Starting phenix.real_space_refine on Thu Jul 2 11:47:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ywm_39638/07_2026/8ywm_39638.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ywm_39638/07_2026/8ywm_39638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ywm_39638/07_2026/8ywm_39638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ywm_39638/07_2026/8ywm_39638.map" model { file = "/net/cci-nas-00/data/ceres_data/8ywm_39638/07_2026/8ywm_39638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ywm_39638/07_2026/8ywm_39638.cif" } resolution = 3.2 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= 0.002 sd= 0.037 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: 5 Type Number sf(0) Gaussians P 34 5.49 5 S 51 5.16 5 C 5455 2.51 5 N 1478 2.21 5 O 1675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8693 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 979, 7980 Classifications: {'peptide': 979} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 934} Chain breaks: 1 Chain: "D" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 339 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "E" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 374 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Time building chain proxies: 2.19, per 1000 atoms: 0.25 Number of scatterers: 8693 At special positions: 0 Unit cell: (89.44, 116.48, 110.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 P 34 15.00 O 1675 8.00 N 1478 7.00 C 5455 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=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 221.3 milliseconds 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1870 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 48.5% alpha, 16.6% beta 16 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 6 through 15 Processing helix chain 'A' and resid 15 through 28 Processing helix chain 'A' and resid 79 through 93 removed outlier: 3.780A pdb=" N GLU A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 142 Processing helix chain 'A' and resid 154 through 163 removed outlier: 3.590A pdb=" N LYS A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 191 No H-bonds generated for 'chain 'A' and resid 189 through 191' Processing helix chain 'A' and resid 271 through 287 Processing helix chain 'A' and resid 299 through 311 removed outlier: 3.650A pdb=" N PHE A 303 " --> pdb=" O TYR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 322 Processing helix chain 'A' and resid 328 through 336 removed outlier: 3.562A pdb=" N TYR A 336 " --> pdb=" O ILE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 374 Processing helix chain 'A' and resid 381 through 389 Processing helix chain 'A' and resid 398 through 409 removed outlier: 3.550A pdb=" N ARG A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 436 removed outlier: 3.607A pdb=" N VAL A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 449 removed outlier: 3.531A pdb=" N ASP A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 458 Processing helix chain 'A' and resid 459 through 475 removed outlier: 4.044A pdb=" N LYS A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 529 Processing helix chain 'A' and resid 532 through 534 No H-bonds generated for 'chain 'A' and resid 532 through 534' Processing helix chain 'A' and resid 539 through 549 Processing helix chain 'A' and resid 575 through 579 Processing helix chain 'A' and resid 580 through 610 Processing helix chain 'A' and resid 616 through 639 Processing helix chain 'A' and resid 640 through 647 Processing helix chain 'A' and resid 654 through 679 Processing helix chain 'A' and resid 697 through 699 No H-bonds generated for 'chain 'A' and resid 697 through 699' Processing helix chain 'A' and resid 700 through 709 removed outlier: 3.973A pdb=" N TYR A 707 " --> pdb=" O VAL A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 748 removed outlier: 3.871A pdb=" N THR A 734 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 815 Processing helix chain 'A' and resid 826 through 841 Processing helix chain 'A' and resid 847 through 851 removed outlier: 3.710A pdb=" N ILE A 851 " --> pdb=" O GLU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 882 Processing helix chain 'A' and resid 921 through 923 No H-bonds generated for 'chain 'A' and resid 921 through 923' Processing helix chain 'A' and resid 928 through 935 Processing helix chain 'A' and resid 939 through 953 removed outlier: 3.616A pdb=" N TYR A 943 " --> pdb=" O ASP A 939 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLY A 950 " --> pdb=" O ASN A 946 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU A 951 " --> pdb=" O TYR A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 990 Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 179 removed outlier: 6.992A pdb=" N PHE A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILE A 39 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N TYR A 52 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 194 " --> pdb=" O GLN A 171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 105 removed outlier: 4.356A pdb=" N VAL A 70 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 268 removed outlier: 3.616A pdb=" N ALA A 249 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N VAL A 232 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR A 215 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY A 293 " --> pdb=" O ILE A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 344 Processing sheet with id=AA5, first strand: chain 'A' and resid 506 through 508 removed outlier: 3.502A pdb=" N PHE A 765 " --> pdb=" O GLY A 506 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TYR A 756 " --> pdb=" O ASP A 517 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASP A 517 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLU A 758 " --> pdb=" O GLY A 515 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 515 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY A 686 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TYR A 692 " --> pdb=" O LYS A 684 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 506 through 508 removed outlier: 3.502A pdb=" N PHE A 765 " --> pdb=" O GLY A 506 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU A 760 " --> pdb=" O HIS A 776 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N HIS A 776 " --> pdb=" O LEU A 760 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LYS A 770 " --> pdb=" O THR A 766 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 536 through 537 Processing sheet with id=AA8, first strand: chain 'A' and resid 852 through 855 418 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 1.84 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2107 1.33 - 1.45: 1932 1.45 - 1.57: 4783 1.57 - 1.69: 67 1.69 - 1.81: 81 Bond restraints: 8970 Sorted by residual: bond pdb=" N LYS A 712 " pdb=" CA LYS A 712 " ideal model delta sigma weight residual 1.460 1.512 -0.052 1.45e-02 4.76e+03 1.29e+01 bond pdb=" C3' DT E 21 " pdb=" C2' DT E 21 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" N ASP A 822 " pdb=" CA ASP A 822 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.16e-02 7.43e+03 8.45e+00 bond pdb=" O3' DA E 22 " pdb=" P DC E 23 " ideal model delta sigma weight residual 1.607 1.650 -0.043 1.50e-02 4.44e+03 8.32e+00 bond pdb=" C3' DC E 14 " pdb=" C2' DC E 14 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.92e+00 ... (remaining 8965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 11934 1.99 - 3.99: 290 3.99 - 5.98: 35 5.98 - 7.98: 10 7.98 - 9.97: 5 Bond angle restraints: 12274 Sorted by residual: angle pdb=" C VAL A 188 " pdb=" N THR A 189 " pdb=" CA THR A 189 " ideal model delta sigma weight residual 120.94 130.79 -9.85 1.90e+00 2.77e-01 2.69e+01 angle pdb=" C GLU A 93 " pdb=" N ASN A 94 " pdb=" CA ASN A 94 " ideal model delta sigma weight residual 121.54 130.10 -8.56 1.91e+00 2.74e-01 2.01e+01 angle pdb=" CB LYS A 260 " pdb=" CG LYS A 260 " pdb=" CD LYS A 260 " ideal model delta sigma weight residual 111.30 121.27 -9.97 2.30e+00 1.89e-01 1.88e+01 angle pdb=" N3 DT E 16 " pdb=" C4 DT E 16 " pdb=" O4 DT E 16 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT D 20 " pdb=" C4 DT D 20 " pdb=" O4 DT D 20 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.66e+01 ... (remaining 12269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.12: 4904 27.12 - 54.24: 365 54.24 - 81.36: 48 81.36 - 108.48: 3 108.48 - 135.61: 1 Dihedral angle restraints: 5321 sinusoidal: 2417 harmonic: 2904 Sorted by residual: dihedral pdb=" CA PHE A 71 " pdb=" C PHE A 71 " pdb=" N PHE A 72 " pdb=" CA PHE A 72 " ideal model delta harmonic sigma weight residual 180.00 160.58 19.42 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA TYR A 700 " pdb=" C TYR A 700 " pdb=" N THR A 701 " pdb=" CA THR A 701 " ideal model delta harmonic sigma weight residual -180.00 -161.07 -18.93 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ILE A 253 " pdb=" C ILE A 253 " pdb=" N THR A 254 " pdb=" CA THR A 254 " ideal model delta harmonic sigma weight residual -180.00 -161.57 -18.43 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 5318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 885 0.039 - 0.079: 317 0.079 - 0.118: 96 0.118 - 0.157: 29 0.157 - 0.196: 5 Chirality restraints: 1332 Sorted by residual: chirality pdb=" CA ASN A 94 " pdb=" N ASN A 94 " pdb=" C ASN A 94 " pdb=" CB ASN A 94 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" CA LYS A 712 " pdb=" N LYS A 712 " pdb=" C LYS A 712 " pdb=" CB LYS A 712 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.45e-01 chirality pdb=" CA ILE A 693 " pdb=" N ILE A 693 " pdb=" C ILE A 693 " pdb=" CB ILE A 693 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.52e-01 ... (remaining 1329 not shown) Planarity restraints: 1448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 857 " 0.045 5.00e-02 4.00e+02 6.87e-02 7.54e+00 pdb=" N PRO A 858 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 858 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 858 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 287 " -0.042 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO A 288 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 99 " 0.176 9.50e-02 1.11e+02 7.96e-02 5.05e+00 pdb=" NE ARG A 99 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 99 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG A 99 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 99 " 0.000 2.00e-02 2.50e+03 ... (remaining 1445 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1039 2.75 - 3.29: 8061 3.29 - 3.83: 14606 3.83 - 4.36: 16262 4.36 - 4.90: 28119 Nonbonded interactions: 68087 Sorted by model distance: nonbonded pdb=" OG SER A 297 " pdb=" OD2 ASP A 365 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR A 471 " pdb=" OD2 ASP A 588 " model vdw 2.286 3.040 nonbonded pdb=" O TYR A 406 " pdb=" NH1 ARG A 409 " model vdw 2.311 3.120 nonbonded pdb=" O ILE A 636 " pdb=" OG1 THR A 640 " model vdw 2.343 3.040 nonbonded pdb=" O THR A 701 " pdb=" OG1 THR A 704 " model vdw 2.360 3.040 ... (remaining 68082 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: 0.710 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: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.900 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 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 : 0.004 0.052 8970 Z= 0.281 Angle : 0.735 9.974 12274 Z= 0.454 Chirality : 0.047 0.196 1332 Planarity : 0.006 0.080 1448 Dihedral : 17.374 135.606 3451 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.69 % Favored : 96.21 % Rotamer: Outliers : 0.23 % Allowed : 0.23 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.26), residues: 975 helix: 0.90 (0.24), residues: 442 sheet: 0.28 (0.42), residues: 151 loop : -0.72 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 99 TYR 0.031 0.002 TYR A 177 PHE 0.037 0.002 PHE A 303 TRP 0.025 0.002 TRP A 325 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.28 ( 8970) covalent geometry : angle 0.73519 / 0.45 (12274) hydrogen bonds : bond 0.15361 / 10.32 ( 452) hydrogen bonds : angle 6.55321 / 4.66 ( 1274) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 348 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6535 (mt-10) REVERT: A 39 ILE cc_start: 0.8175 (mm) cc_final: 0.7801 (mm) REVERT: A 41 GLU cc_start: 0.7266 (pt0) cc_final: 0.7033 (pt0) REVERT: A 75 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7540 (tm-30) REVERT: A 127 LYS cc_start: 0.8069 (ttmm) cc_final: 0.7802 (ttmm) REVERT: A 134 LYS cc_start: 0.7786 (mmmm) cc_final: 0.7530 (mmmm) REVERT: A 163 LYS cc_start: 0.8204 (mmtm) cc_final: 0.7947 (mmtp) REVERT: A 180 ARG cc_start: 0.7177 (mtm110) cc_final: 0.6637 (mtm110) REVERT: A 191 GLU cc_start: 0.7134 (mp0) cc_final: 0.6889 (mp0) REVERT: A 206 ILE cc_start: 0.7710 (mt) cc_final: 0.7401 (mm) REVERT: A 278 SER cc_start: 0.8347 (t) cc_final: 0.8129 (t) REVERT: A 285 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.7121 (mtp85) REVERT: A 334 LYS cc_start: 0.8333 (tppp) cc_final: 0.8030 (tppp) REVERT: A 340 GLU cc_start: 0.7257 (mt-10) cc_final: 0.7040 (mt-10) REVERT: A 349 LYS cc_start: 0.7831 (tttt) cc_final: 0.7544 (mttm) REVERT: A 399 TYR cc_start: 0.7509 (m-80) cc_final: 0.6604 (m-80) REVERT: A 474 HIS cc_start: 0.7477 (m90) cc_final: 0.7204 (m170) REVERT: A 476 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6792 (tm-30) REVERT: A 513 THR cc_start: 0.6775 (t) cc_final: 0.6496 (p) REVERT: A 517 ASP cc_start: 0.6609 (t70) cc_final: 0.6254 (t70) REVERT: A 593 ARG cc_start: 0.7998 (ttt90) cc_final: 0.7774 (ttt180) REVERT: A 630 LYS cc_start: 0.8035 (mttt) cc_final: 0.7756 (mtpp) REVERT: A 632 LYS cc_start: 0.8017 (tptt) cc_final: 0.7751 (ttmm) REVERT: A 636 ILE cc_start: 0.8157 (tt) cc_final: 0.7946 (tt) REVERT: A 687 ASP cc_start: 0.6487 (t0) cc_final: 0.5806 (t0) REVERT: A 738 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7271 (mt-10) REVERT: A 824 ARG cc_start: 0.6503 (mtt-85) cc_final: 0.6177 (mtt-85) REVERT: A 846 ASN cc_start: 0.6664 (p0) cc_final: 0.6117 (p0) REVERT: A 863 LYS cc_start: 0.7210 (mmmm) cc_final: 0.6961 (mmmm) REVERT: A 924 LYS cc_start: 0.7449 (mttp) cc_final: 0.6785 (mttm) REVERT: A 937 PRO cc_start: 0.7002 (Cg_endo) cc_final: 0.5930 (Cg_exo) REVERT: A 947 TYR cc_start: 0.7645 (m-80) cc_final: 0.7428 (m-10) outliers start: 2 outliers final: 2 residues processed: 350 average time/residue: 0.1006 time to fit residues: 46.4675 Evaluate side-chains 302 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 300 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 938 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS A 319 ASN ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN A 963 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.151887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.125648 restraints weight = 13042.599| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.55 r_work: 0.3459 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8970 Z= 0.198 Angle : 0.667 8.112 12274 Z= 0.359 Chirality : 0.047 0.209 1332 Planarity : 0.005 0.051 1448 Dihedral : 18.698 136.868 1464 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.18 % Favored : 96.72 % Rotamer: Outliers : 2.62 % Allowed : 13.54 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.27), residues: 975 helix: 1.37 (0.24), residues: 445 sheet: 0.27 (0.39), residues: 164 loop : -0.61 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 13 TYR 0.024 0.002 TYR A 405 PHE 0.030 0.002 PHE A 294 TRP 0.022 0.002 TRP A 325 HIS 0.005 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.20 ( 8970) covalent geometry : angle 0.66690 / 0.36 (12274) hydrogen bonds : bond 0.06747 / 4.20 ( 452) hydrogen bonds : angle 4.53314 / 3.19 ( 1274) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 311 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8628 (tp40) cc_final: 0.8262 (tp-100) REVERT: A 41 GLU cc_start: 0.8152 (pt0) cc_final: 0.7645 (pt0) REVERT: A 54 SER cc_start: 0.8298 (m) cc_final: 0.7957 (t) REVERT: A 62 GLU cc_start: 0.7560 (tt0) cc_final: 0.7274 (tt0) REVERT: A 75 GLN cc_start: 0.8477 (tm-30) cc_final: 0.8153 (tm-30) REVERT: A 127 LYS cc_start: 0.8532 (ttmm) cc_final: 0.8194 (ttmm) REVERT: A 134 LYS cc_start: 0.8099 (mmmm) cc_final: 0.7835 (mmmm) REVERT: A 149 ASP cc_start: 0.7524 (p0) cc_final: 0.7146 (p0) REVERT: A 163 LYS cc_start: 0.8490 (mmtm) cc_final: 0.8166 (tppt) REVERT: A 180 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7121 (mtt90) REVERT: A 191 GLU cc_start: 0.7670 (mp0) cc_final: 0.7332 (mp0) REVERT: A 206 ILE cc_start: 0.7911 (mt) cc_final: 0.7658 (mm) REVERT: A 207 VAL cc_start: 0.8335 (t) cc_final: 0.8036 (m) REVERT: A 285 ARG cc_start: 0.8402 (ttm-80) cc_final: 0.7962 (mmm-85) REVERT: A 313 ILE cc_start: 0.8577 (pt) cc_final: 0.8321 (pt) REVERT: A 334 LYS cc_start: 0.8528 (tppp) cc_final: 0.8159 (tppp) REVERT: A 349 LYS cc_start: 0.8211 (tttt) cc_final: 0.7965 (mttm) REVERT: A 376 LYS cc_start: 0.8269 (mmtt) cc_final: 0.8013 (mmtm) REVERT: A 399 TYR cc_start: 0.7840 (m-80) cc_final: 0.6788 (m-80) REVERT: A 469 ILE cc_start: 0.8466 (mt) cc_final: 0.8101 (tt) REVERT: A 474 HIS cc_start: 0.7784 (m90) cc_final: 0.7536 (m170) REVERT: A 476 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7234 (tm-30) REVERT: A 513 THR cc_start: 0.7267 (t) cc_final: 0.6968 (p) REVERT: A 517 ASP cc_start: 0.7292 (t70) cc_final: 0.6848 (t70) REVERT: A 549 LYS cc_start: 0.8545 (ptmt) cc_final: 0.8128 (ptmt) REVERT: A 579 MET cc_start: 0.7721 (ttm) cc_final: 0.7413 (ttm) REVERT: A 593 ARG cc_start: 0.8200 (ttt90) cc_final: 0.7977 (ttt90) REVERT: A 630 LYS cc_start: 0.8223 (mttt) cc_final: 0.7992 (mtpp) REVERT: A 632 LYS cc_start: 0.8164 (tptt) cc_final: 0.7845 (ttmm) REVERT: A 635 LYS cc_start: 0.8352 (tttt) cc_final: 0.8102 (ttpt) REVERT: A 647 ASN cc_start: 0.8059 (t0) cc_final: 0.7791 (t0) REVERT: A 687 ASP cc_start: 0.7110 (t0) cc_final: 0.6773 (t0) REVERT: A 738 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8150 (mt-10) REVERT: A 846 ASN cc_start: 0.7365 (p0) cc_final: 0.6899 (p0) REVERT: A 848 GLU cc_start: 0.7804 (mp0) cc_final: 0.7513 (mp0) REVERT: A 863 LYS cc_start: 0.7693 (mmmm) cc_final: 0.7449 (mmmm) REVERT: A 900 TYR cc_start: 0.7858 (p90) cc_final: 0.7056 (p90) REVERT: A 924 LYS cc_start: 0.7992 (mttp) cc_final: 0.6954 (mttm) REVERT: A 947 TYR cc_start: 0.8120 (m-80) cc_final: 0.7873 (m-10) outliers start: 23 outliers final: 14 residues processed: 319 average time/residue: 0.1091 time to fit residues: 45.5075 Evaluate side-chains 315 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 301 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 489 LYS Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 938 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 71 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 0.0070 chunk 76 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN A 282 GLN A 319 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.148360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.121783 restraints weight = 12819.475| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.52 r_work: 0.3395 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8970 Z= 0.202 Angle : 0.647 9.046 12274 Z= 0.348 Chirality : 0.046 0.212 1332 Planarity : 0.005 0.044 1448 Dihedral : 18.694 135.196 1460 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.28 % Favored : 96.62 % Rotamer: Outliers : 3.41 % Allowed : 16.72 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.27), residues: 975 helix: 1.46 (0.24), residues: 444 sheet: 0.07 (0.37), residues: 164 loop : -0.59 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 824 TYR 0.024 0.002 TYR A 772 PHE 0.018 0.002 PHE A 294 TRP 0.015 0.002 TRP A 325 HIS 0.004 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 ( 8970) covalent geometry : angle 0.64700 / 0.35 (12274) hydrogen bonds : bond 0.05995 / 3.82 ( 452) hydrogen bonds : angle 4.34823 / 3.07 ( 1274) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 342 time to evaluate : 0.262 Fit side-chains REVERT: A 5 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.6997 (ttt) REVERT: A 41 GLU cc_start: 0.8143 (pt0) cc_final: 0.7635 (pt0) REVERT: A 54 SER cc_start: 0.8401 (m) cc_final: 0.8010 (p) REVERT: A 56 GLU cc_start: 0.7679 (pt0) cc_final: 0.7175 (pt0) REVERT: A 59 TYR cc_start: 0.8172 (m-10) cc_final: 0.7790 (m-80) REVERT: A 62 GLU cc_start: 0.7639 (tt0) cc_final: 0.7409 (tt0) REVERT: A 75 GLN cc_start: 0.8490 (tm-30) cc_final: 0.7822 (tm-30) REVERT: A 85 PHE cc_start: 0.8994 (t80) cc_final: 0.8581 (t80) REVERT: A 109 MET cc_start: 0.7744 (mmm) cc_final: 0.7505 (mmt) REVERT: A 127 LYS cc_start: 0.8512 (ttmm) cc_final: 0.8191 (ttmm) REVERT: A 134 LYS cc_start: 0.8156 (mmmm) cc_final: 0.7870 (mmmm) REVERT: A 142 MET cc_start: 0.8048 (mmm) cc_final: 0.7743 (tmm) REVERT: A 149 ASP cc_start: 0.7588 (p0) cc_final: 0.6939 (p0) REVERT: A 180 ARG cc_start: 0.7942 (mtm110) cc_final: 0.7392 (mtm110) REVERT: A 183 VAL cc_start: 0.8581 (m) cc_final: 0.8365 (p) REVERT: A 191 GLU cc_start: 0.7772 (mp0) cc_final: 0.7422 (mp0) REVERT: A 285 ARG cc_start: 0.8533 (ttm-80) cc_final: 0.7958 (mmm-85) REVERT: A 307 LYS cc_start: 0.8410 (mmtt) cc_final: 0.7690 (mmmt) REVERT: A 320 LYS cc_start: 0.8709 (ttmm) cc_final: 0.8479 (ttmm) REVERT: A 334 LYS cc_start: 0.8530 (tppp) cc_final: 0.8137 (tppp) REVERT: A 349 LYS cc_start: 0.8333 (tttt) cc_final: 0.8088 (tttm) REVERT: A 369 MET cc_start: 0.8041 (mmp) cc_final: 0.7788 (mmt) REVERT: A 376 LYS cc_start: 0.8324 (mmtt) cc_final: 0.8036 (mmtm) REVERT: A 397 LEU cc_start: 0.8593 (tp) cc_final: 0.8382 (tp) REVERT: A 399 TYR cc_start: 0.7918 (m-80) cc_final: 0.6927 (m-80) REVERT: A 404 LYS cc_start: 0.8167 (tttm) cc_final: 0.7894 (tttm) REVERT: A 426 GLN cc_start: 0.8609 (tp40) cc_final: 0.7737 (tm-30) REVERT: A 467 MET cc_start: 0.8142 (ttp) cc_final: 0.7751 (ttm) REVERT: A 476 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7440 (tm-30) REVERT: A 484 THR cc_start: 0.7791 (m) cc_final: 0.7449 (p) REVERT: A 511 LYS cc_start: 0.8296 (ptpp) cc_final: 0.7348 (ptpp) REVERT: A 513 THR cc_start: 0.7620 (t) cc_final: 0.7331 (p) REVERT: A 517 ASP cc_start: 0.7510 (t70) cc_final: 0.7052 (t70) REVERT: A 549 LYS cc_start: 0.8593 (ptmt) cc_final: 0.8238 (ptmt) REVERT: A 579 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7596 (ttm) REVERT: A 593 ARG cc_start: 0.8228 (ttt90) cc_final: 0.7916 (ttt90) REVERT: A 630 LYS cc_start: 0.8249 (mttt) cc_final: 0.8003 (mttp) REVERT: A 632 LYS cc_start: 0.8191 (tptt) cc_final: 0.7723 (ttmm) REVERT: A 635 LYS cc_start: 0.8313 (tttt) cc_final: 0.7712 (ttmm) REVERT: A 636 ILE cc_start: 0.8363 (tt) cc_final: 0.8148 (tt) REVERT: A 644 GLU cc_start: 0.7439 (tp30) cc_final: 0.6984 (tp30) REVERT: A 647 ASN cc_start: 0.8237 (t0) cc_final: 0.7954 (t0) REVERT: A 687 ASP cc_start: 0.7244 (t0) cc_final: 0.6890 (t0) REVERT: A 718 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6684 (mt-10) REVERT: A 738 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8316 (mt-10) REVERT: A 810 ILE cc_start: 0.8577 (mt) cc_final: 0.8285 (tp) REVERT: A 846 ASN cc_start: 0.7934 (p0) cc_final: 0.6955 (p0) REVERT: A 848 GLU cc_start: 0.7819 (mp0) cc_final: 0.7096 (mp0) REVERT: A 863 LYS cc_start: 0.7913 (mmmm) cc_final: 0.7353 (mmmm) REVERT: A 867 ILE cc_start: 0.7661 (mm) cc_final: 0.7415 (mm) REVERT: A 888 GLN cc_start: 0.8135 (pm20) cc_final: 0.7814 (pm20) REVERT: A 900 TYR cc_start: 0.7869 (p90) cc_final: 0.7297 (p90) REVERT: A 924 LYS cc_start: 0.7902 (mttp) cc_final: 0.7408 (mttm) REVERT: A 947 TYR cc_start: 0.8287 (m-80) cc_final: 0.7978 (m-10) outliers start: 30 outliers final: 15 residues processed: 350 average time/residue: 0.1046 time to fit residues: 48.1443 Evaluate side-chains 340 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 322 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 938 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 60 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 GLN A 429 GLN A 976 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.147755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.120888 restraints weight = 12940.912| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.53 r_work: 0.3429 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8970 Z= 0.177 Angle : 0.614 9.908 12274 Z= 0.327 Chirality : 0.044 0.213 1332 Planarity : 0.005 0.045 1448 Dihedral : 18.684 135.832 1460 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.28 % Favored : 96.62 % Rotamer: Outliers : 3.30 % Allowed : 18.77 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.27), residues: 975 helix: 1.64 (0.24), residues: 445 sheet: -0.01 (0.38), residues: 164 loop : -0.64 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 99 TYR 0.018 0.001 TYR A 405 PHE 0.031 0.002 PHE A 72 TRP 0.011 0.001 TRP A 325 HIS 0.004 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 ( 8970) covalent geometry : angle 0.61359 / 0.33 (12274) hydrogen bonds : bond 0.05370 / 3.41 ( 452) hydrogen bonds : angle 4.21115 / 2.99 ( 1274) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 341 time to evaluate : 0.289 Fit side-chains REVERT: A 5 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6871 (ttp) REVERT: A 41 GLU cc_start: 0.8072 (pt0) cc_final: 0.7603 (pt0) REVERT: A 54 SER cc_start: 0.8404 (m) cc_final: 0.8065 (t) REVERT: A 56 GLU cc_start: 0.7620 (pt0) cc_final: 0.7153 (pt0) REVERT: A 59 TYR cc_start: 0.8296 (m-10) cc_final: 0.8013 (m-80) REVERT: A 62 GLU cc_start: 0.7601 (tt0) cc_final: 0.7378 (tt0) REVERT: A 75 GLN cc_start: 0.8475 (tm-30) cc_final: 0.7817 (tm-30) REVERT: A 85 PHE cc_start: 0.8973 (t80) cc_final: 0.8550 (t80) REVERT: A 109 MET cc_start: 0.7760 (mmm) cc_final: 0.7527 (mmt) REVERT: A 127 LYS cc_start: 0.8535 (ttmm) cc_final: 0.8129 (ttmm) REVERT: A 134 LYS cc_start: 0.8193 (mmmm) cc_final: 0.7914 (mmmm) REVERT: A 142 MET cc_start: 0.8004 (mmm) cc_final: 0.7700 (tmm) REVERT: A 149 ASP cc_start: 0.7578 (p0) cc_final: 0.6972 (p0) REVERT: A 180 ARG cc_start: 0.7903 (mtm110) cc_final: 0.7377 (mtm110) REVERT: A 191 GLU cc_start: 0.7771 (mp0) cc_final: 0.7470 (mp0) REVERT: A 230 ASP cc_start: 0.7458 (m-30) cc_final: 0.7083 (m-30) REVERT: A 285 ARG cc_start: 0.8497 (ttm-80) cc_final: 0.8047 (mmm-85) REVERT: A 307 LYS cc_start: 0.8422 (mmtt) cc_final: 0.7746 (mmmt) REVERT: A 320 LYS cc_start: 0.8713 (ttmm) cc_final: 0.8476 (ttmm) REVERT: A 334 LYS cc_start: 0.8458 (tppp) cc_final: 0.8071 (tppp) REVERT: A 349 LYS cc_start: 0.8330 (tttt) cc_final: 0.8085 (tttm) REVERT: A 376 LYS cc_start: 0.8333 (mmtt) cc_final: 0.8072 (mmtm) REVERT: A 395 VAL cc_start: 0.7467 (m) cc_final: 0.7141 (p) REVERT: A 397 LEU cc_start: 0.8618 (tp) cc_final: 0.8414 (tp) REVERT: A 399 TYR cc_start: 0.7978 (m-80) cc_final: 0.7071 (m-80) REVERT: A 404 LYS cc_start: 0.8238 (tttm) cc_final: 0.7973 (tttm) REVERT: A 424 ASP cc_start: 0.8108 (t0) cc_final: 0.7603 (t0) REVERT: A 426 GLN cc_start: 0.8586 (tp40) cc_final: 0.8175 (tm-30) REVERT: A 467 MET cc_start: 0.8101 (ttp) cc_final: 0.7714 (ttm) REVERT: A 475 ASP cc_start: 0.7274 (t0) cc_final: 0.7016 (t0) REVERT: A 476 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7327 (tm-30) REVERT: A 511 LYS cc_start: 0.8309 (ptpp) cc_final: 0.8002 (ptpp) REVERT: A 513 THR cc_start: 0.7845 (t) cc_final: 0.7597 (p) REVERT: A 517 ASP cc_start: 0.7636 (t70) cc_final: 0.7259 (t70) REVERT: A 549 LYS cc_start: 0.8569 (ptmt) cc_final: 0.8257 (ptmt) REVERT: A 579 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7552 (ttm) REVERT: A 597 LYS cc_start: 0.8015 (mmtm) cc_final: 0.7702 (tppp) REVERT: A 630 LYS cc_start: 0.8335 (mttt) cc_final: 0.8069 (mttp) REVERT: A 632 LYS cc_start: 0.8226 (tptt) cc_final: 0.7772 (ttmm) REVERT: A 635 LYS cc_start: 0.8456 (tttt) cc_final: 0.7891 (ttmm) REVERT: A 636 ILE cc_start: 0.8469 (tt) cc_final: 0.8095 (tp) REVERT: A 644 GLU cc_start: 0.7452 (tp30) cc_final: 0.7074 (tp30) REVERT: A 647 ASN cc_start: 0.8346 (t0) cc_final: 0.8047 (t0) REVERT: A 670 LYS cc_start: 0.8566 (ttmm) cc_final: 0.8272 (ttmm) REVERT: A 676 VAL cc_start: 0.8588 (t) cc_final: 0.8248 (m) REVERT: A 687 ASP cc_start: 0.7323 (t0) cc_final: 0.7028 (t0) REVERT: A 721 CYS cc_start: 0.7779 (m) cc_final: 0.7329 (m) REVERT: A 747 ASN cc_start: 0.8173 (p0) cc_final: 0.7915 (p0) REVERT: A 778 ASN cc_start: 0.8702 (m-40) cc_final: 0.8392 (m-40) REVERT: A 810 ILE cc_start: 0.8700 (mt) cc_final: 0.8413 (tp) REVERT: A 816 LYS cc_start: 0.8558 (ptpp) cc_final: 0.8325 (ptpp) REVERT: A 819 ARG cc_start: 0.6565 (mtm-85) cc_final: 0.6347 (mtm-85) REVERT: A 863 LYS cc_start: 0.8051 (mmmm) cc_final: 0.7558 (mmmm) REVERT: A 900 TYR cc_start: 0.7913 (p90) cc_final: 0.7053 (p90) REVERT: A 924 LYS cc_start: 0.8020 (mttp) cc_final: 0.7310 (mttm) REVERT: A 925 MET cc_start: 0.7533 (mmm) cc_final: 0.6766 (mmm) REVERT: A 947 TYR cc_start: 0.8336 (m-80) cc_final: 0.8059 (m-10) REVERT: A 963 GLN cc_start: 0.8344 (mm110) cc_final: 0.8127 (mm110) outliers start: 29 outliers final: 15 residues processed: 346 average time/residue: 0.1029 time to fit residues: 46.7917 Evaluate side-chains 336 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 319 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 958 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 84 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 82 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 976 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.148898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.122445 restraints weight = 12877.228| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.44 r_work: 0.3447 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8970 Z= 0.139 Angle : 0.587 10.501 12274 Z= 0.313 Chirality : 0.043 0.221 1332 Planarity : 0.004 0.040 1448 Dihedral : 18.629 134.933 1460 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.30 % Allowed : 20.25 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.27), residues: 975 helix: 1.76 (0.24), residues: 445 sheet: 0.02 (0.38), residues: 164 loop : -0.65 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 13 TYR 0.015 0.001 TYR A 405 PHE 0.030 0.002 PHE A 986 TRP 0.008 0.001 TRP A 325 HIS 0.004 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 8970) covalent geometry : angle 0.58707 / 0.31 (12274) hydrogen bonds : bond 0.04941 / 3.15 ( 452) hydrogen bonds : angle 4.13850 / 2.95 ( 1274) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 327 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.5305 (ttt) REVERT: A 9 GLU cc_start: 0.7613 (tt0) cc_final: 0.6973 (tt0) REVERT: A 27 GLN cc_start: 0.8603 (tp40) cc_final: 0.8340 (tp-100) REVERT: A 41 GLU cc_start: 0.8100 (pt0) cc_final: 0.7669 (pt0) REVERT: A 54 SER cc_start: 0.8375 (m) cc_final: 0.8102 (t) REVERT: A 56 GLU cc_start: 0.7608 (pt0) cc_final: 0.7129 (pt0) REVERT: A 59 TYR cc_start: 0.8297 (m-10) cc_final: 0.8084 (m-80) REVERT: A 62 GLU cc_start: 0.7636 (tt0) cc_final: 0.7427 (tt0) REVERT: A 75 GLN cc_start: 0.8423 (tm-30) cc_final: 0.8028 (tm-30) REVERT: A 85 PHE cc_start: 0.8970 (t80) cc_final: 0.8558 (t80) REVERT: A 127 LYS cc_start: 0.8551 (ttmm) cc_final: 0.8147 (ttmm) REVERT: A 134 LYS cc_start: 0.8145 (mmmm) cc_final: 0.7868 (mmmm) REVERT: A 142 MET cc_start: 0.8026 (mmm) cc_final: 0.7720 (tmm) REVERT: A 149 ASP cc_start: 0.7616 (p0) cc_final: 0.7128 (p0) REVERT: A 180 ARG cc_start: 0.7885 (mtm110) cc_final: 0.7324 (mtm110) REVERT: A 191 GLU cc_start: 0.7756 (mp0) cc_final: 0.7457 (mp0) REVERT: A 194 VAL cc_start: 0.8528 (p) cc_final: 0.8174 (m) REVERT: A 208 MET cc_start: 0.8055 (ttm) cc_final: 0.7845 (ttp) REVERT: A 230 ASP cc_start: 0.7488 (m-30) cc_final: 0.7116 (m-30) REVERT: A 285 ARG cc_start: 0.8478 (ttm-80) cc_final: 0.7932 (mmm-85) REVERT: A 289 ASP cc_start: 0.7991 (m-30) cc_final: 0.7529 (m-30) REVERT: A 307 LYS cc_start: 0.8449 (mmtt) cc_final: 0.7781 (mmmt) REVERT: A 334 LYS cc_start: 0.8495 (tppp) cc_final: 0.8086 (tppp) REVERT: A 349 LYS cc_start: 0.8342 (tttt) cc_final: 0.8109 (tttm) REVERT: A 369 MET cc_start: 0.8014 (mmp) cc_final: 0.7757 (mmt) REVERT: A 376 LYS cc_start: 0.8316 (mmtt) cc_final: 0.8054 (mmtm) REVERT: A 395 VAL cc_start: 0.7556 (m) cc_final: 0.7204 (p) REVERT: A 397 LEU cc_start: 0.8618 (tp) cc_final: 0.8417 (tp) REVERT: A 399 TYR cc_start: 0.8008 (m-80) cc_final: 0.7040 (m-80) REVERT: A 404 LYS cc_start: 0.8246 (tttm) cc_final: 0.7982 (tttm) REVERT: A 424 ASP cc_start: 0.8175 (t0) cc_final: 0.7607 (t0) REVERT: A 434 ARG cc_start: 0.8292 (mmm160) cc_final: 0.7990 (tpt90) REVERT: A 476 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7238 (tm-30) REVERT: A 511 LYS cc_start: 0.8409 (ptpp) cc_final: 0.8095 (ptpt) REVERT: A 513 THR cc_start: 0.7805 (t) cc_final: 0.7526 (p) REVERT: A 579 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7548 (ttm) REVERT: A 597 LYS cc_start: 0.8067 (mmtm) cc_final: 0.7730 (tppp) REVERT: A 630 LYS cc_start: 0.8366 (mttt) cc_final: 0.8099 (mttp) REVERT: A 632 LYS cc_start: 0.8247 (tptt) cc_final: 0.7761 (ttmm) REVERT: A 636 ILE cc_start: 0.8475 (tt) cc_final: 0.8016 (tp) REVERT: A 644 GLU cc_start: 0.7406 (tp30) cc_final: 0.7040 (tp30) REVERT: A 647 ASN cc_start: 0.8285 (t0) cc_final: 0.7967 (t0) REVERT: A 670 LYS cc_start: 0.8552 (ttmm) cc_final: 0.8239 (ttmm) REVERT: A 676 VAL cc_start: 0.8568 (t) cc_final: 0.8191 (m) REVERT: A 687 ASP cc_start: 0.7385 (t0) cc_final: 0.7131 (t0) REVERT: A 715 LYS cc_start: 0.8160 (mmtm) cc_final: 0.7930 (mmtm) REVERT: A 721 CYS cc_start: 0.7815 (m) cc_final: 0.7331 (m) REVERT: A 747 ASN cc_start: 0.8111 (p0) cc_final: 0.7873 (p0) REVERT: A 778 ASN cc_start: 0.8806 (m-40) cc_final: 0.8424 (m-40) REVERT: A 793 ASP cc_start: 0.7703 (t0) cc_final: 0.7334 (t0) REVERT: A 804 LYS cc_start: 0.8257 (mmtt) cc_final: 0.7958 (mmtt) REVERT: A 810 ILE cc_start: 0.8633 (mt) cc_final: 0.8360 (tp) REVERT: A 819 ARG cc_start: 0.6542 (mtm-85) cc_final: 0.6341 (ttm-80) REVERT: A 863 LYS cc_start: 0.8075 (mmmm) cc_final: 0.7702 (mmmm) REVERT: A 867 ILE cc_start: 0.7758 (mm) cc_final: 0.7469 (mm) REVERT: A 900 TYR cc_start: 0.7910 (p90) cc_final: 0.7221 (p90) REVERT: A 924 LYS cc_start: 0.7901 (mttp) cc_final: 0.7215 (mttm) REVERT: A 932 LYS cc_start: 0.8605 (mtmm) cc_final: 0.8251 (mtmm) REVERT: A 946 ASN cc_start: 0.8472 (m110) cc_final: 0.8011 (m110) outliers start: 29 outliers final: 20 residues processed: 334 average time/residue: 0.0979 time to fit residues: 42.9778 Evaluate side-chains 343 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 321 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 849 ASP Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 958 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 90 optimal weight: 0.0470 chunk 72 optimal weight: 3.9990 chunk 78 optimal weight: 0.2980 chunk 11 optimal weight: 0.0000 chunk 75 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 overall best weight: 0.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.149612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.123051 restraints weight = 12883.142| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.45 r_work: 0.3460 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8970 Z= 0.120 Angle : 0.574 10.972 12274 Z= 0.303 Chirality : 0.042 0.222 1332 Planarity : 0.004 0.037 1448 Dihedral : 18.624 135.110 1460 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.50 % Allowed : 22.07 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.27), residues: 975 helix: 1.92 (0.25), residues: 443 sheet: -0.06 (0.38), residues: 169 loop : -0.61 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 593 TYR 0.016 0.001 TYR A 138 PHE 0.035 0.002 PHE A 294 TRP 0.007 0.001 TRP A 325 HIS 0.004 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 8970) covalent geometry : angle 0.57439 / 0.30 (12274) hydrogen bonds : bond 0.04558 / 2.90 ( 452) hydrogen bonds : angle 4.05720 / 2.90 ( 1274) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 327 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.5585 (ttp) REVERT: A 9 GLU cc_start: 0.7566 (tt0) cc_final: 0.7091 (tt0) REVERT: A 27 GLN cc_start: 0.8593 (tp40) cc_final: 0.8325 (tp-100) REVERT: A 41 GLU cc_start: 0.8033 (pt0) cc_final: 0.7601 (pt0) REVERT: A 54 SER cc_start: 0.8378 (m) cc_final: 0.8086 (t) REVERT: A 56 GLU cc_start: 0.7613 (pt0) cc_final: 0.7109 (pt0) REVERT: A 75 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8004 (tm-30) REVERT: A 85 PHE cc_start: 0.8967 (t80) cc_final: 0.8573 (t80) REVERT: A 109 MET cc_start: 0.7711 (mmm) cc_final: 0.7404 (mmt) REVERT: A 126 PHE cc_start: 0.8296 (m-10) cc_final: 0.7991 (m-10) REVERT: A 127 LYS cc_start: 0.8551 (ttmm) cc_final: 0.8113 (ttmm) REVERT: A 134 LYS cc_start: 0.8126 (mmmm) cc_final: 0.7831 (mmmm) REVERT: A 142 MET cc_start: 0.8007 (mmm) cc_final: 0.7686 (tmm) REVERT: A 149 ASP cc_start: 0.7600 (p0) cc_final: 0.7071 (p0) REVERT: A 180 ARG cc_start: 0.7831 (mtm110) cc_final: 0.7269 (mtm110) REVERT: A 191 GLU cc_start: 0.7760 (mp0) cc_final: 0.7447 (mp0) REVERT: A 194 VAL cc_start: 0.8532 (p) cc_final: 0.8194 (m) REVERT: A 285 ARG cc_start: 0.8451 (ttm-80) cc_final: 0.7884 (mmm-85) REVERT: A 289 ASP cc_start: 0.7975 (m-30) cc_final: 0.7532 (m-30) REVERT: A 307 LYS cc_start: 0.8511 (mmtt) cc_final: 0.7881 (mmmt) REVERT: A 334 LYS cc_start: 0.8492 (tppp) cc_final: 0.8074 (tppp) REVERT: A 349 LYS cc_start: 0.8336 (tttt) cc_final: 0.8114 (tttm) REVERT: A 376 LYS cc_start: 0.8327 (mmtt) cc_final: 0.8056 (mmtm) REVERT: A 387 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7657 (mm-30) REVERT: A 395 VAL cc_start: 0.7517 (m) cc_final: 0.7151 (p) REVERT: A 397 LEU cc_start: 0.8610 (tp) cc_final: 0.8389 (tp) REVERT: A 399 TYR cc_start: 0.7971 (m-80) cc_final: 0.6994 (m-80) REVERT: A 404 LYS cc_start: 0.8233 (tttm) cc_final: 0.7968 (tttm) REVERT: A 417 VAL cc_start: 0.8483 (t) cc_final: 0.8268 (t) REVERT: A 424 ASP cc_start: 0.8146 (t0) cc_final: 0.7605 (t0) REVERT: A 433 VAL cc_start: 0.8371 (t) cc_final: 0.8152 (p) REVERT: A 434 ARG cc_start: 0.8242 (mmm160) cc_final: 0.7926 (tpt90) REVERT: A 474 HIS cc_start: 0.7839 (m90) cc_final: 0.7637 (m170) REVERT: A 476 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7206 (tm-30) REVERT: A 511 LYS cc_start: 0.8595 (ptpp) cc_final: 0.7890 (ptpp) REVERT: A 513 THR cc_start: 0.7781 (t) cc_final: 0.7482 (p) REVERT: A 579 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7570 (ttm) REVERT: A 597 LYS cc_start: 0.8092 (mmtm) cc_final: 0.7754 (tppp) REVERT: A 630 LYS cc_start: 0.8351 (mttt) cc_final: 0.8078 (mttp) REVERT: A 632 LYS cc_start: 0.8235 (tptt) cc_final: 0.7745 (ttmm) REVERT: A 635 LYS cc_start: 0.8408 (ttpp) cc_final: 0.7801 (ttmm) REVERT: A 636 ILE cc_start: 0.8417 (tt) cc_final: 0.8059 (tp) REVERT: A 644 GLU cc_start: 0.7470 (tp30) cc_final: 0.6886 (tp30) REVERT: A 647 ASN cc_start: 0.8268 (t0) cc_final: 0.7951 (t0) REVERT: A 676 VAL cc_start: 0.8523 (t) cc_final: 0.8155 (m) REVERT: A 687 ASP cc_start: 0.7437 (t0) cc_final: 0.7172 (t0) REVERT: A 690 SER cc_start: 0.8246 (t) cc_final: 0.7838 (m) REVERT: A 721 CYS cc_start: 0.7813 (m) cc_final: 0.7314 (m) REVERT: A 778 ASN cc_start: 0.8837 (m-40) cc_final: 0.8452 (m-40) REVERT: A 793 ASP cc_start: 0.7687 (t0) cc_final: 0.7322 (t0) REVERT: A 794 ILE cc_start: 0.7373 (tp) cc_final: 0.7135 (tp) REVERT: A 804 LYS cc_start: 0.8221 (mmtt) cc_final: 0.7882 (mmtt) REVERT: A 810 ILE cc_start: 0.8610 (mt) cc_final: 0.8351 (tp) REVERT: A 819 ARG cc_start: 0.6478 (mtm-85) cc_final: 0.6099 (ttm110) REVERT: A 842 MET cc_start: 0.7532 (ttt) cc_final: 0.7218 (tpp) REVERT: A 863 LYS cc_start: 0.8060 (mmmm) cc_final: 0.7701 (mmmm) REVERT: A 893 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6819 (mm-30) REVERT: A 900 TYR cc_start: 0.7860 (p90) cc_final: 0.7176 (p90) REVERT: A 924 LYS cc_start: 0.7867 (mttp) cc_final: 0.7165 (mttm) REVERT: A 932 LYS cc_start: 0.8579 (mtmm) cc_final: 0.8244 (mtmm) REVERT: A 946 ASN cc_start: 0.8508 (m110) cc_final: 0.8030 (m110) outliers start: 22 outliers final: 14 residues processed: 333 average time/residue: 0.0998 time to fit residues: 43.4482 Evaluate side-chains 340 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 324 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 958 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 23 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 84 optimal weight: 0.2980 chunk 20 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 HIS A 945 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.149097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.122512 restraints weight = 12881.571| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.44 r_work: 0.3432 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8970 Z= 0.136 Angle : 0.579 11.039 12274 Z= 0.306 Chirality : 0.043 0.230 1332 Planarity : 0.004 0.057 1448 Dihedral : 18.565 135.123 1460 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.07 % Allowed : 21.50 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.27), residues: 975 helix: 1.96 (0.25), residues: 444 sheet: -0.11 (0.38), residues: 164 loop : -0.63 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 99 TYR 0.020 0.001 TYR A 59 PHE 0.025 0.002 PHE A 283 TRP 0.007 0.001 TRP A 241 HIS 0.005 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 8970) covalent geometry : angle 0.57861 / 0.31 (12274) hydrogen bonds : bond 0.04515 / 2.89 ( 452) hydrogen bonds : angle 4.07802 / 2.90 ( 1274) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 327 time to evaluate : 0.270 Fit side-chains REVERT: A 5 MET cc_start: 0.7006 (OUTLIER) cc_final: 0.5376 (ttp) REVERT: A 9 GLU cc_start: 0.7615 (tt0) cc_final: 0.7083 (tt0) REVERT: A 27 GLN cc_start: 0.8606 (tp40) cc_final: 0.8328 (tp-100) REVERT: A 41 GLU cc_start: 0.8018 (pt0) cc_final: 0.7619 (pt0) REVERT: A 54 SER cc_start: 0.8388 (m) cc_final: 0.8077 (t) REVERT: A 59 TYR cc_start: 0.8225 (m-80) cc_final: 0.7807 (m-80) REVERT: A 62 GLU cc_start: 0.7721 (tt0) cc_final: 0.6831 (tt0) REVERT: A 75 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8006 (tm-30) REVERT: A 85 PHE cc_start: 0.8973 (t80) cc_final: 0.8594 (t80) REVERT: A 127 LYS cc_start: 0.8586 (ttmm) cc_final: 0.8143 (ttmm) REVERT: A 134 LYS cc_start: 0.8144 (mmmm) cc_final: 0.7853 (mmmm) REVERT: A 142 MET cc_start: 0.8045 (mmm) cc_final: 0.7737 (tmm) REVERT: A 149 ASP cc_start: 0.7616 (p0) cc_final: 0.7087 (p0) REVERT: A 180 ARG cc_start: 0.7824 (mtm110) cc_final: 0.5889 (mtm110) REVERT: A 191 GLU cc_start: 0.7768 (mp0) cc_final: 0.7455 (mp0) REVERT: A 194 VAL cc_start: 0.8547 (p) cc_final: 0.8210 (m) REVERT: A 277 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8158 (mm) REVERT: A 285 ARG cc_start: 0.8491 (ttm-80) cc_final: 0.8037 (mmm-85) REVERT: A 289 ASP cc_start: 0.8102 (m-30) cc_final: 0.7741 (m-30) REVERT: A 307 LYS cc_start: 0.8509 (mmtt) cc_final: 0.7908 (mmmt) REVERT: A 334 LYS cc_start: 0.8487 (tppp) cc_final: 0.8078 (tppp) REVERT: A 349 LYS cc_start: 0.8362 (tttt) cc_final: 0.8155 (tttm) REVERT: A 369 MET cc_start: 0.7891 (mmp) cc_final: 0.7638 (mmt) REVERT: A 376 LYS cc_start: 0.8335 (mmtt) cc_final: 0.8060 (mmtm) REVERT: A 387 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7659 (mm-30) REVERT: A 395 VAL cc_start: 0.7569 (m) cc_final: 0.7213 (p) REVERT: A 397 LEU cc_start: 0.8619 (tp) cc_final: 0.8408 (tp) REVERT: A 399 TYR cc_start: 0.8005 (m-80) cc_final: 0.7071 (m-80) REVERT: A 404 LYS cc_start: 0.8285 (tttm) cc_final: 0.8029 (tttm) REVERT: A 417 VAL cc_start: 0.8509 (t) cc_final: 0.8298 (t) REVERT: A 424 ASP cc_start: 0.8138 (t0) cc_final: 0.7626 (t0) REVERT: A 433 VAL cc_start: 0.8464 (t) cc_final: 0.8252 (p) REVERT: A 434 ARG cc_start: 0.8282 (mmm160) cc_final: 0.7976 (tpt90) REVERT: A 476 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7196 (tm-30) REVERT: A 511 LYS cc_start: 0.8646 (ptpp) cc_final: 0.8314 (ptpp) REVERT: A 513 THR cc_start: 0.7863 (t) cc_final: 0.7591 (p) REVERT: A 527 MET cc_start: 0.8107 (mtt) cc_final: 0.7757 (mtp) REVERT: A 579 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7649 (ttm) REVERT: A 597 LYS cc_start: 0.8088 (mmtm) cc_final: 0.7710 (tppp) REVERT: A 630 LYS cc_start: 0.8373 (mttt) cc_final: 0.8068 (mttp) REVERT: A 632 LYS cc_start: 0.8253 (tptt) cc_final: 0.7764 (ttmm) REVERT: A 636 ILE cc_start: 0.8466 (tt) cc_final: 0.8089 (tp) REVERT: A 644 GLU cc_start: 0.7575 (tp30) cc_final: 0.7041 (tp30) REVERT: A 647 ASN cc_start: 0.8291 (t0) cc_final: 0.7965 (t0) REVERT: A 676 VAL cc_start: 0.8512 (t) cc_final: 0.8172 (m) REVERT: A 687 ASP cc_start: 0.7433 (t0) cc_final: 0.7177 (t0) REVERT: A 690 SER cc_start: 0.8254 (t) cc_final: 0.7815 (m) REVERT: A 721 CYS cc_start: 0.7891 (m) cc_final: 0.7433 (m) REVERT: A 747 ASN cc_start: 0.8267 (p0) cc_final: 0.7850 (p0) REVERT: A 778 ASN cc_start: 0.8806 (m-40) cc_final: 0.8379 (m-40) REVERT: A 793 ASP cc_start: 0.7727 (t0) cc_final: 0.7369 (t0) REVERT: A 794 ILE cc_start: 0.7376 (tp) cc_final: 0.7108 (tp) REVERT: A 804 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7888 (mmtt) REVERT: A 810 ILE cc_start: 0.8617 (mt) cc_final: 0.8330 (tp) REVERT: A 819 ARG cc_start: 0.6604 (mtm-85) cc_final: 0.6232 (ttm110) REVERT: A 828 ILE cc_start: 0.8358 (pt) cc_final: 0.8003 (mt) REVERT: A 842 MET cc_start: 0.7598 (ttt) cc_final: 0.7325 (tpp) REVERT: A 893 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6797 (mm-30) REVERT: A 924 LYS cc_start: 0.7895 (mttp) cc_final: 0.7392 (mttm) REVERT: A 946 ASN cc_start: 0.8525 (m110) cc_final: 0.8015 (m110) REVERT: A 954 ARG cc_start: 0.8323 (mmt180) cc_final: 0.7954 (mmm-85) outliers start: 27 outliers final: 16 residues processed: 335 average time/residue: 0.0885 time to fit residues: 39.2414 Evaluate side-chains 337 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 318 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 958 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 93 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 509 GLN A 945 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.148420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.121932 restraints weight = 12876.839| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.41 r_work: 0.3432 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8970 Z= 0.133 Angle : 0.595 11.028 12274 Z= 0.313 Chirality : 0.043 0.236 1332 Planarity : 0.005 0.092 1448 Dihedral : 18.501 135.246 1460 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.39 % Allowed : 23.89 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.27), residues: 975 helix: 1.99 (0.25), residues: 445 sheet: -0.17 (0.39), residues: 160 loop : -0.66 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 180 TYR 0.019 0.001 TYR A 138 PHE 0.024 0.002 PHE A 986 TRP 0.007 0.001 TRP A 241 HIS 0.005 0.001 HIS A 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 8970) covalent geometry : angle 0.59544 / 0.31 (12274) hydrogen bonds : bond 0.04354 / 2.79 ( 452) hydrogen bonds : angle 4.06950 / 2.91 ( 1274) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 319 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7007 (OUTLIER) cc_final: 0.5381 (ttp) REVERT: A 9 GLU cc_start: 0.7631 (tt0) cc_final: 0.7145 (tt0) REVERT: A 27 GLN cc_start: 0.8586 (tp40) cc_final: 0.8263 (tp-100) REVERT: A 41 GLU cc_start: 0.7984 (pt0) cc_final: 0.7584 (pt0) REVERT: A 54 SER cc_start: 0.8473 (m) cc_final: 0.8190 (t) REVERT: A 62 GLU cc_start: 0.7444 (tt0) cc_final: 0.7203 (tt0) REVERT: A 75 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8012 (tm-30) REVERT: A 85 PHE cc_start: 0.8968 (t80) cc_final: 0.8574 (t80) REVERT: A 126 PHE cc_start: 0.8266 (m-10) cc_final: 0.8044 (m-10) REVERT: A 127 LYS cc_start: 0.8572 (ttmm) cc_final: 0.8122 (ttmm) REVERT: A 134 LYS cc_start: 0.8149 (mmmm) cc_final: 0.7856 (mmmm) REVERT: A 142 MET cc_start: 0.8064 (mmm) cc_final: 0.7730 (tmm) REVERT: A 149 ASP cc_start: 0.7596 (p0) cc_final: 0.7049 (p0) REVERT: A 163 LYS cc_start: 0.8407 (tppt) cc_final: 0.8155 (mmtp) REVERT: A 191 GLU cc_start: 0.7776 (mp0) cc_final: 0.7458 (mp0) REVERT: A 194 VAL cc_start: 0.8508 (p) cc_final: 0.8196 (m) REVERT: A 255 MET cc_start: 0.8231 (mmt) cc_final: 0.7848 (mmt) REVERT: A 285 ARG cc_start: 0.8489 (ttm-80) cc_final: 0.7996 (mmm-85) REVERT: A 289 ASP cc_start: 0.8103 (m-30) cc_final: 0.7646 (m-30) REVERT: A 307 LYS cc_start: 0.8496 (mmtt) cc_final: 0.7869 (mmmt) REVERT: A 321 MET cc_start: 0.8218 (ttp) cc_final: 0.7928 (ttm) REVERT: A 334 LYS cc_start: 0.8499 (tppp) cc_final: 0.8086 (tppp) REVERT: A 339 LYS cc_start: 0.8423 (mtmm) cc_final: 0.8126 (mtpp) REVERT: A 349 LYS cc_start: 0.8355 (tttt) cc_final: 0.8142 (tttm) REVERT: A 369 MET cc_start: 0.7872 (mmp) cc_final: 0.7575 (mmp) REVERT: A 376 LYS cc_start: 0.8330 (mmtt) cc_final: 0.8057 (mmtm) REVERT: A 387 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7640 (mm-30) REVERT: A 395 VAL cc_start: 0.7608 (m) cc_final: 0.7257 (p) REVERT: A 397 LEU cc_start: 0.8631 (tp) cc_final: 0.8412 (tp) REVERT: A 399 TYR cc_start: 0.8037 (m-80) cc_final: 0.7019 (m-80) REVERT: A 404 LYS cc_start: 0.8260 (tttm) cc_final: 0.7983 (tttm) REVERT: A 417 VAL cc_start: 0.8487 (t) cc_final: 0.8283 (t) REVERT: A 424 ASP cc_start: 0.8142 (t0) cc_final: 0.7708 (t0) REVERT: A 433 VAL cc_start: 0.8448 (t) cc_final: 0.8240 (p) REVERT: A 434 ARG cc_start: 0.8289 (mmm160) cc_final: 0.7983 (tpt90) REVERT: A 476 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7345 (tm-30) REVERT: A 511 LYS cc_start: 0.8631 (ptpp) cc_final: 0.8403 (ptpp) REVERT: A 513 THR cc_start: 0.7893 (t) cc_final: 0.7637 (p) REVERT: A 579 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7599 (mtp) REVERT: A 593 ARG cc_start: 0.8235 (ttt90) cc_final: 0.8033 (ttt90) REVERT: A 597 LYS cc_start: 0.8084 (mmtm) cc_final: 0.7756 (tppp) REVERT: A 630 LYS cc_start: 0.8341 (mttt) cc_final: 0.8036 (mttp) REVERT: A 632 LYS cc_start: 0.8223 (tptt) cc_final: 0.7724 (ttmm) REVERT: A 636 ILE cc_start: 0.8433 (tt) cc_final: 0.8078 (tp) REVERT: A 644 GLU cc_start: 0.7594 (tp30) cc_final: 0.7057 (tp30) REVERT: A 647 ASN cc_start: 0.8332 (t0) cc_final: 0.8005 (t0) REVERT: A 676 VAL cc_start: 0.8478 (t) cc_final: 0.8118 (m) REVERT: A 687 ASP cc_start: 0.7482 (t0) cc_final: 0.7267 (t0) REVERT: A 690 SER cc_start: 0.8234 (t) cc_final: 0.7845 (m) REVERT: A 711 GLN cc_start: 0.8220 (tp40) cc_final: 0.7783 (tp40) REVERT: A 721 CYS cc_start: 0.7929 (m) cc_final: 0.7469 (m) REVERT: A 747 ASN cc_start: 0.8196 (p0) cc_final: 0.7839 (p0) REVERT: A 770 LYS cc_start: 0.7894 (mttp) cc_final: 0.7677 (mttp) REVERT: A 778 ASN cc_start: 0.8835 (m-40) cc_final: 0.8464 (m-40) REVERT: A 793 ASP cc_start: 0.7735 (t0) cc_final: 0.7368 (t0) REVERT: A 794 ILE cc_start: 0.7356 (tp) cc_final: 0.7120 (tp) REVERT: A 804 LYS cc_start: 0.8200 (mmtt) cc_final: 0.7869 (mmtt) REVERT: A 810 ILE cc_start: 0.8611 (mt) cc_final: 0.8320 (tp) REVERT: A 819 ARG cc_start: 0.6635 (mtm-85) cc_final: 0.6259 (ttm110) REVERT: A 828 ILE cc_start: 0.8372 (pt) cc_final: 0.8067 (mt) REVERT: A 842 MET cc_start: 0.7676 (ttt) cc_final: 0.7387 (tpp) REVERT: A 924 LYS cc_start: 0.7933 (mttp) cc_final: 0.7346 (mttm) REVERT: A 946 ASN cc_start: 0.8456 (m110) cc_final: 0.8149 (m110) REVERT: A 954 ARG cc_start: 0.8311 (mmt180) cc_final: 0.7972 (mmm-85) outliers start: 21 outliers final: 14 residues processed: 324 average time/residue: 0.0904 time to fit residues: 38.4928 Evaluate side-chains 330 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 314 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 958 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 0.0970 chunk 33 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 ASN ** A 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.146384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.119741 restraints weight = 12718.801| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.39 r_work: 0.3408 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8970 Z= 0.178 Angle : 0.621 10.995 12274 Z= 0.327 Chirality : 0.044 0.230 1332 Planarity : 0.005 0.051 1448 Dihedral : 18.402 135.459 1458 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.16 % Allowed : 24.00 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.27), residues: 975 helix: 1.97 (0.25), residues: 444 sheet: -0.15 (0.37), residues: 170 loop : -0.64 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 185 TYR 0.018 0.001 TYR A 138 PHE 0.024 0.002 PHE A 986 TRP 0.009 0.001 TRP A 169 HIS 0.005 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 ( 8970) covalent geometry : angle 0.62108 / 0.33 (12274) hydrogen bonds : bond 0.04522 / 2.89 ( 452) hydrogen bonds : angle 4.14337 / 2.96 ( 1274) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 331 time to evaluate : 0.306 Fit side-chains REVERT: A 5 MET cc_start: 0.6958 (OUTLIER) cc_final: 0.5249 (ttp) REVERT: A 9 GLU cc_start: 0.7611 (tt0) cc_final: 0.7126 (tt0) REVERT: A 18 ILE cc_start: 0.8775 (mm) cc_final: 0.8527 (mm) REVERT: A 22 VAL cc_start: 0.8594 (t) cc_final: 0.8371 (t) REVERT: A 27 GLN cc_start: 0.8600 (tp40) cc_final: 0.8200 (tp-100) REVERT: A 41 GLU cc_start: 0.7941 (pt0) cc_final: 0.7555 (pt0) REVERT: A 54 SER cc_start: 0.8517 (m) cc_final: 0.8187 (p) REVERT: A 75 GLN cc_start: 0.8435 (tm-30) cc_final: 0.8022 (tm-30) REVERT: A 85 PHE cc_start: 0.9004 (t80) cc_final: 0.8633 (t80) REVERT: A 109 MET cc_start: 0.7887 (mmm) cc_final: 0.7652 (mmt) REVERT: A 127 LYS cc_start: 0.8581 (ttmm) cc_final: 0.8127 (ttmm) REVERT: A 134 LYS cc_start: 0.8189 (mmmm) cc_final: 0.7864 (mmmm) REVERT: A 142 MET cc_start: 0.8072 (mmm) cc_final: 0.7736 (tmm) REVERT: A 149 ASP cc_start: 0.7582 (p0) cc_final: 0.7055 (p0) REVERT: A 163 LYS cc_start: 0.8412 (tppt) cc_final: 0.8169 (mmtp) REVERT: A 180 ARG cc_start: 0.7346 (mtm180) cc_final: 0.6866 (mtm-85) REVERT: A 191 GLU cc_start: 0.7788 (mp0) cc_final: 0.7464 (mp0) REVERT: A 194 VAL cc_start: 0.8520 (p) cc_final: 0.8220 (m) REVERT: A 255 MET cc_start: 0.8260 (mmt) cc_final: 0.7918 (mmt) REVERT: A 285 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.7983 (mmm-85) REVERT: A 289 ASP cc_start: 0.8164 (m-30) cc_final: 0.7701 (m-30) REVERT: A 307 LYS cc_start: 0.8521 (mmtt) cc_final: 0.7939 (mmmt) REVERT: A 321 MET cc_start: 0.8219 (ttp) cc_final: 0.7941 (ttm) REVERT: A 334 LYS cc_start: 0.8535 (tppp) cc_final: 0.8120 (tppp) REVERT: A 349 LYS cc_start: 0.8415 (tttt) cc_final: 0.8194 (tttm) REVERT: A 365 ASP cc_start: 0.6946 (t0) cc_final: 0.6714 (t0) REVERT: A 369 MET cc_start: 0.7949 (mmp) cc_final: 0.7657 (mmp) REVERT: A 376 LYS cc_start: 0.8328 (mmtt) cc_final: 0.8041 (mmtm) REVERT: A 387 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7681 (mm-30) REVERT: A 395 VAL cc_start: 0.7723 (m) cc_final: 0.7393 (p) REVERT: A 397 LEU cc_start: 0.8628 (tp) cc_final: 0.8407 (tp) REVERT: A 399 TYR cc_start: 0.7989 (m-80) cc_final: 0.7027 (m-80) REVERT: A 404 LYS cc_start: 0.8348 (tttm) cc_final: 0.8100 (tttm) REVERT: A 417 VAL cc_start: 0.8521 (t) cc_final: 0.8309 (t) REVERT: A 424 ASP cc_start: 0.8219 (t0) cc_final: 0.7806 (t0) REVERT: A 433 VAL cc_start: 0.8469 (t) cc_final: 0.8263 (p) REVERT: A 434 ARG cc_start: 0.8329 (mmm160) cc_final: 0.8029 (tpt90) REVERT: A 475 ASP cc_start: 0.7639 (t0) cc_final: 0.7411 (t0) REVERT: A 476 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7406 (tm-30) REVERT: A 513 THR cc_start: 0.7967 (t) cc_final: 0.7742 (p) REVERT: A 558 PHE cc_start: 0.7878 (p90) cc_final: 0.7663 (p90) REVERT: A 579 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7725 (ttm) REVERT: A 593 ARG cc_start: 0.8296 (ttt90) cc_final: 0.8094 (ttt90) REVERT: A 597 LYS cc_start: 0.8119 (mmtm) cc_final: 0.7787 (tppp) REVERT: A 630 LYS cc_start: 0.8357 (mttt) cc_final: 0.8043 (mttp) REVERT: A 632 LYS cc_start: 0.8283 (tptt) cc_final: 0.7782 (ttmm) REVERT: A 636 ILE cc_start: 0.8479 (tt) cc_final: 0.8108 (tp) REVERT: A 644 GLU cc_start: 0.7593 (tp30) cc_final: 0.7064 (tp30) REVERT: A 647 ASN cc_start: 0.8339 (t0) cc_final: 0.7996 (t0) REVERT: A 676 VAL cc_start: 0.8488 (t) cc_final: 0.8146 (m) REVERT: A 687 ASP cc_start: 0.7460 (t0) cc_final: 0.7228 (t0) REVERT: A 690 SER cc_start: 0.8234 (t) cc_final: 0.7870 (m) REVERT: A 711 GLN cc_start: 0.8226 (tp40) cc_final: 0.7815 (tp40) REVERT: A 721 CYS cc_start: 0.8096 (m) cc_final: 0.7583 (m) REVERT: A 747 ASN cc_start: 0.8195 (p0) cc_final: 0.7850 (p0) REVERT: A 770 LYS cc_start: 0.7993 (mttp) cc_final: 0.7686 (mttp) REVERT: A 778 ASN cc_start: 0.8806 (m-40) cc_final: 0.8408 (m-40) REVERT: A 793 ASP cc_start: 0.7790 (t0) cc_final: 0.7411 (t0) REVERT: A 794 ILE cc_start: 0.7426 (tp) cc_final: 0.7134 (tp) REVERT: A 804 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7851 (mmtt) REVERT: A 810 ILE cc_start: 0.8595 (mt) cc_final: 0.8248 (tp) REVERT: A 818 ARG cc_start: 0.7974 (mtt90) cc_final: 0.7715 (mtt90) REVERT: A 819 ARG cc_start: 0.6955 (mtm-85) cc_final: 0.6675 (ttm-80) REVERT: A 828 ILE cc_start: 0.8468 (pt) cc_final: 0.8162 (mt) REVERT: A 842 MET cc_start: 0.7723 (ttt) cc_final: 0.7494 (tpp) REVERT: A 851 ILE cc_start: 0.8675 (mt) cc_final: 0.8444 (mp) REVERT: A 924 LYS cc_start: 0.7990 (mttp) cc_final: 0.7396 (mttm) REVERT: A 925 MET cc_start: 0.7526 (mmm) cc_final: 0.7224 (mmm) REVERT: A 945 ASN cc_start: 0.8329 (m-40) cc_final: 0.8129 (t0) REVERT: A 946 ASN cc_start: 0.8490 (m110) cc_final: 0.8023 (m110) REVERT: A 952 CYS cc_start: 0.8276 (t) cc_final: 0.7823 (t) outliers start: 19 outliers final: 15 residues processed: 333 average time/residue: 0.1049 time to fit residues: 45.6824 Evaluate side-chains 346 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 329 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 958 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 58 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 462 HIS ** 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 = 0.3931 r_free = 0.3931 target = 0.147652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.120793 restraints weight = 12811.260| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.43 r_work: 0.3423 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8970 Z= 0.140 Angle : 0.622 10.077 12274 Z= 0.325 Chirality : 0.043 0.249 1332 Planarity : 0.005 0.070 1448 Dihedral : 18.356 135.586 1458 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.93 % Allowed : 25.26 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.27), residues: 975 helix: 1.98 (0.25), residues: 442 sheet: -0.12 (0.38), residues: 166 loop : -0.63 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 180 TYR 0.019 0.001 TYR A 138 PHE 0.025 0.002 PHE A 986 TRP 0.008 0.001 TRP A 241 HIS 0.005 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 8970) covalent geometry : angle 0.62158 / 0.33 (12274) hydrogen bonds : bond 0.04306 / 2.74 ( 452) hydrogen bonds : angle 4.10023 / 2.95 ( 1274) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 328 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 5 MET cc_start: 0.6955 (OUTLIER) cc_final: 0.5264 (ttp) REVERT: A 9 GLU cc_start: 0.7607 (tt0) cc_final: 0.7117 (tt0) REVERT: A 18 ILE cc_start: 0.8784 (mm) cc_final: 0.8530 (mm) REVERT: A 22 VAL cc_start: 0.8598 (t) cc_final: 0.8377 (t) REVERT: A 23 THR cc_start: 0.8719 (t) cc_final: 0.8420 (p) REVERT: A 27 GLN cc_start: 0.8591 (tp40) cc_final: 0.8182 (tp-100) REVERT: A 41 GLU cc_start: 0.7940 (pt0) cc_final: 0.7552 (pt0) REVERT: A 54 SER cc_start: 0.8503 (m) cc_final: 0.8165 (p) REVERT: A 75 GLN cc_start: 0.8424 (tm-30) cc_final: 0.8027 (tm-30) REVERT: A 85 PHE cc_start: 0.8985 (t80) cc_final: 0.8622 (t80) REVERT: A 127 LYS cc_start: 0.8578 (ttmm) cc_final: 0.8132 (ttmm) REVERT: A 134 LYS cc_start: 0.8152 (mmmm) cc_final: 0.7845 (mmmm) REVERT: A 142 MET cc_start: 0.8062 (mmm) cc_final: 0.7706 (tmm) REVERT: A 149 ASP cc_start: 0.7593 (p0) cc_final: 0.7011 (p0) REVERT: A 163 LYS cc_start: 0.8399 (tppt) cc_final: 0.8159 (mmtp) REVERT: A 191 GLU cc_start: 0.7791 (mp0) cc_final: 0.7473 (mp0) REVERT: A 194 VAL cc_start: 0.8520 (p) cc_final: 0.8229 (m) REVERT: A 211 ASP cc_start: 0.7780 (t70) cc_final: 0.7512 (t0) REVERT: A 285 ARG cc_start: 0.8466 (ttm-80) cc_final: 0.8004 (mmm-85) REVERT: A 289 ASP cc_start: 0.8115 (m-30) cc_final: 0.7663 (m-30) REVERT: A 307 LYS cc_start: 0.8505 (mmtt) cc_final: 0.7931 (mmmt) REVERT: A 321 MET cc_start: 0.8108 (ttp) cc_final: 0.7847 (ttm) REVERT: A 334 LYS cc_start: 0.8530 (tppp) cc_final: 0.8114 (tppp) REVERT: A 349 LYS cc_start: 0.8357 (tttt) cc_final: 0.8151 (tttm) REVERT: A 365 ASP cc_start: 0.6939 (t0) cc_final: 0.6721 (t0) REVERT: A 369 MET cc_start: 0.7864 (mmp) cc_final: 0.7603 (mmt) REVERT: A 376 LYS cc_start: 0.8319 (mmtt) cc_final: 0.8043 (mmtm) REVERT: A 387 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7683 (mm-30) REVERT: A 395 VAL cc_start: 0.7721 (m) cc_final: 0.7389 (p) REVERT: A 397 LEU cc_start: 0.8625 (tp) cc_final: 0.8406 (tp) REVERT: A 399 TYR cc_start: 0.7907 (m-80) cc_final: 0.6968 (m-80) REVERT: A 404 LYS cc_start: 0.8342 (tttm) cc_final: 0.8098 (tttm) REVERT: A 417 VAL cc_start: 0.8501 (t) cc_final: 0.8293 (t) REVERT: A 424 ASP cc_start: 0.8219 (t0) cc_final: 0.7733 (t0) REVERT: A 433 VAL cc_start: 0.8494 (t) cc_final: 0.8284 (p) REVERT: A 434 ARG cc_start: 0.8315 (mmm160) cc_final: 0.8016 (tpt90) REVERT: A 476 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7411 (tm-30) REVERT: A 579 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7706 (ttm) REVERT: A 597 LYS cc_start: 0.8124 (mmtm) cc_final: 0.7794 (tppp) REVERT: A 630 LYS cc_start: 0.8377 (mttt) cc_final: 0.8059 (mttp) REVERT: A 632 LYS cc_start: 0.8303 (tptt) cc_final: 0.7786 (ttmm) REVERT: A 636 ILE cc_start: 0.8488 (tt) cc_final: 0.8107 (tp) REVERT: A 644 GLU cc_start: 0.7609 (tp30) cc_final: 0.7091 (tp30) REVERT: A 647 ASN cc_start: 0.8353 (t0) cc_final: 0.8006 (t0) REVERT: A 676 VAL cc_start: 0.8492 (t) cc_final: 0.8150 (m) REVERT: A 690 SER cc_start: 0.8281 (t) cc_final: 0.7916 (m) REVERT: A 711 GLN cc_start: 0.8213 (tp40) cc_final: 0.7801 (tp40) REVERT: A 721 CYS cc_start: 0.8082 (m) cc_final: 0.7561 (m) REVERT: A 747 ASN cc_start: 0.8176 (p0) cc_final: 0.7790 (p0) REVERT: A 770 LYS cc_start: 0.7988 (mttp) cc_final: 0.7673 (mttp) REVERT: A 778 ASN cc_start: 0.8807 (m-40) cc_final: 0.8392 (m-40) REVERT: A 782 PHE cc_start: 0.8683 (m-80) cc_final: 0.8456 (m-80) REVERT: A 793 ASP cc_start: 0.7769 (t0) cc_final: 0.7381 (t0) REVERT: A 794 ILE cc_start: 0.7413 (tp) cc_final: 0.7147 (tp) REVERT: A 804 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7833 (mmtt) REVERT: A 810 ILE cc_start: 0.8587 (mt) cc_final: 0.8249 (tp) REVERT: A 818 ARG cc_start: 0.8036 (mtt90) cc_final: 0.7757 (mtt90) REVERT: A 819 ARG cc_start: 0.6965 (mtm-85) cc_final: 0.6680 (ttm-80) REVERT: A 828 ILE cc_start: 0.8457 (pt) cc_final: 0.8166 (mt) REVERT: A 842 MET cc_start: 0.7740 (ttt) cc_final: 0.7500 (tpp) REVERT: A 851 ILE cc_start: 0.8698 (mt) cc_final: 0.8470 (mp) REVERT: A 869 MET cc_start: 0.7776 (mmm) cc_final: 0.7527 (mmm) REVERT: A 923 ASP cc_start: 0.7812 (m-30) cc_final: 0.7311 (m-30) REVERT: A 924 LYS cc_start: 0.7967 (mttp) cc_final: 0.7111 (mtpp) REVERT: A 946 ASN cc_start: 0.8541 (m110) cc_final: 0.8178 (m-40) REVERT: A 952 CYS cc_start: 0.8286 (t) cc_final: 0.7828 (t) outliers start: 17 outliers final: 14 residues processed: 330 average time/residue: 0.1159 time to fit residues: 50.6005 Evaluate side-chains 344 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 328 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 958 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 40 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 462 HIS ** 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 = 0.3918 r_free = 0.3918 target = 0.146551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.119771 restraints weight = 12693.709| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.40 r_work: 0.3406 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8970 Z= 0.172 Angle : 0.640 9.932 12274 Z= 0.338 Chirality : 0.044 0.197 1332 Planarity : 0.005 0.070 1448 Dihedral : 18.328 135.894 1458 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.93 % Allowed : 25.60 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.28), residues: 975 helix: 1.97 (0.25), residues: 442 sheet: -0.11 (0.38), residues: 165 loop : -0.62 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 185 TYR 0.021 0.001 TYR A 138 PHE 0.040 0.002 PHE A 558 TRP 0.009 0.001 TRP A 241 HIS 0.005 0.001 HIS A 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 8970) covalent geometry : angle 0.64043 / 0.34 (12274) hydrogen bonds : bond 0.04462 / 2.86 ( 452) hydrogen bonds : angle 4.18164 / 3.01 ( 1274) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2019.60 seconds wall clock time: 35 minutes 23.51 seconds (2123.51 seconds total)