 3.040 nonbonded pdb=" OH TYR B 21 " pdb=" OD1 ASP B 68 " model vdw 2.435 3.040 nonbonded pdb=" OE1 GLU A 306 " pdb=" OH TYR A 334 " model vdw 2.438 3.040 ... (remaining 16586 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: 2.370 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.160 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 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 : 0.005 0.048 1999 Z= 0.260 Angle : 0.857 9.568 2719 Z= 0.432 Chirality : 0.069 0.595 335 Planarity : 0.015 0.234 327 Dihedral : 15.891 104.405 819 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 0.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.52 % Allowed : 0.00 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.50), residues: 236 helix: 0.71 (0.48), residues: 95 sheet: 0.48 (0.65), residues: 58 loop : -0.93 (0.60), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 98 TYR 0.031 0.005 TYR A 398 PHE 0.016 0.002 PHE A 363 TRP 0.021 0.005 TRP B 102 HIS 0.006 0.003 HIS B 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.24 ( 1989) covalent geometry : angle 0.76034 / 0.41 ( 2692) SS BOND : bond 0.00243 / 0.13 ( 3) SS BOND : angle 1.55713 / 0.65 ( 6) hydrogen bonds : bond 0.11990 / 7.07 ( 94) hydrogen bonds : angle 6.33197 / 4.44 ( 282) link_ALPHA1-3 : bond 0.04559 / 2.40 ( 1) link_ALPHA1-3 : angle 5.10986 / 2.72 ( 3) link_ALPHA1-6 : bond 0.03682 / 1.94 ( 1) link_ALPHA1-6 : angle 3.96672 / 2.01 ( 3) link_BETA1-4 : bond 0.03872 / 1.94 ( 3) link_BETA1-4 : angle 4.99736 / 2.32 ( 9) link_NAG-ASN : bond 0.01317 / 0.69 ( 2) link_NAG-ASN : angle 3.60029 / 1.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.087 Fit side-chains REVERT: B 34 LYS cc_start: 0.8605 (mmtm) cc_final: 0.8230 (mmmt) REVERT: B 58 ARG cc_start: 0.7649 (mtp85) cc_final: 0.7336 (mtp85) outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.9052 time to fit residues: 59.5484 Evaluate side-chains 56 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.0370 chunk 4 optimal weight: 1.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 346 ASN A 370 ASN B 15 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.084289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.065288 restraints weight = 4395.789| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.53 r_work: 0.2832 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 1999 Z= 0.143 Angle : 0.639 5.566 2719 Z= 0.333 Chirality : 0.043 0.190 335 Planarity : 0.004 0.031 327 Dihedral : 10.992 68.274 398 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.65 % Allowed : 13.02 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.52), residues: 236 helix: 2.20 (0.48), residues: 97 sheet: 0.53 (0.72), residues: 54 loop : -0.65 (0.60), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 401 TYR 0.015 0.002 TYR B 125 PHE 0.010 0.001 PHE B 27 TRP 0.010 0.002 TRP A 396 HIS 0.004 0.001 HIS B 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 1989) covalent geometry : angle 0.61108 / 0.33 ( 2692) SS BOND : bond 0.00144 / 0.07 ( 3) SS BOND : angle 2.20065 / 1.13 ( 6) hydrogen bonds : bond 0.03754 / 2.51 ( 94) hydrogen bonds : angle 4.44587 / 3.20 ( 282) link_ALPHA1-3 : bond 0.00620 / 0.33 ( 1) link_ALPHA1-3 : angle 1.58187 / 0.91 ( 3) link_ALPHA1-6 : bond 0.00355 / 0.19 ( 1) link_ALPHA1-6 : angle 1.64879 / 0.93 ( 3) link_BETA1-4 : bond 0.00271 / 0.14 ( 3) link_BETA1-4 : angle 2.44199 / 0.97 ( 9) link_NAG-ASN : bond 0.00066 / 0.03 ( 2) link_NAG-ASN : angle 0.95280 / 0.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: A 344 GLU cc_start: 0.8088 (tt0) cc_final: 0.7598 (tt0) REVERT: B 26 GLU cc_start: 0.8869 (mp0) cc_final: 0.8377 (mp0) REVERT: B 34 LYS cc_start: 0.9026 (mmtm) cc_final: 0.8460 (mmmt) REVERT: B 68 ASP cc_start: 0.9093 (t0) cc_final: 0.8878 (t0) REVERT: B 72 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8329 (mp0) REVERT: B 87 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.6967 (t70) REVERT: B 93 ASP cc_start: 0.8914 (m-30) cc_final: 0.8675 (m-30) REVERT: B 100 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8726 (tp30) outliers start: 7 outliers final: 1 residues processed: 63 average time/residue: 0.7748 time to fit residues: 49.4490 Evaluate side-chains 58 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 100 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 2 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.082584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.063802 restraints weight = 4439.521| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.54 r_work: 0.2803 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 1999 Z= 0.136 Angle : 0.584 7.150 2719 Z= 0.301 Chirality : 0.042 0.171 335 Planarity : 0.004 0.042 327 Dihedral : 7.011 41.812 398 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.60 % Allowed : 14.58 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.55), residues: 236 helix: 2.77 (0.49), residues: 98 sheet: 0.01 (0.67), residues: 64 loop : -0.32 (0.69), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG B 58 TYR 0.022 0.001 TYR B 125 PHE 0.010 0.001 PHE B 27 TRP 0.009 0.001 TRP A 396 HIS 0.001 0.000 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 ( 1989) covalent geometry : angle 0.55629 / 0.29 ( 2692) SS BOND : bond 0.00527 / 0.27 ( 3) SS BOND : angle 2.51077 / 1.31 ( 6) hydrogen bonds : bond 0.03255 / 2.19 ( 94) hydrogen bonds : angle 4.08428 / 2.96 ( 282) link_ALPHA1-3 : bond 0.01256 / 0.66 ( 1) link_ALPHA1-3 : angle 1.14244 / 0.59 ( 3) link_ALPHA1-6 : bond 0.00914 / 0.48 ( 1) link_ALPHA1-6 : angle 1.19119 / 0.68 ( 3) link_BETA1-4 : bond 0.00322 / 0.16 ( 3) link_BETA1-4 : angle 2.09079 / 0.86 ( 9) link_NAG-ASN : bond 0.00191 / 0.10 ( 2) link_NAG-ASN : angle 1.21749 / 0.55 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: A 344 GLU cc_start: 0.8204 (tt0) cc_final: 0.7558 (tt0) REVERT: A 348 MET cc_start: 0.8186 (mtm) cc_final: 0.7694 (ptp) REVERT: A 364 ASP cc_start: 0.8709 (m-30) cc_final: 0.8444 (m-30) REVERT: A 388 MET cc_start: 0.9387 (OUTLIER) cc_final: 0.8667 (mmt) REVERT: B 25 GLU cc_start: 0.8921 (pm20) cc_final: 0.8603 (pm20) REVERT: B 26 GLU cc_start: 0.8963 (mp0) cc_final: 0.8239 (mp0) REVERT: B 34 LYS cc_start: 0.9069 (mmtm) cc_final: 0.8448 (mmmt) REVERT: B 45 LYS cc_start: 0.9560 (mmmm) cc_final: 0.9301 (tptp) REVERT: B 68 ASP cc_start: 0.9096 (t0) cc_final: 0.8783 (t0) REVERT: B 72 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8333 (mp0) REVERT: B 87 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7051 (t70) outliers start: 5 outliers final: 1 residues processed: 59 average time/residue: 0.7967 time to fit residues: 47.6690 Evaluate side-chains 59 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 87 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 0.0050 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.080169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.061293 restraints weight = 4517.390| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.62 r_work: 0.2759 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 1999 Z= 0.194 Angle : 0.602 7.848 2719 Z= 0.310 Chirality : 0.043 0.187 335 Planarity : 0.004 0.041 327 Dihedral : 5.469 26.491 398 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.17 % Allowed : 14.58 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.56), residues: 236 helix: 3.05 (0.49), residues: 98 sheet: -0.03 (0.67), residues: 64 loop : -0.44 (0.71), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG A 322 TYR 0.006 0.001 TYR A 398 PHE 0.008 0.001 PHE B 27 TRP 0.006 0.001 TRP A 396 HIS 0.003 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 ( 1989) covalent geometry : angle 0.57517 / 0.30 ( 2692) SS BOND : bond 0.00588 / 0.31 ( 3) SS BOND : angle 2.56044 / 1.34 ( 6) hydrogen bonds : bond 0.03466 / 2.43 ( 94) hydrogen bonds : angle 4.05186 / 2.94 ( 282) link_ALPHA1-3 : bond 0.01220 / 0.64 ( 1) link_ALPHA1-3 : angle 1.62419 / 0.81 ( 3) link_ALPHA1-6 : bond 0.00941 / 0.50 ( 1) link_ALPHA1-6 : angle 1.42582 / 0.69 ( 3) link_BETA1-4 : bond 0.00287 / 0.14 ( 3) link_BETA1-4 : angle 1.91906 / 0.77 ( 9) link_NAG-ASN : bond 0.00275 / 0.14 ( 2) link_NAG-ASN : angle 1.24945 / 0.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.098 Fit side-chains revert: symmetry clash REVERT: A 322 ARG cc_start: 0.8156 (mmt90) cc_final: 0.7563 (mmt-90) REVERT: A 344 GLU cc_start: 0.8286 (tt0) cc_final: 0.7739 (tt0) REVERT: A 348 MET cc_start: 0.8335 (mtm) cc_final: 0.7848 (ptp) REVERT: A 410 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7893 (tt0) REVERT: B 25 GLU cc_start: 0.8895 (pm20) cc_final: 0.8531 (pm20) REVERT: B 26 GLU cc_start: 0.8976 (mp0) cc_final: 0.8194 (mp0) REVERT: B 34 LYS cc_start: 0.9116 (mmtm) cc_final: 0.8473 (mmmt) REVERT: B 45 LYS cc_start: 0.9610 (OUTLIER) cc_final: 0.9380 (tptp) REVERT: B 68 ASP cc_start: 0.9099 (t0) cc_final: 0.8789 (t0) REVERT: B 72 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8379 (mp0) REVERT: B 87 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7419 (t70) REVERT: B 126 ASN cc_start: 0.9038 (m-40) cc_final: 0.8815 (m-40) outliers start: 8 outliers final: 1 residues processed: 60 average time/residue: 0.8151 time to fit residues: 49.5282 Evaluate side-chains 60 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 87 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 0.0570 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.080758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.061869 restraints weight = 4565.994| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.67 r_work: 0.2767 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 1999 Z= 0.152 Angle : 0.600 8.597 2719 Z= 0.312 Chirality : 0.042 0.192 335 Planarity : 0.004 0.035 327 Dihedral : 4.896 20.342 398 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.65 % Allowed : 17.19 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.56), residues: 236 helix: 3.20 (0.49), residues: 98 sheet: 0.09 (0.69), residues: 64 loop : -0.36 (0.73), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG A 401 TYR 0.006 0.001 TYR A 398 PHE 0.008 0.001 PHE B 27 TRP 0.007 0.001 TRP A 396 HIS 0.002 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 1989) covalent geometry : angle 0.57516 / 0.30 ( 2692) SS BOND : bond 0.00648 / 0.34 ( 3) SS BOND : angle 2.55858 / 1.34 ( 6) hydrogen bonds : bond 0.03142 / 2.18 ( 94) hydrogen bonds : angle 3.87484 / 2.81 ( 282) link_ALPHA1-3 : bond 0.01091 / 0.57 ( 1) link_ALPHA1-3 : angle 1.43149 / 0.71 ( 3) link_ALPHA1-6 : bond 0.00730 / 0.38 ( 1) link_ALPHA1-6 : angle 1.46037 / 0.68 ( 3) link_BETA1-4 : bond 0.00363 / 0.18 ( 3) link_BETA1-4 : angle 1.80683 / 0.75 ( 9) link_NAG-ASN : bond 0.00130 / 0.07 ( 2) link_NAG-ASN : angle 1.12055 / 0.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: A 322 ARG cc_start: 0.8081 (mmt90) cc_final: 0.7525 (mmt-90) REVERT: A 344 GLU cc_start: 0.8320 (tt0) cc_final: 0.7760 (tt0) REVERT: A 348 MET cc_start: 0.8469 (mtm) cc_final: 0.8111 (ptp) REVERT: A 410 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: B 25 GLU cc_start: 0.8949 (pm20) cc_final: 0.8579 (pm20) REVERT: B 26 GLU cc_start: 0.8954 (mp0) cc_final: 0.8209 (mp0) REVERT: B 34 LYS cc_start: 0.9113 (mmtm) cc_final: 0.8470 (mmmt) REVERT: B 45 LYS cc_start: 0.9606 (OUTLIER) cc_final: 0.9377 (tptp) REVERT: B 68 ASP cc_start: 0.9112 (t0) cc_final: 0.8798 (t0) REVERT: B 72 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: B 87 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7396 (t70) outliers start: 7 outliers final: 2 residues processed: 60 average time/residue: 0.7888 time to fit residues: 47.9256 Evaluate side-chains 61 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 87 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 0.3980 chunk 0 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 0.0980 chunk 22 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 370 ASN A 412 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.081144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.062422 restraints weight = 4444.058| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.63 r_work: 0.2791 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 1999 Z= 0.128 Angle : 0.580 9.114 2719 Z= 0.302 Chirality : 0.041 0.179 335 Planarity : 0.004 0.031 327 Dihedral : 4.546 18.606 398 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 5.73 % Allowed : 15.62 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.57), residues: 236 helix: 3.39 (0.48), residues: 98 sheet: 0.03 (0.69), residues: 64 loop : -0.20 (0.74), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 342 TYR 0.021 0.001 TYR B 125 PHE 0.008 0.001 PHE B 27 TRP 0.008 0.001 TRP A 396 HIS 0.002 0.000 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 1989) covalent geometry : angle 0.55667 / 0.30 ( 2692) SS BOND : bond 0.00655 / 0.34 ( 3) SS BOND : angle 2.42343 / 1.27 ( 6) hydrogen bonds : bond 0.02894 / 2.01 ( 94) hydrogen bonds : angle 3.72612 / 2.71 ( 282) link_ALPHA1-3 : bond 0.00891 / 0.47 ( 1) link_ALPHA1-3 : angle 1.34127 / 0.66 ( 3) link_ALPHA1-6 : bond 0.00626 / 0.33 ( 1) link_ALPHA1-6 : angle 1.52869 / 0.69 ( 3) link_BETA1-4 : bond 0.00317 / 0.15 ( 3) link_BETA1-4 : angle 1.68481 / 0.70 ( 9) link_NAG-ASN : bond 0.00025 / 0.01 ( 2) link_NAG-ASN : angle 1.05863 / 0.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.063 Fit side-chains revert: symmetry clash REVERT: A 322 ARG cc_start: 0.8043 (mmt90) cc_final: 0.7492 (mmt-90) REVERT: A 342 ARG cc_start: 0.8669 (ttp80) cc_final: 0.8218 (ttp80) REVERT: A 344 GLU cc_start: 0.8299 (tt0) cc_final: 0.7909 (tt0) REVERT: A 348 MET cc_start: 0.8482 (mtm) cc_final: 0.8112 (ptp) REVERT: A 388 MET cc_start: 0.9413 (mmt) cc_final: 0.8644 (mmt) REVERT: A 410 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: B 25 GLU cc_start: 0.8947 (pm20) cc_final: 0.8544 (pm20) REVERT: B 26 GLU cc_start: 0.8983 (mp0) cc_final: 0.8172 (mp0) REVERT: B 34 LYS cc_start: 0.9128 (mmtm) cc_final: 0.8489 (mmmt) REVERT: B 45 LYS cc_start: 0.9606 (OUTLIER) cc_final: 0.9380 (tptp) REVERT: B 68 ASP cc_start: 0.9083 (t0) cc_final: 0.8767 (t0) REVERT: B 72 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8392 (mp0) REVERT: B 87 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7395 (t70) REVERT: B 89 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8215 (tmmm) outliers start: 11 outliers final: 1 residues processed: 60 average time/residue: 0.8024 time to fit residues: 48.7582 Evaluate side-chains 62 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 89 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.080280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.061739 restraints weight = 4496.076| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.61 r_work: 0.2759 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 1999 Z= 0.156 Angle : 0.615 9.626 2719 Z= 0.317 Chirality : 0.041 0.172 335 Planarity : 0.003 0.028 327 Dihedral : 4.457 18.965 398 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.12 % Allowed : 19.79 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.57), residues: 236 helix: 3.45 (0.48), residues: 98 sheet: 0.05 (0.69), residues: 64 loop : -0.17 (0.74), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 401 TYR 0.006 0.001 TYR A 398 PHE 0.008 0.001 PHE B 27 TRP 0.006 0.001 TRP A 396 HIS 0.002 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 1989) covalent geometry : angle 0.59262 / 0.31 ( 2692) SS BOND : bond 0.00733 / 0.38 ( 3) SS BOND : angle 2.45372 / 1.29 ( 6) hydrogen bonds : bond 0.03014 / 2.11 ( 94) hydrogen bonds : angle 3.76758 / 2.73 ( 282) link_ALPHA1-3 : bond 0.00890 / 0.47 ( 1) link_ALPHA1-3 : angle 1.42428 / 0.71 ( 3) link_ALPHA1-6 : bond 0.00570 / 0.30 ( 1) link_ALPHA1-6 : angle 1.57931 / 0.70 ( 3) link_BETA1-4 : bond 0.00318 / 0.15 ( 3) link_BETA1-4 : angle 1.65753 / 0.70 ( 9) link_NAG-ASN : bond 0.00111 / 0.06 ( 2) link_NAG-ASN : angle 1.09813 / 0.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.048 Fit side-chains REVERT: A 320 GLU cc_start: 0.6587 (mt-10) cc_final: 0.6283 (mt-10) REVERT: A 322 ARG cc_start: 0.8062 (mmt90) cc_final: 0.7683 (mmt90) REVERT: A 344 GLU cc_start: 0.8306 (tt0) cc_final: 0.7814 (tt0) REVERT: A 348 MET cc_start: 0.8584 (mtm) cc_final: 0.8187 (ptp) REVERT: A 410 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7890 (tt0) REVERT: B 25 GLU cc_start: 0.8962 (pm20) cc_final: 0.8554 (pm20) REVERT: B 26 GLU cc_start: 0.8985 (mp0) cc_final: 0.8179 (mp0) REVERT: B 34 LYS cc_start: 0.9084 (mmtm) cc_final: 0.8470 (mmmt) REVERT: B 68 ASP cc_start: 0.9064 (t0) cc_final: 0.8744 (t0) REVERT: B 72 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8371 (mp0) REVERT: B 87 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7422 (t70) REVERT: B 89 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8397 (tppp) outliers start: 6 outliers final: 1 residues processed: 57 average time/residue: 0.5388 time to fit residues: 31.0775 Evaluate side-chains 59 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 89 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.079905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.061551 restraints weight = 4532.176| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.59 r_work: 0.2756 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 1999 Z= 0.182 Angle : 0.745 13.756 2719 Z= 0.377 Chirality : 0.046 0.354 335 Planarity : 0.003 0.036 327 Dihedral : 4.489 18.822 398 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 5.21 % Allowed : 18.75 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.58), residues: 236 helix: 3.52 (0.49), residues: 98 sheet: 0.08 (0.71), residues: 64 loop : -0.16 (0.74), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 342 TYR 0.006 0.001 TYR A 398 PHE 0.007 0.001 PHE B 27 TRP 0.005 0.001 TRP A 396 HIS 0.003 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 ( 1989) covalent geometry : angle 0.69130 / 0.36 ( 2692) SS BOND : bond 0.00895 / 0.47 ( 3) SS BOND : angle 5.42749 / 3.08 ( 6) hydrogen bonds : bond 0.03223 / 2.23 ( 94) hydrogen bonds : angle 3.78885 / 2.75 ( 282) link_ALPHA1-3 : bond 0.00841 / 0.44 ( 1) link_ALPHA1-3 : angle 1.44168 / 0.72 ( 3) link_ALPHA1-6 : bond 0.00511 / 0.27 ( 1) link_ALPHA1-6 : angle 1.58875 / 0.70 ( 3) link_BETA1-4 : bond 0.00329 / 0.16 ( 3) link_BETA1-4 : angle 1.64090 / 0.69 ( 9) link_NAG-ASN : bond 0.00146 / 0.08 ( 2) link_NAG-ASN : angle 1.11358 / 0.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.057 Fit side-chains REVERT: A 320 GLU cc_start: 0.6682 (mt-10) cc_final: 0.6369 (mt-10) REVERT: A 322 ARG cc_start: 0.8085 (mmt90) cc_final: 0.7710 (mmt90) REVERT: A 344 GLU cc_start: 0.8292 (tt0) cc_final: 0.7801 (tt0) REVERT: A 348 MET cc_start: 0.8596 (mtm) cc_final: 0.8191 (ptp) REVERT: A 410 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: B 26 GLU cc_start: 0.8988 (mp0) cc_final: 0.8357 (mp0) REVERT: B 34 LYS cc_start: 0.9105 (mmtm) cc_final: 0.8492 (mmmt) REVERT: B 68 ASP cc_start: 0.9065 (t0) cc_final: 0.8743 (t0) REVERT: B 72 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8376 (mp0) REVERT: B 87 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7501 (t70) outliers start: 10 outliers final: 1 residues processed: 57 average time/residue: 0.5240 time to fit residues: 30.2485 Evaluate side-chains 58 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 87 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.0370 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.080466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.061698 restraints weight = 4374.702| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.61 r_work: 0.2761 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 1999 Z= 0.171 Angle : 0.888 22.836 2719 Z= 0.448 Chirality : 0.048 0.401 335 Planarity : 0.004 0.035 327 Dihedral : 4.487 23.353 398 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.08 % Allowed : 21.35 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.58), residues: 236 helix: 3.60 (0.49), residues: 98 sheet: -0.02 (0.70), residues: 64 loop : -0.12 (0.74), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 342 TYR 0.006 0.001 TYR A 398 PHE 0.010 0.001 PHE A 377 TRP 0.006 0.001 TRP A 396 HIS 0.003 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 1989) covalent geometry : angle 0.83349 / 0.43 ( 2692) SS BOND : bond 0.01374 / 0.72 ( 3) SS BOND : angle 6.17285 / 3.49 ( 6) hydrogen bonds : bond 0.03272 / 2.18 ( 94) hydrogen bonds : angle 3.73134 / 2.71 ( 282) link_ALPHA1-3 : bond 0.00775 / 0.41 ( 1) link_ALPHA1-3 : angle 1.39318 / 0.69 ( 3) link_ALPHA1-6 : bond 0.00491 / 0.26 ( 1) link_ALPHA1-6 : angle 1.58757 / 0.69 ( 3) link_BETA1-4 : bond 0.00322 / 0.16 ( 3) link_BETA1-4 : angle 1.60132 / 0.68 ( 9) link_NAG-ASN : bond 0.00089 / 0.05 ( 2) link_NAG-ASN : angle 1.08789 / 0.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.056 Fit side-chains REVERT: A 322 ARG cc_start: 0.8089 (mmt90) cc_final: 0.7809 (mmt90) REVERT: A 342 ARG cc_start: 0.8676 (ttp80) cc_final: 0.8224 (ttp80) REVERT: A 344 GLU cc_start: 0.8290 (tt0) cc_final: 0.7937 (tt0) REVERT: A 348 MET cc_start: 0.8612 (mtm) cc_final: 0.8190 (ptp) REVERT: B 26 GLU cc_start: 0.9008 (mp0) cc_final: 0.8397 (mp0) REVERT: B 34 LYS cc_start: 0.9097 (mmtm) cc_final: 0.8484 (mmmt) REVERT: B 68 ASP cc_start: 0.9060 (t0) cc_final: 0.8735 (t0) REVERT: B 72 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8364 (mp0) REVERT: B 87 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7482 (t70) REVERT: B 110 GLU cc_start: 0.8812 (mp0) cc_final: 0.8260 (mp0) outliers start: 4 outliers final: 1 residues processed: 56 average time/residue: 0.5171 time to fit residues: 29.3203 Evaluate side-chains 57 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 87 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 GLN B 126 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.081034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.062079 restraints weight = 4561.780| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.69 r_work: 0.2761 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 1999 Z= 0.157 Angle : 0.817 20.403 2719 Z= 0.411 Chirality : 0.046 0.345 335 Planarity : 0.003 0.034 327 Dihedral : 4.488 24.929 398 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.12 % Allowed : 20.83 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.58), residues: 236 helix: 3.64 (0.50), residues: 98 sheet: -0.01 (0.70), residues: 64 loop : -0.07 (0.74), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 342 TYR 0.006 0.001 TYR A 398 PHE 0.009 0.001 PHE A 377 TRP 0.006 0.001 TRP A 396 HIS 0.002 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 1989) covalent geometry : angle 0.76076 / 0.39 ( 2692) SS BOND : bond 0.01112 / 0.58 ( 3) SS BOND : angle 5.99784 / 3.40 ( 6) hydrogen bonds : bond 0.03172 / 2.09 ( 94) hydrogen bonds : angle 3.73573 / 2.70 ( 282) link_ALPHA1-3 : bond 0.00691 / 0.36 ( 1) link_ALPHA1-3 : angle 1.34222 / 0.66 ( 3) link_ALPHA1-6 : bond 0.00449 / 0.24 ( 1) link_ALPHA1-6 : angle 1.58572 / 0.69 ( 3) link_BETA1-4 : bond 0.00325 / 0.16 ( 3) link_BETA1-4 : angle 1.57261 / 0.67 ( 9) link_NAG-ASN : bond 0.00074 / 0.04 ( 2) link_NAG-ASN : angle 1.06500 / 0.51 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 472 Ramachandran restraints generated. 236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.048 Fit side-chains REVERT: A 322 ARG cc_start: 0.8077 (mmt90) cc_final: 0.7653 (mmt90) REVERT: A 342 ARG cc_start: 0.8660 (ttp80) cc_final: 0.8149 (ttp80) REVERT: A 344 GLU cc_start: 0.8296 (tt0) cc_final: 0.7930 (tt0) REVERT: A 348 MET cc_start: 0.8610 (mtm) cc_final: 0.8183 (ptp) REVERT: B 26 GLU cc_start: 0.8997 (mp0) cc_final: 0.8374 (mp0) REVERT: B 34 LYS cc_start: 0.9111 (mmtm) cc_final: 0.8506 (mmmt) REVERT: B 68 ASP cc_start: 0.9057 (t0) cc_final: 0.8731 (t0) REVERT: B 72 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8368 (mp0) REVERT: B 87 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7442 (t70) REVERT: B 110 GLU cc_start: 0.8778 (mp0) cc_final: 0.8239 (mp0) outliers start: 6 outliers final: 1 residues processed: 56 average time/residue: 0.5676 time to fit residues: 32.1961 Evaluate side-chains 56 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 87 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 23 random chunks: chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.080944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.062348 restraints weight = 4642.325| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.66 r_work: 0.2765 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 1999 Z= 0.176 Angle : 0.915 19.418 2719 Z= 0.459 Chirality : 0.045 0.321 335 Planarity : 0.003 0.034 327 Dihedral : 4.679 25.854 398 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.08 % Allowed : 22.92 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.58), residues: 236 helix: 3.66 (0.49), residues: 98 sheet: 0.08 (0.70), residues: 64 loop : -0.14 (0.74), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 342 TYR 0.018 0.001 TYR B 125 PHE 0.008 0.001 PHE A 377 TRP 0.006 0.001 TRP A 396 HIS 0.003 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 ( 1989) covalent geometry : angle 0.84089 / 0.43 ( 2692) SS BOND : bond 0.01097 / 0.57 ( 3) SS BOND : angle 7.42836 / 3.70 ( 6) hydrogen bonds : bond 0.03244 / 2.16 ( 94) hydrogen bonds : angle 3.74130 / 2.69 ( 282) link_ALPHA1-3 : bond 0.00737 / 0.39 ( 1) link_ALPHA1-3 : angle 1.40761 / 0.70 ( 3) link_ALPHA1-6 : bond 0.00457 / 0.24 ( 1) link_ALPHA1-6 : angle 1.60046 / 0.69 ( 3) link_BETA1-4 : bond 0.00328 / 0.16 ( 3) link_BETA1-4 : angle 1.56568 / 0.67 ( 9) link_NAG-ASN : bond 0.00104 / 0.05 ( 2) link_NAG-ASN : angle 1.09698 / 0.53 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1086.95 seconds wall clock time: 19 minutes 18.67 seconds (1158.67 seconds total)