Starting phenix.real_space_refine on Tue Aug 4 19:09:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cak_45394/08_2026/9cak_45394_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cak_45394/08_2026/9cak_45394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cak_45394/08_2026/9cak_45394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cak_45394/08_2026/9cak_45394.map" model { file = "/net/cci-nas-00/data/ceres_data/9cak_45394/08_2026/9cak_45394_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cak_45394/08_2026/9cak_45394_neut.cif" } resolution = 3.01 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= 0.001 sd= 0.020 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 Mn 2 7.51 5 P 10 5.49 5 S 40 5.16 5 C 3927 2.51 5 N 1083 2.21 5 O 1206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s 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: 6268 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4844 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 30, 'TRANS': 581} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1219 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "D" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 146 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "E" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Classifications: {'DNA': 3} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.20, per 1000 atoms: 0.19 Number of scatterers: 6268 At special positions: 0 Unit cell: (70.55, 88.81, 138.61, 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) Mn 2 24.99 S 40 16.00 P 10 15.00 O 1206 8.00 N 1083 7.00 C 3927 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 321.8 milliseconds 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1442 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 5 sheets defined 43.2% alpha, 19.1% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 10 through 23 removed outlier: 3.555A pdb=" N ARG A 23 " --> pdb=" O LYS A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 82 removed outlier: 3.942A pdb=" N PHE A 82 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 106 Processing helix chain 'A' and resid 119 through 134 removed outlier: 3.600A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 166 Processing helix chain 'A' and resid 171 through 204 removed outlier: 3.748A pdb=" N ALA A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY A 202 " --> pdb=" O LYS A 198 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 204 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 208 removed outlier: 3.550A pdb=" N ASP A 208 " --> pdb=" O GLY A 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 205 through 208' Processing helix chain 'A' and resid 217 through 234 removed outlier: 3.723A pdb=" N CYS A 225 " --> pdb=" O THR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 252 removed outlier: 3.572A pdb=" N ASP A 252 " --> pdb=" O THR A 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 252' Processing helix chain 'A' and resid 266 through 279 removed outlier: 3.623A pdb=" N THR A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEU A 279 " --> pdb=" O ASN A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 317 through 332 Processing helix chain 'A' and resid 349 through 357 removed outlier: 4.014A pdb=" N GLN A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 373 Processing helix chain 'A' and resid 404 through 421 removed outlier: 3.625A pdb=" N LEU A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 removed outlier: 3.580A pdb=" N GLU A 454 " --> pdb=" O GLY A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 506 Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 538 through 552 Processing helix chain 'A' and resid 553 through 556 Processing helix chain 'A' and resid 559 through 573 removed outlier: 3.549A pdb=" N LEU A 570 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE A 571 " --> pdb=" O GLN A 567 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 599 removed outlier: 3.566A pdb=" N LYS A 592 " --> pdb=" O VAL A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 609 removed outlier: 3.766A pdb=" N LEU A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 13 Processing helix chain 'B' and resid 17 through 24 Processing helix chain 'B' and resid 32 through 43 Processing helix chain 'B' and resid 44 through 49 removed outlier: 4.063A pdb=" N ILE B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 5.740A pdb=" N SER A 37 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER A 56 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LYS A 2 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LYS A 53 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 4 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N THR A 55 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N MET A 6 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR A 3 " --> pdb=" O ASP A 110 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE A 112 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU A 5 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N LEU A 114 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL A 7 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 66 Processing sheet with id=AA3, first strand: chain 'A' and resid 446 through 449 removed outlier: 7.070A pdb=" N LYS A 425 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N SER A 443 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N LEU A 256 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA A 245 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TRP A 259 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LEU A 243 " --> pdb=" O TRP A 259 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A 480 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL A 285 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG A 434 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA A 287 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A 291 " --> pdb=" O GLN A 428 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 527 through 530 Processing sheet with id=AA5, first strand: chain 'B' and resid 64 through 66 removed outlier: 4.718A pdb=" N ASP B 134 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LEU B 95 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ARG B 96 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE B 76 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLN B 98 " --> pdb=" O GLN B 74 " (cutoff:3.500A) 282 hydrogen bonds defined for protein. 798 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1945 1.33 - 1.45: 897 1.45 - 1.57: 3494 1.57 - 1.69: 15 1.69 - 1.81: 63 Bond restraints: 6414 Sorted by residual: bond pdb=" OH PTR A 336 " pdb=" P PTR A 336 " ideal model delta sigma weight residual 1.769 1.608 0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" C SER A 335 " pdb=" N PTR A 336 " ideal model delta sigma weight residual 1.329 1.431 -0.102 1.40e-02 5.10e+03 5.31e+01 bond pdb=" O3' DG D 2 " pdb=" P DA D 3 " ideal model delta sigma weight residual 1.607 1.552 0.055 1.20e-02 6.94e+03 2.14e+01 bond pdb=" O3' DA D 1 " pdb=" P DG D 2 " ideal model delta sigma weight residual 1.607 1.559 0.048 1.20e-02 6.94e+03 1.62e+01 bond pdb=" O3' DC D 0 " pdb=" P DA D 1 " ideal model delta sigma weight residual 1.607 1.567 0.040 1.20e-02 6.94e+03 1.11e+01 ... (remaining 6409 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 8632 2.61 - 5.22: 82 5.22 - 7.83: 4 7.83 - 10.43: 2 10.43 - 13.04: 1 Bond angle restraints: 8721 Sorted by residual: angle pdb=" C SER A 335 " pdb=" N PTR A 336 " pdb=" CA PTR A 336 " ideal model delta sigma weight residual 121.70 108.66 13.04 1.80e+00 3.09e-01 5.25e+01 angle pdb=" N3 DT E 6 " pdb=" C4 DT E 6 " pdb=" O4 DT E 6 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT E 7 " pdb=" C4 DT E 7 " pdb=" O4 DT E 7 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" CA SER A 335 " pdb=" C SER A 335 " pdb=" N PTR A 336 " ideal model delta sigma weight residual 116.20 108.29 7.91 2.00e+00 2.50e-01 1.57e+01 angle pdb=" O4 DT E 6 " pdb=" C4 DT E 6 " pdb=" C5 DT E 6 " ideal model delta sigma weight residual 124.90 122.30 2.60 7.00e-01 2.04e+00 1.38e+01 ... (remaining 8716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 3383 17.68 - 35.36: 378 35.36 - 53.03: 83 53.03 - 70.71: 24 70.71 - 88.39: 5 Dihedral angle restraints: 3873 sinusoidal: 1639 harmonic: 2234 Sorted by residual: dihedral pdb=" CD ARG B 77 " pdb=" NE ARG B 77 " pdb=" CZ ARG B 77 " pdb=" NH1 ARG B 77 " ideal model delta sinusoidal sigma weight residual 0.00 -65.13 65.13 1 1.00e+01 1.00e-02 5.56e+01 dihedral pdb=" CD ARG A 414 " pdb=" NE ARG A 414 " pdb=" CZ ARG A 414 " pdb=" NH1 ARG A 414 " ideal model delta sinusoidal sigma weight residual 0.00 61.72 -61.72 1 1.00e+01 1.00e-02 5.05e+01 dihedral pdb=" CD ARG A 379 " pdb=" NE ARG A 379 " pdb=" CZ ARG A 379 " pdb=" NH1 ARG A 379 " ideal model delta sinusoidal sigma weight residual 0.00 -56.50 56.50 1 1.00e+01 1.00e-02 4.30e+01 ... (remaining 3870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 666 0.037 - 0.073: 228 0.073 - 0.110: 68 0.110 - 0.146: 12 0.146 - 0.183: 3 Chirality restraints: 977 Sorted by residual: chirality pdb=" CB ILE A 155 " pdb=" CA ILE A 155 " pdb=" CG1 ILE A 155 " pdb=" CG2 ILE A 155 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" CA PTR A 336 " pdb=" N PTR A 336 " pdb=" C PTR A 336 " pdb=" CB PTR A 336 " both_signs ideal model delta sigma weight residual False 2.35 2.52 -0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CA ASP A 250 " pdb=" N ASP A 250 " pdb=" C ASP A 250 " pdb=" CB ASP A 250 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.87e-01 ... (remaining 974 not shown) Planarity restraints: 1092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 77 " 0.996 9.50e-02 1.11e+02 4.46e-01 1.20e+02 pdb=" NE ARG B 77 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG B 77 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 77 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 77 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 414 " 0.966 9.50e-02 1.11e+02 4.33e-01 1.14e+02 pdb=" NE ARG A 414 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG A 414 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 414 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 414 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 379 " -0.912 9.50e-02 1.11e+02 4.09e-01 1.01e+02 pdb=" NE ARG A 379 " 0.055 2.00e-02 2.50e+03 pdb=" CZ ARG A 379 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 379 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 379 " -0.024 2.00e-02 2.50e+03 ... (remaining 1089 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 49 2.59 - 3.17: 4996 3.17 - 3.74: 9359 3.74 - 4.32: 12981 4.32 - 4.90: 21975 Nonbonded interactions: 49360 Sorted by model distance: nonbonded pdb=" OD2 ASP A 511 " pdb="MN MN A 702 " model vdw 2.010 2.320 nonbonded pdb=" OD2 ASP A 117 " pdb="MN MN A 701 " model vdw 2.085 2.320 nonbonded pdb=" OE2 GLU A 9 " pdb="MN MN A 701 " model vdw 2.099 2.320 nonbonded pdb=" OE2 GLU A 340 " pdb="MN MN A 702 " model vdw 2.145 2.320 nonbonded pdb=" CG2 THR A 303 " pdb=" O PRO A 337 " model vdw 2.225 3.460 ... (remaining 49355 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: 4.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.820 Find NCS groups from input model: 0.020 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 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 0.161 6415 Z= 0.293 Angle : 0.623 13.044 8721 Z= 0.345 Chirality : 0.041 0.183 977 Planarity : 0.026 0.446 1092 Dihedral : 15.870 88.388 2431 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: -0.27 (0.30), residues: 766 helix: 0.71 (0.30), residues: 294 sheet: -0.15 (0.43), residues: 138 loop : -0.93 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 434 TYR 0.012 0.001 TYR A 41 PHE 0.009 0.001 PHE A 127 TRP 0.025 0.002 TRP A 259 HIS 0.004 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.26 ( 6414) covalent geometry : angle 0.62333 / 0.35 ( 8721) hydrogen bonds : bond 0.16589 / 11.10 ( 282) hydrogen bonds : angle 6.10630 / 4.15 ( 798) Misc. bond : bond 0.10652 / 5.61 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.230 Fit side-chains REVERT: A 75 LYS cc_start: 0.8622 (tptt) cc_final: 0.8349 (mptt) REVERT: A 126 CYS cc_start: 0.6467 (m) cc_final: 0.6222 (m) REVERT: A 213 SER cc_start: 0.8286 (m) cc_final: 0.8003 (p) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.0741 time to fit residues: 15.9816 Evaluate side-chains 157 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.2980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 GLN B 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.113195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.101559 restraints weight = 9321.169| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.01 r_work: 0.3195 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 6415 Z= 0.224 Angle : 0.621 8.052 8721 Z= 0.331 Chirality : 0.043 0.155 977 Planarity : 0.005 0.070 1092 Dihedral : 11.818 74.868 946 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.90 % Allowed : 9.15 % Favored : 89.96 % 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: 0.08 (0.30), residues: 766 helix: 1.13 (0.30), residues: 299 sheet: -0.04 (0.43), residues: 138 loop : -0.87 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 379 TYR 0.014 0.002 TYR A 41 PHE 0.012 0.002 PHE A 127 TRP 0.014 0.002 TRP A 259 HIS 0.005 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.22 ( 6414) covalent geometry : angle 0.62068 / 0.33 ( 8721) hydrogen bonds : bond 0.05076 / 3.44 ( 282) hydrogen bonds : angle 4.94088 / 3.37 ( 798) Misc. bond : bond 0.00221 / 0.12 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 155 time to evaluate : 0.190 Fit side-chains REVERT: A 75 LYS cc_start: 0.8782 (tptt) cc_final: 0.8499 (mptt) REVERT: A 120 LYS cc_start: 0.8520 (mtpp) cc_final: 0.8217 (mtpp) REVERT: A 126 CYS cc_start: 0.7480 (m) cc_final: 0.7058 (m) REVERT: A 213 SER cc_start: 0.8697 (m) cc_final: 0.8458 (p) REVERT: A 227 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7554 (tm-30) outliers start: 6 outliers final: 3 residues processed: 157 average time/residue: 0.0755 time to fit residues: 14.9185 Evaluate side-chains 154 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 151 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain B residue 55 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 70 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 6 optimal weight: 0.3980 chunk 52 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 48 optimal weight: 0.0470 chunk 13 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.113484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.101859 restraints weight = 9148.502| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.97 r_work: 0.3202 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6415 Z= 0.194 Angle : 0.585 8.830 8721 Z= 0.311 Chirality : 0.043 0.169 977 Planarity : 0.004 0.057 1092 Dihedral : 11.881 71.058 946 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.20 % Allowed : 12.59 % Favored : 86.21 % 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: 0.22 (0.31), residues: 766 helix: 1.29 (0.30), residues: 299 sheet: 0.05 (0.44), residues: 138 loop : -0.84 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 308 TYR 0.014 0.002 TYR A 41 PHE 0.012 0.002 PHE A 127 TRP 0.011 0.002 TRP A 259 HIS 0.004 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 ( 6414) covalent geometry : angle 0.58489 / 0.31 ( 8721) hydrogen bonds : bond 0.04454 / 3.01 ( 282) hydrogen bonds : angle 4.74157 / 3.26 ( 798) Misc. bond : bond 0.00150 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 0.152 Fit side-chains REVERT: A 32 LEU cc_start: 0.8500 (pt) cc_final: 0.8215 (pp) REVERT: A 75 LYS cc_start: 0.8747 (tptt) cc_final: 0.8486 (mptt) REVERT: A 120 LYS cc_start: 0.8613 (mtpp) cc_final: 0.8306 (mtpp) REVERT: A 126 CYS cc_start: 0.7522 (m) cc_final: 0.7059 (m) REVERT: A 213 SER cc_start: 0.8664 (m) cc_final: 0.8432 (p) REVERT: A 230 ASP cc_start: 0.7812 (m-30) cc_final: 0.7546 (m-30) outliers start: 8 outliers final: 4 residues processed: 157 average time/residue: 0.0776 time to fit residues: 15.3137 Evaluate side-chains 159 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 155 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain B residue 55 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 50 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 12 optimal weight: 0.0770 chunk 44 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 chunk 63 optimal weight: 0.0870 chunk 22 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN A 573 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.114748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.102978 restraints weight = 9243.046| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.99 r_work: 0.3217 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6415 Z= 0.136 Angle : 0.553 7.338 8721 Z= 0.294 Chirality : 0.041 0.162 977 Planarity : 0.004 0.048 1092 Dihedral : 11.867 66.240 946 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.95 % Allowed : 13.79 % Favored : 84.26 % 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: 0.36 (0.31), residues: 766 helix: 1.40 (0.30), residues: 300 sheet: 0.12 (0.44), residues: 138 loop : -0.77 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 308 TYR 0.013 0.001 TYR A 411 PHE 0.011 0.001 PHE A 214 TRP 0.010 0.001 TRP A 259 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 6414) covalent geometry : angle 0.55309 / 0.29 ( 8721) hydrogen bonds : bond 0.03871 / 2.60 ( 282) hydrogen bonds : angle 4.56948 / 3.14 ( 798) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.141 Fit side-chains REVERT: A 52 PHE cc_start: 0.8450 (m-80) cc_final: 0.8150 (m-80) REVERT: A 75 LYS cc_start: 0.8780 (tptt) cc_final: 0.8540 (mptt) REVERT: A 88 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7435 (mt-10) REVERT: A 120 LYS cc_start: 0.8576 (mtpp) cc_final: 0.8285 (mtpp) REVERT: A 126 CYS cc_start: 0.7405 (m) cc_final: 0.6916 (m) REVERT: A 230 ASP cc_start: 0.7773 (m-30) cc_final: 0.7518 (m-30) outliers start: 13 outliers final: 9 residues processed: 156 average time/residue: 0.0823 time to fit residues: 16.2382 Evaluate side-chains 160 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 144 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 33 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 40 optimal weight: 0.0870 chunk 1 optimal weight: 0.0980 chunk 59 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 0.0980 overall best weight: 0.2558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 GLN A 347 ASN A 573 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.115390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.103506 restraints weight = 9357.505| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.00 r_work: 0.3227 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6415 Z= 0.122 Angle : 0.539 9.914 8721 Z= 0.286 Chirality : 0.041 0.166 977 Planarity : 0.004 0.046 1092 Dihedral : 11.871 65.692 946 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.55 % Allowed : 15.14 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.31), residues: 766 helix: 1.46 (0.30), residues: 301 sheet: 0.14 (0.44), residues: 138 loop : -0.71 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 308 TYR 0.013 0.001 TYR A 411 PHE 0.010 0.001 PHE A 148 TRP 0.010 0.001 TRP A 259 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 6414) covalent geometry : angle 0.53917 / 0.29 ( 8721) hydrogen bonds : bond 0.03625 / 2.42 ( 282) hydrogen bonds : angle 4.44453 / 3.06 ( 798) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.139 Fit side-chains REVERT: A 52 PHE cc_start: 0.8407 (m-80) cc_final: 0.8115 (m-80) REVERT: A 75 LYS cc_start: 0.8782 (tptt) cc_final: 0.8543 (mptt) REVERT: A 126 CYS cc_start: 0.7367 (m) cc_final: 0.6882 (m) REVERT: A 230 ASP cc_start: 0.7751 (m-30) cc_final: 0.7493 (m-30) REVERT: A 367 VAL cc_start: 0.8011 (t) cc_final: 0.7753 (t) outliers start: 17 outliers final: 9 residues processed: 161 average time/residue: 0.0838 time to fit residues: 16.9413 Evaluate side-chains 159 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 141 HIS Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 144 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 27 optimal weight: 0.2980 chunk 56 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 323 GLN A 573 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.113515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.101779 restraints weight = 9276.458| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.99 r_work: 0.3200 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6415 Z= 0.211 Angle : 0.577 7.547 8721 Z= 0.303 Chirality : 0.043 0.166 977 Planarity : 0.004 0.046 1092 Dihedral : 11.901 66.625 946 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.70 % Allowed : 15.59 % Favored : 81.71 % 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: 0.32 (0.31), residues: 766 helix: 1.43 (0.30), residues: 300 sheet: 0.05 (0.43), residues: 138 loop : -0.82 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 308 TYR 0.015 0.002 TYR A 240 PHE 0.014 0.002 PHE A 214 TRP 0.009 0.002 TRP A 458 HIS 0.005 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 ( 6414) covalent geometry : angle 0.57715 / 0.30 ( 8721) hydrogen bonds : bond 0.04075 / 2.74 ( 282) hydrogen bonds : angle 4.49040 / 3.09 ( 798) Misc. bond : bond 0.00082 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.165 Fit side-chains REVERT: A 32 LEU cc_start: 0.8443 (pt) cc_final: 0.8144 (pp) REVERT: A 52 PHE cc_start: 0.8474 (m-80) cc_final: 0.8203 (m-80) REVERT: A 75 LYS cc_start: 0.8781 (tptt) cc_final: 0.8541 (mptt) REVERT: A 98 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.8001 (mmm) REVERT: A 126 CYS cc_start: 0.7603 (m) cc_final: 0.7102 (m) REVERT: A 230 ASP cc_start: 0.7748 (m-30) cc_final: 0.7494 (m-30) outliers start: 18 outliers final: 12 residues processed: 156 average time/residue: 0.0770 time to fit residues: 15.0354 Evaluate side-chains 166 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 141 HIS Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 144 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 33 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 chunk 31 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 39 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 0.0980 chunk 15 optimal weight: 0.4980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.114425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.102627 restraints weight = 9187.278| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.00 r_work: 0.3215 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6415 Z= 0.151 Angle : 0.558 8.548 8721 Z= 0.293 Chirality : 0.041 0.190 977 Planarity : 0.004 0.044 1092 Dihedral : 11.905 66.799 946 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.85 % Allowed : 15.29 % Favored : 81.86 % 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: 0.35 (0.31), residues: 766 helix: 1.47 (0.30), residues: 300 sheet: 0.03 (0.43), residues: 138 loop : -0.81 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 308 TYR 0.013 0.002 TYR A 41 PHE 0.010 0.001 PHE A 127 TRP 0.007 0.001 TRP A 458 HIS 0.004 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 6414) covalent geometry : angle 0.55780 / 0.29 ( 8721) hydrogen bonds : bond 0.03812 / 2.54 ( 282) hydrogen bonds : angle 4.45820 / 3.06 ( 798) Misc. bond : bond 0.00026 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.175 Fit side-chains REVERT: A 32 LEU cc_start: 0.8464 (pt) cc_final: 0.8203 (pp) REVERT: A 52 PHE cc_start: 0.8454 (m-80) cc_final: 0.8147 (m-80) REVERT: A 75 LYS cc_start: 0.8790 (tptt) cc_final: 0.8555 (mptt) REVERT: A 98 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7965 (mmm) REVERT: A 126 CYS cc_start: 0.7512 (m) cc_final: 0.7008 (m) REVERT: A 230 ASP cc_start: 0.7736 (m-30) cc_final: 0.7474 (m-30) REVERT: A 357 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7689 (mt0) outliers start: 19 outliers final: 15 residues processed: 157 average time/residue: 0.0818 time to fit residues: 16.0326 Evaluate side-chains 169 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 155 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 30 optimal weight: 0.4980 chunk 43 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 49 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.0980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 GLN B 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.114802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.102926 restraints weight = 9281.964| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.00 r_work: 0.3220 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6415 Z= 0.143 Angle : 0.551 8.477 8721 Z= 0.288 Chirality : 0.041 0.193 977 Planarity : 0.004 0.044 1092 Dihedral : 12.015 67.129 946 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.70 % Allowed : 16.04 % Favored : 81.26 % 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: 0.37 (0.31), residues: 766 helix: 1.50 (0.30), residues: 300 sheet: 0.04 (0.43), residues: 138 loop : -0.81 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 434 TYR 0.013 0.001 TYR A 411 PHE 0.016 0.001 PHE A 214 TRP 0.008 0.001 TRP A 458 HIS 0.004 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 6414) covalent geometry : angle 0.55133 / 0.29 ( 8721) hydrogen bonds : bond 0.03693 / 2.45 ( 282) hydrogen bonds : angle 4.41511 / 3.03 ( 798) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.134 Fit side-chains REVERT: A 32 LEU cc_start: 0.8436 (pt) cc_final: 0.8137 (pp) REVERT: A 75 LYS cc_start: 0.8791 (tptt) cc_final: 0.8557 (mptt) REVERT: A 98 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7957 (mmm) REVERT: A 126 CYS cc_start: 0.7468 (m) cc_final: 0.6954 (m) REVERT: A 227 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7498 (tm-30) REVERT: A 230 ASP cc_start: 0.7718 (m-30) cc_final: 0.7455 (m-30) REVERT: A 357 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7686 (mt0) REVERT: A 367 VAL cc_start: 0.8020 (t) cc_final: 0.7760 (t) outliers start: 18 outliers final: 15 residues processed: 158 average time/residue: 0.0760 time to fit residues: 15.1347 Evaluate side-chains 169 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 141 HIS Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 155 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 21 optimal weight: 0.0980 chunk 52 optimal weight: 0.7980 chunk 45 optimal weight: 0.0970 chunk 48 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 51 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.115390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.103418 restraints weight = 9325.674| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.01 r_work: 0.3228 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6415 Z= 0.128 Angle : 0.553 9.696 8721 Z= 0.286 Chirality : 0.040 0.169 977 Planarity : 0.004 0.043 1092 Dihedral : 12.080 67.688 946 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.00 % Allowed : 16.04 % Favored : 80.96 % 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: 0.43 (0.31), residues: 766 helix: 1.54 (0.30), residues: 300 sheet: 0.07 (0.44), residues: 138 loop : -0.77 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 434 TYR 0.013 0.001 TYR A 411 PHE 0.010 0.001 PHE A 148 TRP 0.008 0.001 TRP A 458 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 6414) covalent geometry : angle 0.55283 / 0.29 ( 8721) hydrogen bonds : bond 0.03549 / 2.35 ( 282) hydrogen bonds : angle 4.37781 / 3.00 ( 798) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.149 Fit side-chains REVERT: A 52 PHE cc_start: 0.8431 (m-80) cc_final: 0.8208 (m-80) REVERT: A 75 LYS cc_start: 0.8788 (tptt) cc_final: 0.8554 (mptt) REVERT: A 98 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7948 (mmm) REVERT: A 126 CYS cc_start: 0.7427 (m) cc_final: 0.6901 (m) REVERT: A 357 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7680 (mt0) REVERT: A 367 VAL cc_start: 0.7991 (t) cc_final: 0.7717 (t) outliers start: 20 outliers final: 16 residues processed: 156 average time/residue: 0.0708 time to fit residues: 13.9129 Evaluate side-chains 165 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 141 HIS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 155 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 39 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 6 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.114555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.102713 restraints weight = 9133.571| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.97 r_work: 0.3216 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6415 Z= 0.177 Angle : 0.573 10.606 8721 Z= 0.298 Chirality : 0.042 0.169 977 Planarity : 0.004 0.043 1092 Dihedral : 12.119 68.252 946 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.70 % Allowed : 16.49 % Favored : 80.81 % 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: 0.35 (0.31), residues: 766 helix: 1.46 (0.30), residues: 300 sheet: 0.11 (0.44), residues: 138 loop : -0.84 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 308 TYR 0.012 0.002 TYR A 578 PHE 0.017 0.002 PHE A 214 TRP 0.008 0.001 TRP A 458 HIS 0.004 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 6414) covalent geometry : angle 0.57259 / 0.30 ( 8721) hydrogen bonds : bond 0.03819 / 2.55 ( 282) hydrogen bonds : angle 4.44278 / 3.05 ( 798) Misc. bond : bond 0.00051 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.143 Fit side-chains REVERT: A 32 LEU cc_start: 0.8439 (pt) cc_final: 0.8144 (pp) REVERT: A 75 LYS cc_start: 0.8781 (tptt) cc_final: 0.8543 (mptt) REVERT: A 98 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7963 (mmm) REVERT: A 126 CYS cc_start: 0.7542 (m) cc_final: 0.7024 (m) REVERT: A 227 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7535 (tm-30) REVERT: A 357 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7699 (mt0) REVERT: A 367 VAL cc_start: 0.8028 (t) cc_final: 0.7770 (t) outliers start: 18 outliers final: 16 residues processed: 151 average time/residue: 0.0791 time to fit residues: 15.0437 Evaluate side-chains 164 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 141 HIS Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 155 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 75 optimal weight: 1.9990 chunk 63 optimal weight: 0.0020 chunk 32 optimal weight: 0.0670 chunk 9 optimal weight: 0.0670 chunk 18 optimal weight: 0.5980 chunk 72 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 2 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 0.2980 overall best weight: 0.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.116646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.104592 restraints weight = 9260.131| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.01 r_work: 0.3246 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 6415 Z= 0.107 Angle : 0.548 9.756 8721 Z= 0.284 Chirality : 0.040 0.173 977 Planarity : 0.004 0.043 1092 Dihedral : 12.072 68.871 946 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.95 % Allowed : 17.09 % Favored : 80.96 % 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: 0.48 (0.31), residues: 766 helix: 1.56 (0.30), residues: 300 sheet: 0.14 (0.44), residues: 138 loop : -0.74 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 434 TYR 0.013 0.001 TYR A 411 PHE 0.009 0.001 PHE A 148 TRP 0.009 0.001 TRP A 259 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 6414) covalent geometry : angle 0.54779 / 0.28 ( 8721) hydrogen bonds : bond 0.03331 / 2.19 ( 282) hydrogen bonds : angle 4.33482 / 2.97 ( 798) Misc. bond : bond 0.00047 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1505.96 seconds wall clock time: 26 minutes 26.15 seconds (1586.15 seconds total)