Starting phenix.real_space_refine on Sat May 10 12:35:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cak_45394/05_2025/9cak_45394_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cak_45394/05_2025/9cak_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_45394/05_2025/9cak_45394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cak_45394/05_2025/9cak_45394.map" model { file = "/net/cci-nas-00/data/ceres_data/9cak_45394/05_2025/9cak_45394_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cak_45394/05_2025/9cak_45394_neut.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.64, per 1000 atoms: 0.74 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: 1.61 Conformation dependent library (CDL) restraints added in 840.9 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: 2.02 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: 2.01 Time building geometry restraints manager: 1.88 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: 8630 2.61 - 5.22: 84 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=" 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=" OH PTR A 336 " pdb=" P PTR A 336 " pdb=" O2P PTR A 336 " ideal model delta sigma weight residual 99.92 109.84 -9.92 3.00e+00 1.11e-01 1.09e+01 angle pdb=" C4' DG D 2 " pdb=" C3' DG D 2 " pdb=" O3' DG D 2 " ideal model delta sigma weight residual 110.00 105.60 4.40 1.50e+00 4.44e-01 8.62e+00 angle pdb=" C THR A 249 " pdb=" N ASP A 250 " pdb=" CA ASP A 250 " ideal model delta sigma weight residual 122.61 127.10 -4.49 1.56e+00 4.11e-01 8.29e+00 ... (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: 668 0.037 - 0.073: 230 0.073 - 0.110: 65 0.110 - 0.146: 11 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: 3.730 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.140 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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= 0.266 Angle : 0.621 13.044 8721 Z= 0.327 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (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 TRP 0.025 0.002 TRP A 259 HIS 0.004 0.001 HIS A 229 PHE 0.009 0.001 PHE A 127 TYR 0.012 0.001 TYR A 41 ARG 0.003 0.000 ARG A 434 Details of bonding type rmsd hydrogen bonds : bond 0.16589 ( 282) hydrogen bonds : angle 6.10630 ( 798) covalent geometry : bond 0.00476 ( 6414) covalent geometry : angle 0.62144 ( 8721) Misc. bond : bond 0.10652 ( 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 : 0.787 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: 0.2231 time to fit residues: 47.8916 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 : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 19 optimal weight: 0.0980 chunk 39 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 0.0000 chunk 36 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 0.0020 overall best weight: 0.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN B 32 ASN B 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.115203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.103492 restraints weight = 9052.715| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.98 r_work: 0.3225 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6415 Z= 0.134 Angle : 0.560 7.887 8721 Z= 0.296 Chirality : 0.040 0.188 977 Planarity : 0.005 0.068 1092 Dihedral : 11.674 65.575 946 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.75 % Allowed : 10.19 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.31), residues: 766 helix: 1.26 (0.30), residues: 301 sheet: 0.11 (0.44), residues: 138 loop : -0.73 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 259 HIS 0.003 0.001 HIS A 229 PHE 0.010 0.001 PHE A 127 TYR 0.013 0.001 TYR A 411 ARG 0.003 0.000 ARG A 379 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 282) hydrogen bonds : angle 4.66540 ( 798) covalent geometry : bond 0.00306 ( 6414) covalent geometry : angle 0.55997 ( 8721) Misc. bond : bond 0.00049 ( 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 160 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 155 time to evaluate : 0.716 Fit side-chains REVERT: A 75 LYS cc_start: 0.8783 (tptt) cc_final: 0.8540 (mptt) REVERT: A 126 CYS cc_start: 0.7242 (m) cc_final: 0.6897 (m) REVERT: A 213 SER cc_start: 0.8627 (m) cc_final: 0.8360 (p) REVERT: A 230 ASP cc_start: 0.7744 (m-30) cc_final: 0.7458 (m-30) REVERT: A 367 VAL cc_start: 0.7984 (t) cc_final: 0.7719 (t) outliers start: 5 outliers final: 1 residues processed: 155 average time/residue: 0.2379 time to fit residues: 45.8336 Evaluate side-chains 150 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 58 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 37 optimal weight: 0.0970 chunk 47 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 55 optimal weight: 0.0770 chunk 46 optimal weight: 0.0010 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 overall best weight: 0.2542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.115849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.104139 restraints weight = 9093.206| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.97 r_work: 0.3234 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6415 Z= 0.123 Angle : 0.538 9.025 8721 Z= 0.284 Chirality : 0.040 0.167 977 Planarity : 0.004 0.055 1092 Dihedral : 11.660 62.826 946 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.31), residues: 766 helix: 1.45 (0.30), residues: 301 sheet: 0.13 (0.44), residues: 138 loop : -0.69 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 259 HIS 0.002 0.001 HIS A 229 PHE 0.009 0.001 PHE A 127 TYR 0.012 0.001 TYR A 411 ARG 0.003 0.000 ARG A 434 Details of bonding type rmsd hydrogen bonds : bond 0.03699 ( 282) hydrogen bonds : angle 4.49016 ( 798) covalent geometry : bond 0.00282 ( 6414) covalent geometry : angle 0.53842 ( 8721) Misc. bond : bond 0.00017 ( 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: 8 poor density : 154 time to evaluate : 0.659 Fit side-chains REVERT: A 75 LYS cc_start: 0.8785 (tptt) cc_final: 0.8540 (mptt) REVERT: A 88 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7380 (mt-10) REVERT: A 126 CYS cc_start: 0.7280 (m) cc_final: 0.6870 (m) REVERT: A 213 SER cc_start: 0.8568 (m) cc_final: 0.8310 (p) REVERT: A 230 ASP cc_start: 0.7720 (m-30) cc_final: 0.7455 (m-30) REVERT: A 367 VAL cc_start: 0.8002 (t) cc_final: 0.7733 (t) outliers start: 8 outliers final: 4 residues processed: 156 average time/residue: 0.2293 time to fit residues: 44.5978 Evaluate side-chains 154 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 149 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 141 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 32 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 34 optimal weight: 0.2980 chunk 54 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3500 r_free = 0.3500 target = 0.114854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.103049 restraints weight = 9215.486| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.98 r_work: 0.3216 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6415 Z= 0.164 Angle : 0.551 8.229 8721 Z= 0.290 Chirality : 0.041 0.160 977 Planarity : 0.004 0.050 1092 Dihedral : 11.760 63.166 946 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.31), residues: 766 helix: 1.47 (0.30), residues: 301 sheet: 0.10 (0.43), residues: 138 loop : -0.69 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 259 HIS 0.004 0.001 HIS A 229 PHE 0.010 0.001 PHE A 127 TYR 0.013 0.002 TYR A 240 ARG 0.004 0.000 ARG A 434 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 282) hydrogen bonds : angle 4.47310 ( 798) covalent geometry : bond 0.00388 ( 6414) covalent geometry : angle 0.55118 ( 8721) Misc. bond : bond 0.00041 ( 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 : 0.660 Fit side-chains REVERT: A 52 PHE cc_start: 0.8433 (m-80) cc_final: 0.8151 (m-80) REVERT: A 75 LYS cc_start: 0.8768 (tptt) cc_final: 0.8534 (mptt) REVERT: A 126 CYS cc_start: 0.7514 (m) cc_final: 0.7028 (m) REVERT: A 230 ASP cc_start: 0.7728 (m-30) cc_final: 0.7473 (m-30) outliers start: 13 outliers final: 8 residues processed: 153 average time/residue: 0.2330 time to fit residues: 44.3237 Evaluate side-chains 156 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 148 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 13 optimal weight: 0.0030 chunk 61 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3491 r_free = 0.3491 target = 0.114053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.102162 restraints weight = 9205.955| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.99 r_work: 0.3207 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6415 Z= 0.175 Angle : 0.553 9.343 8721 Z= 0.290 Chirality : 0.041 0.158 977 Planarity : 0.004 0.047 1092 Dihedral : 11.976 63.377 946 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.80 % Allowed : 16.19 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.31), residues: 766 helix: 1.46 (0.30), residues: 301 sheet: 0.10 (0.43), residues: 138 loop : -0.71 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 259 HIS 0.004 0.001 HIS A 229 PHE 0.011 0.001 PHE A 127 TYR 0.013 0.002 TYR A 41 ARG 0.005 0.000 ARG A 434 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 282) hydrogen bonds : angle 4.45398 ( 798) covalent geometry : bond 0.00418 ( 6414) covalent geometry : angle 0.55336 ( 8721) Misc. bond : bond 0.00058 ( 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 164 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.717 Fit side-chains REVERT: A 52 PHE cc_start: 0.8442 (m-80) cc_final: 0.8181 (m-80) REVERT: A 75 LYS cc_start: 0.8754 (tptt) cc_final: 0.8509 (mptt) REVERT: A 126 CYS cc_start: 0.7530 (m) cc_final: 0.7024 (m) REVERT: A 230 ASP cc_start: 0.7711 (m-30) cc_final: 0.7454 (m-30) REVERT: A 573 GLN cc_start: 0.8243 (mt0) cc_final: 0.7975 (mt0) outliers start: 12 outliers final: 8 residues processed: 155 average time/residue: 0.2374 time to fit residues: 45.5858 Evaluate side-chains 158 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 141 HIS 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 28 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 46 optimal weight: 0.0980 chunk 43 optimal weight: 0.7980 chunk 40 optimal weight: 0.0060 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 0.0970 chunk 54 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.115636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.103677 restraints weight = 9054.749| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.98 r_work: 0.3228 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6415 Z= 0.124 Angle : 0.525 7.846 8721 Z= 0.276 Chirality : 0.040 0.161 977 Planarity : 0.004 0.044 1092 Dihedral : 12.013 63.215 946 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.25 % Allowed : 16.19 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.31), residues: 766 helix: 1.51 (0.30), residues: 302 sheet: 0.15 (0.44), residues: 138 loop : -0.70 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 259 HIS 0.003 0.001 HIS A 229 PHE 0.012 0.001 PHE A 214 TYR 0.013 0.001 TYR A 411 ARG 0.004 0.000 ARG A 434 Details of bonding type rmsd hydrogen bonds : bond 0.03464 ( 282) hydrogen bonds : angle 4.33881 ( 798) covalent geometry : bond 0.00290 ( 6414) covalent geometry : angle 0.52494 ( 8721) Misc. bond : bond 0.00017 ( 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 164 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.754 Fit side-chains REVERT: A 32 LEU cc_start: 0.8383 (pt) cc_final: 0.8047 (pp) REVERT: A 75 LYS cc_start: 0.8753 (tptt) cc_final: 0.8503 (mptt) REVERT: A 126 CYS cc_start: 0.7365 (m) cc_final: 0.6859 (m) REVERT: A 230 ASP cc_start: 0.7669 (m-30) cc_final: 0.7219 (m-30) REVERT: A 367 VAL cc_start: 0.7983 (t) cc_final: 0.7712 (t) outliers start: 15 outliers final: 10 residues processed: 151 average time/residue: 0.2434 time to fit residues: 45.7840 Evaluate side-chains 158 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 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 66 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 65 optimal weight: 0.0980 chunk 75 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.114403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.102439 restraints weight = 9175.974| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.99 r_work: 0.3211 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6415 Z= 0.178 Angle : 0.551 9.130 8721 Z= 0.290 Chirality : 0.041 0.175 977 Planarity : 0.004 0.044 1092 Dihedral : 12.116 63.740 946 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.70 % Allowed : 16.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.31), residues: 766 helix: 1.51 (0.30), residues: 301 sheet: 0.11 (0.43), residues: 138 loop : -0.78 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 73 HIS 0.004 0.001 HIS A 229 PHE 0.010 0.001 PHE A 127 TYR 0.013 0.002 TYR A 240 ARG 0.005 0.000 ARG A 434 Details of bonding type rmsd hydrogen bonds : bond 0.03811 ( 282) hydrogen bonds : angle 4.41949 ( 798) covalent geometry : bond 0.00426 ( 6414) covalent geometry : angle 0.55122 ( 8721) Misc. bond : bond 0.00058 ( 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 170 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.710 Fit side-chains REVERT: A 75 LYS cc_start: 0.8773 (tptt) cc_final: 0.8532 (mptt) REVERT: A 126 CYS cc_start: 0.7541 (m) cc_final: 0.7028 (m) REVERT: A 230 ASP cc_start: 0.7696 (m-30) cc_final: 0.7266 (m-30) REVERT: A 367 VAL cc_start: 0.8016 (t) cc_final: 0.7765 (t) outliers start: 18 outliers final: 13 residues processed: 155 average time/residue: 0.2327 time to fit residues: 45.3261 Evaluate side-chains 164 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 453 THR Chi-restraints excluded: chain B residue 48 ILE 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 59 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 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 = 0.113898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.101974 restraints weight = 9160.408| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.98 r_work: 0.3203 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 6415 Z= 0.204 Angle : 0.565 8.375 8721 Z= 0.296 Chirality : 0.042 0.166 977 Planarity : 0.004 0.045 1092 Dihedral : 12.154 63.078 946 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.40 % Allowed : 16.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.30), residues: 766 helix: 1.44 (0.30), residues: 301 sheet: 0.07 (0.43), residues: 138 loop : -0.82 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 73 HIS 0.004 0.001 HIS A 229 PHE 0.012 0.002 PHE A 127 TYR 0.014 0.002 TYR A 578 ARG 0.006 0.000 ARG A 434 Details of bonding type rmsd hydrogen bonds : bond 0.03981 ( 282) hydrogen bonds : angle 4.48749 ( 798) covalent geometry : bond 0.00490 ( 6414) covalent geometry : angle 0.56467 ( 8721) Misc. bond : bond 0.00075 ( 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 167 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.658 Fit side-chains REVERT: A 32 LEU cc_start: 0.8462 (pt) cc_final: 0.8172 (pp) REVERT: A 52 PHE cc_start: 0.8453 (m-80) cc_final: 0.8216 (m-80) REVERT: A 75 LYS cc_start: 0.8768 (tptt) cc_final: 0.8527 (mptt) REVERT: A 126 CYS cc_start: 0.7573 (m) cc_final: 0.7064 (m) REVERT: A 230 ASP cc_start: 0.7694 (m-30) cc_final: 0.7267 (m-30) outliers start: 16 outliers final: 15 residues processed: 155 average time/residue: 0.2386 time to fit residues: 46.4872 Evaluate side-chains 165 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 453 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain B residue 44 ASP Chi-restraints excluded: chain B residue 48 ILE 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 48 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 14 optimal weight: 0.0070 chunk 11 optimal weight: 0.5980 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.114461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.102424 restraints weight = 9205.392| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.00 r_work: 0.3218 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6415 Z= 0.146 Angle : 0.552 9.613 8721 Z= 0.287 Chirality : 0.041 0.184 977 Planarity : 0.004 0.045 1092 Dihedral : 12.151 63.152 946 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.55 % Allowed : 16.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.31), residues: 766 helix: 1.52 (0.30), residues: 301 sheet: 0.06 (0.43), residues: 138 loop : -0.79 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 458 HIS 0.003 0.001 HIS A 229 PHE 0.010 0.001 PHE A 127 TYR 0.012 0.001 TYR A 411 ARG 0.005 0.000 ARG A 434 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 282) hydrogen bonds : angle 4.41401 ( 798) covalent geometry : bond 0.00346 ( 6414) covalent geometry : angle 0.55154 ( 8721) Misc. bond : bond 0.00036 ( 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 167 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.716 Fit side-chains REVERT: A 75 LYS cc_start: 0.8773 (tptt) cc_final: 0.8539 (mptt) REVERT: A 126 CYS cc_start: 0.7465 (m) cc_final: 0.6941 (m) REVERT: A 230 ASP cc_start: 0.7684 (m-30) cc_final: 0.7246 (m-30) REVERT: A 367 VAL cc_start: 0.7997 (t) cc_final: 0.7741 (t) outliers start: 17 outliers final: 15 residues processed: 154 average time/residue: 0.2343 time to fit residues: 45.0358 Evaluate side-chains 165 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 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 45 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.0870 chunk 70 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 13 optimal weight: 0.0770 chunk 76 optimal weight: 0.0970 overall best weight: 0.2914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.115886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.103798 restraints weight = 9256.525| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.01 r_work: 0.3232 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6415 Z= 0.129 Angle : 0.543 10.556 8721 Z= 0.284 Chirality : 0.040 0.169 977 Planarity : 0.004 0.045 1092 Dihedral : 12.188 64.453 946 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.10 % Allowed : 17.69 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.31), residues: 766 helix: 1.58 (0.30), residues: 302 sheet: 0.06 (0.43), residues: 138 loop : -0.80 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 259 HIS 0.003 0.001 HIS A 229 PHE 0.011 0.001 PHE A 214 TYR 0.013 0.001 TYR A 411 ARG 0.006 0.000 ARG A 434 Details of bonding type rmsd hydrogen bonds : bond 0.03495 ( 282) hydrogen bonds : angle 4.37160 ( 798) covalent geometry : bond 0.00302 ( 6414) covalent geometry : angle 0.54263 ( 8721) Misc. bond : bond 0.00023 ( 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 164 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.779 Fit side-chains REVERT: A 32 LEU cc_start: 0.8390 (pt) cc_final: 0.8078 (pp) REVERT: A 52 PHE cc_start: 0.8399 (m-80) cc_final: 0.8137 (m-80) REVERT: A 75 LYS cc_start: 0.8773 (tptt) cc_final: 0.8535 (mptt) REVERT: A 126 CYS cc_start: 0.7400 (m) cc_final: 0.6879 (m) REVERT: A 159 ASP cc_start: 0.7515 (m-30) cc_final: 0.7268 (m-30) REVERT: A 230 ASP cc_start: 0.7666 (m-30) cc_final: 0.7226 (m-30) REVERT: A 367 VAL cc_start: 0.7935 (t) cc_final: 0.7654 (t) outliers start: 14 outliers final: 14 residues processed: 152 average time/residue: 0.2340 time to fit residues: 44.4276 Evaluate side-chains 162 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 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 75 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 65 optimal weight: 0.1980 chunk 67 optimal weight: 0.8980 chunk 55 optimal weight: 0.0980 chunk 41 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 61 optimal weight: 0.0870 chunk 42 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.2358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.116602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.104562 restraints weight = 9291.155| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.00 r_work: 0.3244 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6415 Z= 0.118 Angle : 0.543 10.236 8721 Z= 0.281 Chirality : 0.039 0.171 977 Planarity : 0.004 0.044 1092 Dihedral : 12.246 65.451 946 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.10 % Allowed : 18.14 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.31), residues: 766 helix: 1.59 (0.30), residues: 302 sheet: 0.08 (0.44), residues: 138 loop : -0.75 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 458 HIS 0.003 0.001 HIS A 229 PHE 0.010 0.001 PHE A 148 TYR 0.013 0.001 TYR A 411 ARG 0.006 0.000 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 282) hydrogen bonds : angle 4.33390 ( 798) covalent geometry : bond 0.00275 ( 6414) covalent geometry : angle 0.54250 ( 8721) Misc. bond : bond 0.00020 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4083.80 seconds wall clock time: 71 minutes 14.41 seconds (4274.41 seconds total)