Starting phenix.real_space_refine on Wed Sep 17 06:39:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cak_45394/09_2025/9cak_45394_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cak_45394/09_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_45394/09_2025/9cak_45394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cak_45394/09_2025/9cak_45394.map" model { file = "/net/cci-nas-00/data/ceres_data/9cak_45394/09_2025/9cak_45394_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cak_45394/09_2025/9cak_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6268 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4844 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 30, 'TRANS': 581} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1219 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "D" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 146 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "E" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Classifications: {'DNA': 3} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.58, per 1000 atoms: 0.25 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: 0.60 Conformation dependent library (CDL) restraints added in 338.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.70 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: 1.11 Time building geometry restraints manager: 0.78 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: 3.230 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.620 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.450 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00476 ( 6414) covalent geometry : angle 0.62144 ( 8721) hydrogen bonds : bond 0.16589 ( 282) hydrogen bonds : angle 6.10630 ( 798) 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 : 0.258 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: 0.1125 time to fit residues: 24.0478 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 : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN B 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.113118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.101398 restraints weight = 9292.960| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.01 r_work: 0.3191 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 6415 Z= 0.231 Angle : 0.609 7.704 8721 Z= 0.321 Chirality : 0.044 0.171 977 Planarity : 0.005 0.070 1092 Dihedral : 11.856 70.152 946 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 1.05 % Allowed : 9.60 % Favored : 89.36 % 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 aren not related in a simple way. whole: 0.12 (0.30), residues: 766 helix: 1.18 (0.30), residues: 299 sheet: -0.02 (0.43), residues: 138 loop : -0.86 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 379 TYR 0.015 0.002 TYR A 41 PHE 0.013 0.002 PHE A 127 TRP 0.016 0.002 TRP A 259 HIS 0.005 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00555 ( 6414) covalent geometry : angle 0.60907 ( 8721) hydrogen bonds : bond 0.04585 ( 282) hydrogen bonds : angle 4.78600 ( 798) Misc. bond : bond 0.00135 ( 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 164 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 157 time to evaluate : 0.245 Fit side-chains REVERT: A 75 LYS cc_start: 0.8779 (tptt) cc_final: 0.8496 (mptt) REVERT: A 120 LYS cc_start: 0.8581 (mtpp) cc_final: 0.8274 (mtpp) REVERT: A 126 CYS cc_start: 0.7548 (m) cc_final: 0.7114 (m) REVERT: A 213 SER cc_start: 0.8693 (m) cc_final: 0.8439 (p) REVERT: A 227 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7538 (tm-30) REVERT: A 230 ASP cc_start: 0.7805 (m-30) cc_final: 0.7526 (m-30) REVERT: A 580 GLN cc_start: 0.8006 (tt0) cc_final: 0.7764 (tt0) outliers start: 7 outliers final: 3 residues processed: 159 average time/residue: 0.1165 time to fit residues: 22.9624 Evaluate side-chains 155 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 152 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain B residue 55 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 70 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 chunk 6 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 48 optimal weight: 0.0000 chunk 13 optimal weight: 0.8980 overall best weight: 0.4362 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.114372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.102655 restraints weight = 9136.076| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.98 r_work: 0.3212 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6415 Z= 0.158 Angle : 0.560 8.976 8721 Z= 0.294 Chirality : 0.042 0.174 977 Planarity : 0.004 0.056 1092 Dihedral : 11.812 60.883 946 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.35 % Allowed : 13.79 % Favored : 84.86 % 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 aren not related in a simple way. whole: 0.29 (0.31), residues: 766 helix: 1.35 (0.30), residues: 301 sheet: 0.04 (0.43), residues: 138 loop : -0.78 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 434 TYR 0.013 0.002 TYR A 41 PHE 0.011 0.001 PHE A 127 TRP 0.012 0.001 TRP A 259 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 6414) covalent geometry : angle 0.56023 ( 8721) hydrogen bonds : bond 0.03964 ( 282) hydrogen bonds : angle 4.57952 ( 798) Misc. bond : bond 0.00083 ( 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 164 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 155 time to evaluate : 0.246 Fit side-chains REVERT: A 75 LYS cc_start: 0.8765 (tptt) cc_final: 0.8521 (mptt) REVERT: A 126 CYS cc_start: 0.7443 (m) cc_final: 0.6969 (m) REVERT: A 213 SER cc_start: 0.8618 (m) cc_final: 0.8410 (p) REVERT: A 230 ASP cc_start: 0.7751 (m-30) cc_final: 0.7484 (m-30) REVERT: A 580 GLN cc_start: 0.7954 (tt0) cc_final: 0.7720 (tt0) outliers start: 9 outliers final: 5 residues processed: 158 average time/residue: 0.1144 time to fit residues: 22.4823 Evaluate side-chains 155 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 150 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 288 THR 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: 0.6980 chunk 52 optimal weight: 0.8980 chunk 12 optimal weight: 0.0770 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 63 optimal weight: 0.0030 chunk 22 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 overall best weight: 0.3148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 323 GLN A 347 ASN A 573 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.114960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.103121 restraints weight = 9202.495| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.99 r_work: 0.3221 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6415 Z= 0.134 Angle : 0.541 6.304 8721 Z= 0.287 Chirality : 0.041 0.157 977 Planarity : 0.004 0.049 1092 Dihedral : 11.827 61.976 946 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.55 % Allowed : 14.39 % Favored : 83.06 % 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 aren not related in a simple way. whole: 0.33 (0.31), residues: 766 helix: 1.41 (0.30), residues: 302 sheet: 0.02 (0.43), residues: 138 loop : -0.79 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 434 TYR 0.013 0.001 TYR A 411 PHE 0.010 0.001 PHE A 148 TRP 0.009 0.001 TRP A 259 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 6414) covalent geometry : angle 0.54076 ( 8721) hydrogen bonds : bond 0.03681 ( 282) hydrogen bonds : angle 4.45580 ( 798) Misc. bond : bond 0.00023 ( 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 172 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.237 Fit side-chains REVERT: A 75 LYS cc_start: 0.8771 (tptt) cc_final: 0.8525 (mptt) REVERT: A 126 CYS cc_start: 0.7418 (m) cc_final: 0.6927 (m) REVERT: A 230 ASP cc_start: 0.7737 (m-30) cc_final: 0.7475 (m-30) REVERT: A 367 VAL cc_start: 0.8019 (t) cc_final: 0.7764 (t) outliers start: 17 outliers final: 11 residues processed: 159 average time/residue: 0.1150 time to fit residues: 22.6784 Evaluate side-chains 163 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 291 LYS Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 393 MET 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: 0.9990 chunk 4 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 40 optimal weight: 0.2980 chunk 1 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.113479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.101566 restraints weight = 9344.972| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.01 r_work: 0.3196 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6415 Z= 0.202 Angle : 0.568 6.823 8721 Z= 0.299 Chirality : 0.042 0.156 977 Planarity : 0.004 0.047 1092 Dihedral : 12.057 63.097 946 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % 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 aren not related in a simple way. whole: 0.28 (0.30), residues: 766 helix: 1.39 (0.30), residues: 301 sheet: 0.01 (0.43), residues: 138 loop : -0.83 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 434 TYR 0.014 0.002 TYR A 578 PHE 0.012 0.002 PHE A 127 TRP 0.009 0.001 TRP A 73 HIS 0.004 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 6414) covalent geometry : angle 0.56774 ( 8721) hydrogen bonds : bond 0.04048 ( 282) hydrogen bonds : angle 4.51743 ( 798) Misc. bond : bond 0.00083 ( 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 173 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.253 Fit side-chains REVERT: A 52 PHE cc_start: 0.8478 (m-80) cc_final: 0.8224 (m-80) REVERT: A 75 LYS cc_start: 0.8771 (tptt) cc_final: 0.8532 (mptt) REVERT: A 120 LYS cc_start: 0.8631 (mtpp) cc_final: 0.8342 (mtpp) REVERT: A 126 CYS cc_start: 0.7613 (m) cc_final: 0.7096 (m) REVERT: A 230 ASP cc_start: 0.7737 (m-30) cc_final: 0.7480 (m-30) outliers start: 17 outliers final: 15 residues processed: 161 average time/residue: 0.1180 time to fit residues: 23.4543 Evaluate side-chains 169 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 56 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3478 r_free = 0.3478 target = 0.113264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.101478 restraints weight = 9211.306| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.98 r_work: 0.3198 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6415 Z= 0.214 Angle : 0.572 7.076 8721 Z= 0.303 Chirality : 0.043 0.176 977 Planarity : 0.004 0.047 1092 Dihedral : 12.089 62.560 946 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.76 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 aren not related in a simple way. whole: 0.20 (0.30), residues: 766 helix: 1.32 (0.30), residues: 301 sheet: -0.03 (0.43), residues: 138 loop : -0.88 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 434 TYR 0.014 0.002 TYR A 578 PHE 0.012 0.002 PHE A 127 TRP 0.009 0.001 TRP A 73 HIS 0.005 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00513 ( 6414) covalent geometry : angle 0.57155 ( 8721) hydrogen bonds : bond 0.04090 ( 282) hydrogen bonds : angle 4.53465 ( 798) Misc. bond : bond 0.00093 ( 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 173 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.270 Fit side-chains REVERT: A 52 PHE cc_start: 0.8448 (m-80) cc_final: 0.8186 (m-80) REVERT: A 75 LYS cc_start: 0.8770 (tptt) cc_final: 0.8539 (mptt) REVERT: A 120 LYS cc_start: 0.8679 (mtpp) cc_final: 0.8379 (mtpp) REVERT: A 126 CYS cc_start: 0.7619 (m) cc_final: 0.7114 (m) REVERT: A 230 ASP cc_start: 0.7709 (m-30) cc_final: 0.7458 (m-30) REVERT: A 357 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7693 (mt0) outliers start: 17 outliers final: 13 residues processed: 160 average time/residue: 0.1126 time to fit residues: 22.4826 Evaluate side-chains 169 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 33 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** A 124 ASN A 573 GLN B 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.113223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.101420 restraints weight = 9130.258| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.98 r_work: 0.3195 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6415 Z= 0.215 Angle : 0.576 7.531 8721 Z= 0.304 Chirality : 0.043 0.186 977 Planarity : 0.004 0.047 1092 Dihedral : 12.126 62.352 946 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.70 % Allowed : 16.94 % Favored : 80.36 % 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 aren not related in a simple way. whole: 0.14 (0.30), residues: 766 helix: 1.27 (0.30), residues: 301 sheet: -0.04 (0.43), residues: 138 loop : -0.92 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 434 TYR 0.015 0.002 TYR A 578 PHE 0.012 0.002 PHE A 127 TRP 0.009 0.002 TRP A 73 HIS 0.004 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 6414) covalent geometry : angle 0.57581 ( 8721) hydrogen bonds : bond 0.04076 ( 282) hydrogen bonds : angle 4.55084 ( 798) Misc. bond : bond 0.00089 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.248 Fit side-chains REVERT: A 52 PHE cc_start: 0.8464 (m-80) cc_final: 0.8165 (m-80) REVERT: A 75 LYS cc_start: 0.8750 (tptt) cc_final: 0.8523 (mptt) REVERT: A 120 LYS cc_start: 0.8681 (mtpp) cc_final: 0.8376 (mtpp) REVERT: A 126 CYS cc_start: 0.7618 (m) cc_final: 0.7103 (m) REVERT: A 227 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7487 (tm-30) REVERT: A 230 ASP cc_start: 0.7719 (m-30) cc_final: 0.7450 (m-30) REVERT: A 357 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7688 (mt0) outliers start: 18 outliers final: 16 residues processed: 156 average time/residue: 0.1130 time to fit residues: 21.9832 Evaluate side-chains 169 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 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 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 30 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 73 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.0020 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 overall best weight: 0.3586 ------------------------------------------------------------------------------- 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** A 124 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 = 0.3501 r_free = 0.3501 target = 0.114960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.102970 restraints weight = 9240.322| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.00 r_work: 0.3218 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6415 Z= 0.142 Angle : 0.547 8.513 8721 Z= 0.287 Chirality : 0.040 0.164 977 Planarity : 0.004 0.046 1092 Dihedral : 12.098 62.387 946 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.95 % Allowed : 17.99 % Favored : 80.06 % 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 aren not related in a simple way. whole: 0.29 (0.30), residues: 766 helix: 1.41 (0.30), residues: 301 sheet: 0.02 (0.43), residues: 138 loop : -0.86 (0.34), residues: 327 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 0.011 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 covalent geometry : bond 0.00333 ( 6414) covalent geometry : angle 0.54732 ( 8721) hydrogen bonds : bond 0.03633 ( 282) hydrogen bonds : angle 4.44311 ( 798) Misc. bond : bond 0.00030 ( 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 166 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.188 Fit side-chains REVERT: A 75 LYS cc_start: 0.8758 (tptt) cc_final: 0.8529 (mptt) REVERT: A 126 CYS cc_start: 0.7468 (m) cc_final: 0.6942 (m) REVERT: A 227 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7469 (tm-30) REVERT: A 230 ASP cc_start: 0.7704 (m-30) cc_final: 0.7432 (m-30) REVERT: A 367 VAL cc_start: 0.8002 (t) cc_final: 0.7744 (t) outliers start: 13 outliers final: 13 residues processed: 154 average time/residue: 0.1122 time to fit residues: 21.6085 Evaluate side-chains 162 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 155 ILE Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 144 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 21 optimal weight: 0.3980 chunk 52 optimal weight: 0.6980 chunk 45 optimal weight: 0.0870 chunk 48 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 0.0270 chunk 51 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.3216 ------------------------------------------------------------------------------- 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** A 124 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 = 0.3507 r_free = 0.3507 target = 0.115317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.103342 restraints weight = 9286.338| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.01 r_work: 0.3224 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6415 Z= 0.134 Angle : 0.547 9.471 8721 Z= 0.285 Chirality : 0.040 0.181 977 Planarity : 0.004 0.045 1092 Dihedral : 12.160 63.984 946 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.95 % Allowed : 18.44 % Favored : 79.61 % 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 aren not related in a simple way. whole: 0.32 (0.30), residues: 766 helix: 1.48 (0.30), residues: 301 sheet: -0.01 (0.43), residues: 138 loop : -0.85 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 434 TYR 0.012 0.001 TYR A 411 PHE 0.011 0.001 PHE A 148 TRP 0.008 0.001 TRP A 458 HIS 0.003 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6414) covalent geometry : angle 0.54654 ( 8721) hydrogen bonds : bond 0.03553 ( 282) hydrogen bonds : angle 4.39950 ( 798) Misc. bond : bond 0.00026 ( 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 162 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.286 Fit side-chains REVERT: A 52 PHE cc_start: 0.8403 (m-80) cc_final: 0.8178 (m-80) REVERT: A 75 LYS cc_start: 0.8781 (tptt) cc_final: 0.8540 (mptt) REVERT: A 126 CYS cc_start: 0.7436 (m) cc_final: 0.6906 (m) REVERT: A 159 ASP cc_start: 0.7513 (m-30) cc_final: 0.7166 (m-30) REVERT: A 227 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7480 (tm-30) REVERT: A 230 ASP cc_start: 0.7706 (m-30) cc_final: 0.7429 (m-30) REVERT: A 367 VAL cc_start: 0.7984 (t) cc_final: 0.7714 (t) outliers start: 13 outliers final: 11 residues processed: 151 average time/residue: 0.1115 time to fit residues: 20.9776 Evaluate side-chains 158 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 155 ILE 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 39 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** A 124 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 = 0.3490 r_free = 0.3490 target = 0.114039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.102254 restraints weight = 9093.767| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.97 r_work: 0.3210 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 6415 Z= 0.192 Angle : 0.576 10.518 8721 Z= 0.301 Chirality : 0.042 0.171 977 Planarity : 0.004 0.045 1092 Dihedral : 12.261 63.984 946 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.25 % Allowed : 18.29 % Favored : 79.46 % 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 aren not related in a simple way. whole: 0.24 (0.30), residues: 766 helix: 1.39 (0.30), residues: 301 sheet: -0.02 (0.43), residues: 138 loop : -0.89 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 434 TYR 0.014 0.002 TYR A 578 PHE 0.012 0.001 PHE A 127 TRP 0.010 0.001 TRP A 458 HIS 0.004 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 6414) covalent geometry : angle 0.57600 ( 8721) hydrogen bonds : bond 0.03924 ( 282) hydrogen bonds : angle 4.49848 ( 798) Misc. bond : bond 0.00062 ( 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 166 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.208 Fit side-chains REVERT: A 75 LYS cc_start: 0.8779 (tptt) cc_final: 0.8534 (mptt) REVERT: A 126 CYS cc_start: 0.7606 (m) cc_final: 0.7072 (m) REVERT: A 230 ASP cc_start: 0.7707 (m-30) cc_final: 0.7269 (m-30) REVERT: A 322 MET cc_start: 0.8405 (tpp) cc_final: 0.8100 (tpp) REVERT: A 357 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7697 (mt0) outliers start: 15 outliers final: 11 residues processed: 154 average time/residue: 0.1079 time to fit residues: 20.8559 Evaluate side-chains 162 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 155 ILE 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 144 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 75 optimal weight: 0.2980 chunk 63 optimal weight: 0.0270 chunk 32 optimal weight: 0.0980 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 0.0980 chunk 27 optimal weight: 0.0970 chunk 54 optimal weight: 0.1980 overall best weight: 0.1036 ------------------------------------------------------------------------------- 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** A 573 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.117601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.105494 restraints weight = 9204.460| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.02 r_work: 0.3257 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 6415 Z= 0.104 Angle : 0.533 10.472 8721 Z= 0.278 Chirality : 0.039 0.170 977 Planarity : 0.004 0.045 1092 Dihedral : 12.160 65.301 946 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.35 % Allowed : 19.04 % Favored : 79.61 % 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 aren not related in a simple way. whole: 0.42 (0.31), residues: 766 helix: 1.58 (0.31), residues: 301 sheet: 0.06 (0.43), residues: 137 loop : -0.83 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 434 TYR 0.013 0.001 TYR A 411 PHE 0.010 0.001 PHE A 148 TRP 0.009 0.001 TRP A 406 HIS 0.002 0.000 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 6414) covalent geometry : angle 0.53283 ( 8721) hydrogen bonds : bond 0.03143 ( 282) hydrogen bonds : angle 4.31638 ( 798) Misc. bond : bond 0.00021 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2089.85 seconds wall clock time: 36 minutes 32.44 seconds (2192.44 seconds total)