Starting phenix.real_space_refine on Thu Jul 2 03:17:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cak_45394/07_2026/9cak_45394_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cak_45394/07_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_45394/07_2026/9cak_45394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cak_45394/07_2026/9cak_45394.map" model { file = "/net/cci-nas-00/data/ceres_data/9cak_45394/07_2026/9cak_45394_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cak_45394/07_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-dev-6108/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, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Time building chain proxies: 1.37, per 1000 atoms: 0.22 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: 0.44 Conformation dependent library (CDL) restraints added in 399.5 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: 0.69 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: 1.24 Time building geometry restraints manager: 0.63 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 1.50e-02 4.44e+03 1.37e+01 bond pdb=" O3' DA D 1 " pdb=" P DG D 2 " ideal model delta sigma weight residual 1.607 1.559 0.048 1.50e-02 4.44e+03 1.04e+01 bond pdb=" O3' DC D 0 " pdb=" P DA D 1 " ideal model delta sigma weight residual 1.607 1.567 0.040 1.50e-02 4.44e+03 7.07e+00 ... (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 3.060 nonbonded pdb=" OD2 ASP A 117 " pdb="MN MN A 701 " model vdw 2.085 3.060 nonbonded pdb=" OE2 GLU A 9 " pdb="MN MN A 701 " model vdw 2.099 3.060 nonbonded pdb=" OE2 GLU A 340 " pdb="MN MN A 702 " model vdw 2.145 3.060 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: 4.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.950 Find NCS groups from input model: 0.040 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.740 ------------------------------------------------------------------------------- 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= 0.288 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 / 0.25 ( 6414) covalent geometry : angle 0.62319 / 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 : 0.232 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: 0.0963 time to fit residues: 20.7678 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 : 0.224 ------------------------------------------------------------------------------- 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: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.112679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.100937 restraints weight = 9377.755| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.05 r_work: 0.3184 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 6415 Z= 0.255 Angle : 0.633 8.147 8721 Z= 0.337 Chirality : 0.044 0.170 977 Planarity : 0.005 0.070 1092 Dihedral : 11.855 76.283 946 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.90 % Allowed : 9.30 % Favored : 89.81 % 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: 0.03 (0.30), residues: 766 helix: 1.09 (0.30), residues: 299 sheet: -0.06 (0.43), residues: 138 loop : -0.90 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.015 0.002 TYR A 41 PHE 0.013 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 0.00601 / 0.26 ( 6414) covalent geometry : angle 0.63292 / 0.34 ( 8721) hydrogen bonds : bond 0.05074 / 3.44 ( 282) hydrogen bonds : angle 4.95109 / 3.38 ( 798) Misc. bond : bond 0.00387 / 0.20 ( 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 159 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 153 time to evaluate : 0.143 Fit side-chains REVERT: A 75 LYS cc_start: 0.8784 (tptt) cc_final: 0.8501 (mptt) REVERT: A 120 LYS cc_start: 0.8558 (mtpp) cc_final: 0.8255 (mtpp) REVERT: A 126 CYS cc_start: 0.7520 (m) cc_final: 0.7080 (m) REVERT: A 213 SER cc_start: 0.8711 (m) cc_final: 0.8455 (p) REVERT: A 227 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7567 (tm-30) outliers start: 6 outliers final: 3 residues processed: 155 average time/residue: 0.0938 time to fit residues: 18.2385 Evaluate side-chains 153 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 150 time to evaluate : 0.162 ------------------------------------------------------------------------------- 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: 0.6980 chunk 2 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 52 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 48 optimal weight: 0.2980 chunk 13 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.113611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.101865 restraints weight = 9170.195| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.00 r_work: 0.3201 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6415 Z= 0.175 Angle : 0.582 8.634 8721 Z= 0.309 Chirality : 0.042 0.165 977 Planarity : 0.004 0.056 1092 Dihedral : 11.852 72.004 946 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.05 % Allowed : 12.89 % Favored : 86.06 % 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: 0.21 (0.31), residues: 766 helix: 1.27 (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 0.004 0.000 ARG A 379 TYR 0.013 0.002 TYR A 578 PHE 0.011 0.001 PHE A 127 TRP 0.011 0.001 TRP A 259 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 6414) covalent geometry : angle 0.58241 / 0.31 ( 8721) hydrogen bonds : bond 0.04401 / 2.97 ( 282) hydrogen bonds : angle 4.76101 / 3.27 ( 798) Misc. bond : bond 0.00094 / 0.05 ( 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 162 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 155 time to evaluate : 0.222 Fit side-chains REVERT: A 32 LEU cc_start: 0.8505 (pt) cc_final: 0.8219 (pp) REVERT: A 75 LYS cc_start: 0.8754 (tptt) cc_final: 0.8474 (mptt) REVERT: A 120 LYS cc_start: 0.8610 (mtpp) cc_final: 0.8291 (mtpp) REVERT: A 126 CYS cc_start: 0.7483 (m) cc_final: 0.7010 (m) REVERT: A 213 SER cc_start: 0.8673 (m) cc_final: 0.8439 (p) REVERT: A 230 ASP cc_start: 0.7819 (m-30) cc_final: 0.7550 (m-30) outliers start: 7 outliers final: 4 residues processed: 157 average time/residue: 0.0874 time to fit residues: 17.3089 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 : 0.136 ------------------------------------------------------------------------------- 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: 0.3980 chunk 52 optimal weight: 0.6980 chunk 12 optimal weight: 0.0770 chunk 44 optimal weight: 0.2980 chunk 27 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 overall best weight: 0.3138 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.114658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.102862 restraints weight = 9291.929| |-----------------------------------------------------------------------------| r_work (start): 0.3330 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: 4.22 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1328 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= 0.138 Angle : 0.550 7.337 8721 Z= 0.294 Chirality : 0.041 0.162 977 Planarity : 0.004 0.048 1092 Dihedral : 11.859 65.266 946 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.95 % Allowed : 13.64 % Favored : 84.41 % 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: 1.38 (0.30), residues: 300 sheet: 0.12 (0.44), residues: 138 loop : -0.76 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 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 0.00312 / 0.14 ( 6414) covalent geometry : angle 0.54981 / 0.29 ( 8721) hydrogen bonds : bond 0.03886 / 2.61 ( 282) hydrogen bonds : angle 4.58433 / 3.15 ( 798) Misc. bond : bond 0.00044 / 0.02 ( 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 165 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.223 Fit side-chains REVERT: A 75 LYS cc_start: 0.8779 (tptt) cc_final: 0.8538 (mptt) REVERT: A 88 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7401 (mt-10) REVERT: A 120 LYS cc_start: 0.8579 (mtpp) cc_final: 0.8291 (mtpp) REVERT: A 126 CYS cc_start: 0.7393 (m) cc_final: 0.6906 (m) REVERT: A 230 ASP cc_start: 0.7783 (m-30) cc_final: 0.7523 (m-30) outliers start: 13 outliers final: 8 residues processed: 155 average time/residue: 0.0895 time to fit residues: 17.3545 Evaluate side-chains 160 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 4 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 47 optimal weight: 0.0000 chunk 6 optimal weight: 0.3980 chunk 32 optimal weight: 0.5980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN A 573 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.114218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.102290 restraints weight = 9419.355| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.03 r_work: 0.3210 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6415 Z= 0.154 Angle : 0.552 8.955 8721 Z= 0.293 Chirality : 0.041 0.166 977 Planarity : 0.004 0.047 1092 Dihedral : 11.852 65.234 946 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.70 % Allowed : 14.99 % 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: 0.37 (0.31), residues: 766 helix: 1.39 (0.30), residues: 301 sheet: 0.15 (0.44), residues: 138 loop : -0.74 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 434 TYR 0.012 0.002 TYR A 41 PHE 0.010 0.001 PHE A 127 TRP 0.008 0.001 TRP A 259 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 6414) covalent geometry : angle 0.55173 / 0.29 ( 8721) hydrogen bonds : bond 0.03870 / 2.60 ( 282) hydrogen bonds : angle 4.52461 / 3.11 ( 798) Misc. bond : bond 0.00045 / 0.02 ( 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 176 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.220 Fit side-chains REVERT: A 75 LYS cc_start: 0.8782 (tptt) cc_final: 0.8538 (mptt) REVERT: A 126 CYS cc_start: 0.7481 (m) cc_final: 0.6966 (m) REVERT: A 230 ASP cc_start: 0.7778 (m-30) cc_final: 0.7516 (m-30) outliers start: 18 outliers final: 11 residues processed: 161 average time/residue: 0.0941 time to fit residues: 18.9816 Evaluate side-chains 165 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 chunk 56 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.113326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.101496 restraints weight = 9295.115| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.00 r_work: 0.3199 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6415 Z= 0.197 Angle : 0.570 7.316 8721 Z= 0.303 Chirality : 0.042 0.165 977 Planarity : 0.004 0.046 1092 Dihedral : 11.875 66.262 946 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.85 % Allowed : 14.99 % Favored : 82.16 % 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: 0.30 (0.31), residues: 766 helix: 1.37 (0.30), residues: 300 sheet: 0.12 (0.44), residues: 138 loop : -0.83 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 434 TYR 0.014 0.002 TYR A 578 PHE 0.015 0.002 PHE A 214 TRP 0.010 0.002 TRP A 259 HIS 0.005 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 ( 6414) covalent geometry : angle 0.56967 / 0.30 ( 8721) hydrogen bonds : bond 0.04080 / 2.74 ( 282) hydrogen bonds : angle 4.52225 / 3.11 ( 798) Misc. bond : bond 0.00081 / 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 174 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.272 Fit side-chains REVERT: A 32 LEU cc_start: 0.8454 (pt) cc_final: 0.8169 (pp) REVERT: A 75 LYS cc_start: 0.8765 (tptt) cc_final: 0.8522 (mptt) REVERT: A 120 LYS cc_start: 0.8626 (mtpp) cc_final: 0.8335 (mtpp) REVERT: A 126 CYS cc_start: 0.7581 (m) cc_final: 0.7086 (m) REVERT: A 230 ASP cc_start: 0.7758 (m-30) cc_final: 0.7504 (m-30) outliers start: 19 outliers final: 13 residues processed: 160 average time/residue: 0.0979 time to fit residues: 19.5517 Evaluate side-chains 168 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 43 optimal weight: 0.5980 chunk 19 optimal weight: 0.0980 chunk 31 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 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 = 0.3487 r_free = 0.3487 target = 0.113748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.101982 restraints weight = 9211.252| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.98 r_work: 0.3207 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6415 Z= 0.178 Angle : 0.567 9.011 8721 Z= 0.301 Chirality : 0.042 0.174 977 Planarity : 0.004 0.045 1092 Dihedral : 11.883 66.532 946 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.70 % Allowed : 15.44 % 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: 0.29 (0.31), residues: 766 helix: 1.41 (0.30), residues: 300 sheet: 0.08 (0.44), residues: 138 loop : -0.86 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 434 TYR 0.014 0.002 TYR A 41 PHE 0.011 0.001 PHE A 127 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 0.56677 / 0.30 ( 8721) hydrogen bonds : bond 0.03954 / 2.64 ( 282) hydrogen bonds : angle 4.52004 / 3.10 ( 798) Misc. bond : bond 0.00056 / 0.03 ( 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 172 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.178 Fit side-chains REVERT: A 52 PHE cc_start: 0.8471 (m-80) cc_final: 0.8216 (m-80) REVERT: A 75 LYS cc_start: 0.8770 (tptt) cc_final: 0.8534 (mptt) REVERT: A 120 LYS cc_start: 0.8637 (mtpp) cc_final: 0.8340 (mtpp) REVERT: A 126 CYS cc_start: 0.7555 (m) cc_final: 0.7038 (m) REVERT: A 230 ASP cc_start: 0.7745 (m-30) cc_final: 0.7491 (m-30) REVERT: A 357 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7684 (mt0) outliers start: 18 outliers final: 13 residues processed: 158 average time/residue: 0.0913 time to fit residues: 18.1253 Evaluate side-chains 168 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 48 GLN 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 44 ASP Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 144 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 30 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 49 optimal weight: 0.0980 chunk 24 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.0970 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.114532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.102609 restraints weight = 9330.088| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.01 r_work: 0.3215 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6415 Z= 0.151 Angle : 0.560 8.627 8721 Z= 0.295 Chirality : 0.042 0.208 977 Planarity : 0.004 0.044 1092 Dihedral : 11.925 66.687 946 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.55 % Allowed : 16.34 % Favored : 81.11 % 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: 0.30 (0.30), residues: 766 helix: 1.44 (0.30), residues: 300 sheet: 0.01 (0.44), residues: 138 loop : -0.85 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 434 TYR 0.013 0.001 TYR A 41 PHE 0.016 0.001 PHE A 214 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 0.00351 / 0.15 ( 6414) covalent geometry : angle 0.55956 / 0.29 ( 8721) hydrogen bonds : bond 0.03776 / 2.52 ( 282) hydrogen bonds : angle 4.47827 / 3.08 ( 798) Misc. bond : bond 0.00021 / 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 174 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.229 Fit side-chains REVERT: A 52 PHE cc_start: 0.8442 (m-80) cc_final: 0.8143 (m-80) REVERT: A 75 LYS cc_start: 0.8777 (tptt) cc_final: 0.8540 (mptt) REVERT: A 120 LYS cc_start: 0.8634 (mtpp) cc_final: 0.8345 (mtpp) REVERT: A 126 CYS cc_start: 0.7489 (m) cc_final: 0.6960 (m) REVERT: A 230 ASP cc_start: 0.7754 (m-30) cc_final: 0.7500 (m-30) REVERT: A 357 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7645 (mt0) REVERT: A 367 VAL cc_start: 0.8023 (t) cc_final: 0.7768 (t) outliers start: 17 outliers final: 13 residues processed: 163 average time/residue: 0.0944 time to fit residues: 19.2136 Evaluate side-chains 171 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 21 optimal weight: 0.4980 chunk 52 optimal weight: 0.4980 chunk 45 optimal weight: 0.0670 chunk 48 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.114192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.102295 restraints weight = 9388.507| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.00 r_work: 0.3212 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6415 Z= 0.168 Angle : 0.572 10.707 8721 Z= 0.299 Chirality : 0.042 0.182 977 Planarity : 0.004 0.044 1092 Dihedral : 12.041 66.906 946 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.40 % Allowed : 16.49 % Favored : 81.11 % 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: 1.42 (0.30), residues: 300 sheet: -0.02 (0.44), residues: 138 loop : -0.88 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 434 TYR 0.014 0.002 TYR A 41 PHE 0.011 0.001 PHE A 127 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 0.00397 / 0.17 ( 6414) covalent geometry : angle 0.57245 / 0.30 ( 8721) hydrogen bonds : bond 0.03841 / 2.56 ( 282) hydrogen bonds : angle 4.47849 / 3.08 ( 798) Misc. bond : bond 0.00036 / 0.02 ( 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 170 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.167 Fit side-chains REVERT: A 75 LYS cc_start: 0.8782 (tptt) cc_final: 0.8548 (mptt) REVERT: A 120 LYS cc_start: 0.8633 (mtpp) cc_final: 0.8343 (mtpp) REVERT: A 126 CYS cc_start: 0.7524 (m) cc_final: 0.7006 (m) REVERT: A 227 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7495 (tm-30) REVERT: A 230 ASP cc_start: 0.7756 (m-30) cc_final: 0.7491 (m-30) REVERT: A 357 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7691 (mt0) outliers start: 16 outliers final: 14 residues processed: 157 average time/residue: 0.0934 time to fit residues: 18.4836 Evaluate side-chains 166 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 48 GLN 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: 1.9990 chunk 25 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 45 optimal weight: 0.0970 chunk 28 optimal weight: 0.0970 chunk 42 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 overall best weight: 0.3576 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.114875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.103033 restraints weight = 9157.825| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.97 r_work: 0.3224 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6415 Z= 0.140 Angle : 0.560 10.586 8721 Z= 0.292 Chirality : 0.041 0.171 977 Planarity : 0.004 0.044 1092 Dihedral : 12.071 67.038 946 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.40 % Allowed : 16.79 % 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: 0.31 (0.31), residues: 766 helix: 1.47 (0.30), residues: 300 sheet: 0.01 (0.44), residues: 138 loop : -0.86 (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 0.018 0.001 PHE A 214 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 0.00325 / 0.14 ( 6414) covalent geometry : angle 0.56019 / 0.29 ( 8721) hydrogen bonds : bond 0.03670 / 2.43 ( 282) hydrogen bonds : angle 4.43884 / 3.05 ( 798) Misc. bond : bond 0.00015 / 0.01 ( 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 171 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.214 Fit side-chains REVERT: A 75 LYS cc_start: 0.8778 (tptt) cc_final: 0.8544 (mptt) REVERT: A 126 CYS cc_start: 0.7436 (m) cc_final: 0.6910 (m) REVERT: A 227 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7467 (tm-30) REVERT: A 230 ASP cc_start: 0.7736 (m-30) cc_final: 0.7471 (m-30) REVERT: A 357 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7648 (mt0) REVERT: A 367 VAL cc_start: 0.8009 (t) cc_final: 0.7748 (t) outliers start: 16 outliers final: 13 residues processed: 158 average time/residue: 0.0894 time to fit residues: 17.6769 Evaluate side-chains 168 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 48 GLN 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 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: 0.5980 chunk 32 optimal weight: 0.2980 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 0.1980 chunk 72 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 0.0060 chunk 2 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 0.3980 overall best weight: 0.2996 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.115245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.103341 restraints weight = 9319.928| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.99 r_work: 0.3227 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6415 Z= 0.131 Angle : 0.560 10.361 8721 Z= 0.291 Chirality : 0.040 0.169 977 Planarity : 0.004 0.044 1092 Dihedral : 12.080 67.627 946 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.40 % Allowed : 16.94 % Favored : 80.66 % 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: 1.50 (0.30), residues: 300 sheet: 0.02 (0.45), residues: 138 loop : -0.85 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 308 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 0.003 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 6414) covalent geometry : angle 0.55995 / 0.29 ( 8721) hydrogen bonds : bond 0.03584 / 2.38 ( 282) hydrogen bonds : angle 4.40279 / 3.02 ( 798) Misc. bond : bond 0.00001 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1768.59 seconds wall clock time: 31 minutes 2.65 seconds (1862.65 seconds total)