Starting phenix.real_space_refine on Thu Feb 13 02:00:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ywm_39638/02_2025/8ywm_39638.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ywm_39638/02_2025/8ywm_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_39638/02_2025/8ywm_39638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ywm_39638/02_2025/8ywm_39638.map" model { file = "/net/cci-nas-00/data/ceres_data/8ywm_39638/02_2025/8ywm_39638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ywm_39638/02_2025/8ywm_39638.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.08, per 1000 atoms: 0.58 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: 2.20 Conformation dependent library (CDL) restraints added in 912.6 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: 2.92 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: 3.51 Time building geometry restraints manager: 2.55 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=" 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=" N ILE A 938 " pdb=" CA ILE A 938 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.05e+00 bond pdb=" N PRO A 820 " pdb=" CA PRO A 820 " ideal model delta sigma weight residual 1.469 1.443 0.026 1.28e-02 6.10e+03 4.09e+00 ... (remaining 8965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 11973 1.99 - 3.99: 254 3.99 - 5.98: 32 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=" CA PRO A 820 " pdb=" N PRO A 820 " pdb=" CD PRO A 820 " ideal model delta sigma weight residual 112.00 106.65 5.35 1.40e+00 5.10e-01 1.46e+01 angle pdb=" C PRO A 820 " pdb=" CA PRO A 820 " pdb=" CB PRO A 820 " ideal model delta sigma weight residual 111.56 105.46 6.10 1.65e+00 3.67e-01 1.36e+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: 924 0.039 - 0.079: 291 0.079 - 0.118: 85 0.118 - 0.157: 27 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.990 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 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= 0.256 Angle : 0.709 9.974 12274 Z= 0.392 Chirality : 0.045 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (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 TRP 0.025 0.002 TRP A 325 HIS 0.003 0.001 HIS A 326 PHE 0.037 0.002 PHE A 303 TYR 0.031 0.002 TYR A 177 ARG 0.019 0.001 ARG A 99 *********************** 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 : 0.931 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: 0.7787 (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: 0.8130 (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: 0.7039 (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: 0.2474 time to fit residues: 112.4741 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 : 0.901 ------------------------------------------------------------------------------- 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 83 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 50 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 0.0980 chunk 89 optimal weight: 3.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN A 509 GLN 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 = 0.4007 r_free = 0.4007 target = 0.154015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.127791 restraints weight = 12777.841| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.54 r_work: 0.3521 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8970 Z= 0.200 Angle : 0.590 10.517 12274 Z= 0.313 Chirality : 0.043 0.211 1332 Planarity : 0.005 0.047 1448 Dihedral : 18.425 137.069 1464 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.97 % Favored : 96.92 % Rotamer: Outliers : 1.48 % Allowed : 15.70 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.27), residues: 975 helix: 1.57 (0.24), residues: 443 sheet: 0.28 (0.39), residues: 164 loop : -0.63 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 325 HIS 0.003 0.001 HIS A 722 PHE 0.019 0.002 PHE A 283 TYR 0.025 0.001 TYR A 772 ARG 0.008 0.001 ARG A 13 *********************** 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 336 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 323 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8547 (tp40) cc_final: 0.8237 (tp-100) REVERT: A 41 GLU cc_start: 0.8041 (pt0) cc_final: 0.7599 (pt0) REVERT: A 54 SER cc_start: 0.8282 (m) cc_final: 0.7963 (p) REVERT: A 59 TYR cc_start: 0.8123 (m-10) cc_final: 0.7592 (m-80) REVERT: A 75 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8171 (tm-30) REVERT: A 127 LYS cc_start: 0.8557 (ttmm) cc_final: 0.8244 (ttmm) REVERT: A 132 ARG cc_start: 0.7654 (ttt-90) cc_final: 0.7409 (ttt180) REVERT: A 134 LYS cc_start: 0.8063 (mmmm) cc_final: 0.7790 (mmmm) REVERT: A 149 ASP cc_start: 0.7496 (p0) cc_final: 0.6965 (p0) REVERT: A 163 LYS cc_start: 0.8489 (mmtm) cc_final: 0.8263 (mmtm) REVERT: A 180 ARG cc_start: 0.7749 (mtm110) cc_final: 0.7460 (mtm110) REVERT: A 191 GLU cc_start: 0.7663 (mp0) cc_final: 0.7341 (mp0) REVERT: A 207 VAL cc_start: 0.8333 (t) cc_final: 0.8070 (m) REVERT: A 237 MET cc_start: 0.7897 (ptt) cc_final: 0.7490 (ptp) REVERT: A 278 SER cc_start: 0.8472 (t) cc_final: 0.8252 (t) REVERT: A 321 MET cc_start: 0.8326 (ttp) cc_final: 0.8077 (ttm) REVERT: A 334 LYS cc_start: 0.8478 (tppp) cc_final: 0.8112 (tppp) REVERT: A 349 LYS cc_start: 0.8172 (tttt) cc_final: 0.7911 (mttm) REVERT: A 376 LYS cc_start: 0.8278 (mmtt) cc_final: 0.8000 (mmtm) REVERT: A 397 LEU cc_start: 0.8440 (tp) cc_final: 0.8238 (tp) REVERT: A 399 TYR cc_start: 0.7833 (m-80) cc_final: 0.6837 (m-80) REVERT: A 476 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7226 (tm-30) REVERT: A 484 THR cc_start: 0.7832 (m) cc_final: 0.7504 (p) REVERT: A 507 LEU cc_start: 0.7915 (mt) cc_final: 0.7715 (mt) REVERT: A 513 THR cc_start: 0.7302 (t) cc_final: 0.6985 (p) REVERT: A 527 MET cc_start: 0.8145 (mtt) cc_final: 0.7897 (mtp) REVERT: A 530 ASN cc_start: 0.7981 (t0) cc_final: 0.7771 (t0) REVERT: A 549 LYS cc_start: 0.8515 (ptmt) cc_final: 0.8117 (ptmt) REVERT: A 579 MET cc_start: 0.7648 (ttm) cc_final: 0.7301 (ttm) REVERT: A 593 ARG cc_start: 0.8257 (ttt90) cc_final: 0.8043 (ttt90) REVERT: A 630 LYS cc_start: 0.8263 (mttt) cc_final: 0.8033 (mtpp) REVERT: A 632 LYS cc_start: 0.8200 (tptt) cc_final: 0.7838 (ttmm) REVERT: A 636 ILE cc_start: 0.8377 (tt) cc_final: 0.7976 (tp) REVERT: A 687 ASP cc_start: 0.7065 (t0) cc_final: 0.6810 (t0) REVERT: A 719 GLN cc_start: 0.8259 (tp40) cc_final: 0.8024 (tp40) REVERT: A 738 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8128 (mt-10) REVERT: A 794 ILE cc_start: 0.7497 (tp) cc_final: 0.7286 (tp) REVERT: A 810 ILE cc_start: 0.8638 (mt) cc_final: 0.8281 (tp) REVERT: A 824 ARG cc_start: 0.7020 (mtt-85) cc_final: 0.6744 (mtt-85) REVERT: A 829 GLU cc_start: 0.7293 (tp30) cc_final: 0.7052 (tp30) REVERT: A 839 VAL cc_start: 0.8499 (t) cc_final: 0.8280 (m) REVERT: A 842 MET cc_start: 0.7320 (ttt) cc_final: 0.6891 (tpp) REVERT: A 846 ASN cc_start: 0.7394 (p0) cc_final: 0.6766 (p0) REVERT: A 848 GLU cc_start: 0.7593 (mp0) cc_final: 0.7364 (mp0) REVERT: A 863 LYS cc_start: 0.7704 (mmmm) cc_final: 0.7451 (mmmm) REVERT: A 876 ARG cc_start: 0.7752 (ttm110) cc_final: 0.7489 (ttm110) REVERT: A 897 ARG cc_start: 0.7912 (mtp85) cc_final: 0.7596 (ttm-80) REVERT: A 900 TYR cc_start: 0.7896 (p90) cc_final: 0.7135 (p90) REVERT: A 924 LYS cc_start: 0.7951 (mttp) cc_final: 0.7310 (mttm) REVERT: A 947 TYR cc_start: 0.8184 (m-80) cc_final: 0.7956 (m-10) outliers start: 13 outliers final: 5 residues processed: 326 average time/residue: 0.2672 time to fit residues: 112.2603 Evaluate side-chains 306 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 301 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 844 GLN 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 47 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 78 optimal weight: 0.0370 chunk 36 optimal weight: 0.8980 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** 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 = 0.3965 r_free = 0.3965 target = 0.150475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.124369 restraints weight = 12972.148| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.50 r_work: 0.3457 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3437 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= 0.209 Angle : 0.573 8.763 12274 Z= 0.303 Chirality : 0.042 0.223 1332 Planarity : 0.004 0.038 1448 Dihedral : 18.200 136.669 1460 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.08 % Favored : 96.82 % Rotamer: Outliers : 2.84 % Allowed : 17.86 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.27), residues: 975 helix: 1.78 (0.24), residues: 444 sheet: 0.23 (0.38), residues: 164 loop : -0.48 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 325 HIS 0.004 0.001 HIS A 722 PHE 0.018 0.002 PHE A 283 TYR 0.023 0.001 TYR A 772 ARG 0.006 0.001 ARG A 824 *********************** 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 349 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 324 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8615 (tp40) cc_final: 0.8340 (tp-100) REVERT: A 41 GLU cc_start: 0.8097 (pt0) cc_final: 0.7712 (pt0) REVERT: A 54 SER cc_start: 0.8397 (m) cc_final: 0.8027 (t) REVERT: A 56 GLU cc_start: 0.7653 (pt0) cc_final: 0.7154 (pt0) REVERT: A 59 TYR cc_start: 0.8271 (m-10) cc_final: 0.7963 (m-80) REVERT: A 75 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8183 (tm-30) REVERT: A 85 PHE cc_start: 0.8884 (t80) cc_final: 0.8435 (t80) REVERT: A 126 PHE cc_start: 0.8215 (m-10) cc_final: 0.7864 (m-10) REVERT: A 127 LYS cc_start: 0.8572 (ttmm) cc_final: 0.8148 (ttmm) REVERT: A 134 LYS cc_start: 0.8112 (mmmm) cc_final: 0.7840 (mmmm) REVERT: A 138 TYR cc_start: 0.8488 (t80) cc_final: 0.8263 (t80) REVERT: A 142 MET cc_start: 0.7901 (mmm) cc_final: 0.7638 (tmm) REVERT: A 149 ASP cc_start: 0.7555 (p0) cc_final: 0.6935 (p0) REVERT: A 180 ARG cc_start: 0.7810 (mtm110) cc_final: 0.7392 (mtm110) REVERT: A 191 GLU cc_start: 0.7758 (mp0) cc_final: 0.7377 (mp0) REVERT: A 285 ARG cc_start: 0.8521 (tpp80) cc_final: 0.7751 (mmm-85) REVERT: A 307 LYS cc_start: 0.8430 (mmtt) cc_final: 0.7688 (mmmt) REVERT: A 320 LYS cc_start: 0.8702 (ttmm) cc_final: 0.8479 (ttmm) REVERT: A 321 MET cc_start: 0.8351 (ttp) cc_final: 0.8100 (ttm) REVERT: A 334 LYS cc_start: 0.8493 (tppp) cc_final: 0.8074 (tppp) REVERT: A 340 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7626 (mt-10) REVERT: A 349 LYS cc_start: 0.8308 (tttt) cc_final: 0.8063 (tttm) REVERT: A 376 LYS cc_start: 0.8281 (mmtt) cc_final: 0.8029 (mmtm) REVERT: A 397 LEU cc_start: 0.8563 (tp) cc_final: 0.8359 (tp) REVERT: A 399 TYR cc_start: 0.7895 (m-80) cc_final: 0.6787 (m-80) REVERT: A 404 LYS cc_start: 0.8169 (tttm) cc_final: 0.7880 (tttm) REVERT: A 424 ASP cc_start: 0.8199 (t0) cc_final: 0.7748 (t0) REVERT: A 433 VAL cc_start: 0.8368 (t) cc_final: 0.8155 (p) REVERT: A 434 ARG cc_start: 0.8277 (mmm160) cc_final: 0.8068 (mmm160) REVERT: A 455 CYS cc_start: 0.7867 (m) cc_final: 0.7640 (m) REVERT: A 469 ILE cc_start: 0.8672 (mt) cc_final: 0.8305 (tt) REVERT: A 476 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7212 (tm-30) REVERT: A 482 CYS cc_start: 0.6900 (p) cc_final: 0.6521 (p) REVERT: A 484 THR cc_start: 0.7829 (m) cc_final: 0.7491 (p) REVERT: A 511 LYS cc_start: 0.8241 (ptpp) cc_final: 0.7581 (ptpt) REVERT: A 513 THR cc_start: 0.7775 (t) cc_final: 0.7534 (p) REVERT: A 527 MET cc_start: 0.8212 (mtt) cc_final: 0.8001 (mtm) REVERT: A 530 ASN cc_start: 0.8246 (t0) cc_final: 0.7979 (t0) REVERT: A 555 TYR cc_start: 0.8336 (t80) cc_final: 0.8116 (t80) REVERT: A 579 MET cc_start: 0.7940 (ttm) cc_final: 0.7622 (ttm) REVERT: A 597 LYS cc_start: 0.8047 (mmtm) cc_final: 0.7829 (tppp) REVERT: A 630 LYS cc_start: 0.8372 (mttt) cc_final: 0.8095 (mttp) REVERT: A 632 LYS cc_start: 0.8252 (tptt) cc_final: 0.7773 (ttmm) REVERT: A 636 ILE cc_start: 0.8416 (tt) cc_final: 0.8195 (tt) REVERT: A 644 GLU cc_start: 0.7416 (tp30) cc_final: 0.6803 (tp30) REVERT: A 647 ASN cc_start: 0.8255 (t0) cc_final: 0.7925 (t0) REVERT: A 678 ASN cc_start: 0.8544 (m-40) cc_final: 0.8335 (m-40) REVERT: A 687 ASP cc_start: 0.7277 (t0) cc_final: 0.7005 (t0) REVERT: A 702 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8191 (tt0) REVERT: A 719 GLN cc_start: 0.8371 (tp40) cc_final: 0.7858 (tp-100) REVERT: A 721 CYS cc_start: 0.7888 (m) cc_final: 0.7373 (m) REVERT: A 778 ASN cc_start: 0.8677 (m-40) cc_final: 0.8241 (m-40) REVERT: A 794 ILE cc_start: 0.7437 (tp) cc_final: 0.7183 (tp) REVERT: A 810 ILE cc_start: 0.8663 (mt) cc_final: 0.8391 (tp) REVERT: A 813 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7803 (mm-30) REVERT: A 829 GLU cc_start: 0.7926 (tp30) cc_final: 0.7434 (tp30) REVERT: A 859 ASP cc_start: 0.7420 (p0) cc_final: 0.7141 (p0) REVERT: A 863 LYS cc_start: 0.7942 (mmmm) cc_final: 0.7388 (mmmm) REVERT: A 867 ILE cc_start: 0.7694 (mm) cc_final: 0.7458 (mm) REVERT: A 897 ARG cc_start: 0.8053 (mtp85) cc_final: 0.7719 (ttm-80) REVERT: A 900 TYR cc_start: 0.8014 (p90) cc_final: 0.7426 (p90) REVERT: A 924 LYS cc_start: 0.8031 (mttp) cc_final: 0.7344 (mttm) REVERT: A 947 TYR cc_start: 0.8279 (m-80) cc_final: 0.7988 (m-10) outliers start: 25 outliers final: 13 residues processed: 330 average time/residue: 0.2668 time to fit residues: 113.6264 Evaluate side-chains 326 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 312 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 811 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 77 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS A 319 ASN A 474 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.148420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.121786 restraints weight = 12799.327| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.47 r_work: 0.3428 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8970 Z= 0.209 Angle : 0.565 9.468 12274 Z= 0.299 Chirality : 0.042 0.245 1332 Planarity : 0.004 0.071 1448 Dihedral : 18.187 136.296 1460 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.77 % Favored : 97.13 % Rotamer: Outliers : 2.62 % Allowed : 21.27 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.27), residues: 975 helix: 1.98 (0.24), residues: 443 sheet: 0.08 (0.37), residues: 169 loop : -0.35 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 325 HIS 0.004 0.001 HIS A 722 PHE 0.030 0.002 PHE A 72 TYR 0.019 0.001 TYR A 772 ARG 0.012 0.001 ARG A 99 *********************** 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 354 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 331 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: A 27 GLN cc_start: 0.8578 (tp40) cc_final: 0.8258 (tp-100) REVERT: A 41 GLU cc_start: 0.8005 (pt0) cc_final: 0.7649 (pt0) REVERT: A 54 SER cc_start: 0.8405 (m) cc_final: 0.8116 (t) REVERT: A 56 GLU cc_start: 0.7728 (pt0) cc_final: 0.7200 (pt0) REVERT: A 62 GLU cc_start: 0.7633 (tt0) cc_final: 0.7367 (tt0) REVERT: A 75 GLN cc_start: 0.8415 (tm-30) cc_final: 0.7752 (tm-30) REVERT: A 85 PHE cc_start: 0.8908 (t80) cc_final: 0.8489 (t80) REVERT: A 127 LYS cc_start: 0.8621 (ttmm) cc_final: 0.8186 (ttmm) REVERT: A 134 LYS cc_start: 0.8126 (mmmm) cc_final: 0.7848 (mmmm) REVERT: A 142 MET cc_start: 0.7981 (mmm) cc_final: 0.7720 (tmm) REVERT: A 149 ASP cc_start: 0.7597 (p0) cc_final: 0.7126 (p0) REVERT: A 163 LYS cc_start: 0.8519 (tptt) cc_final: 0.8119 (mptt) REVERT: A 180 ARG cc_start: 0.7836 (mtm110) cc_final: 0.7508 (mtm110) REVERT: A 191 GLU cc_start: 0.7764 (mp0) cc_final: 0.7426 (mp0) REVERT: A 255 MET cc_start: 0.8271 (mmt) cc_final: 0.7781 (mmt) REVERT: A 272 GLU cc_start: 0.7360 (tt0) cc_final: 0.6997 (tt0) REVERT: A 285 ARG cc_start: 0.8547 (tpp80) cc_final: 0.7783 (mmm-85) REVERT: A 289 ASP cc_start: 0.7813 (m-30) cc_final: 0.7416 (m-30) REVERT: A 307 LYS cc_start: 0.8554 (mmtt) cc_final: 0.7931 (mmmt) REVERT: A 320 LYS cc_start: 0.8724 (ttmm) cc_final: 0.8515 (ttmm) REVERT: A 321 MET cc_start: 0.8279 (ttp) cc_final: 0.8033 (ttm) REVERT: A 340 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7610 (mt-10) REVERT: A 349 LYS cc_start: 0.8340 (tttt) cc_final: 0.8117 (tttm) REVERT: A 369 MET cc_start: 0.8015 (mmp) cc_final: 0.7793 (mmt) REVERT: A 375 PRO cc_start: 0.8457 (Cg_endo) cc_final: 0.8170 (Cg_exo) REVERT: A 376 LYS cc_start: 0.8279 (mmtt) cc_final: 0.7972 (mmtm) REVERT: A 395 VAL cc_start: 0.7616 (m) cc_final: 0.7272 (p) REVERT: A 397 LEU cc_start: 0.8568 (tp) cc_final: 0.8349 (tp) REVERT: A 399 TYR cc_start: 0.7923 (m-80) cc_final: 0.7043 (m-80) REVERT: A 404 LYS cc_start: 0.8295 (tttm) cc_final: 0.8017 (tttm) REVERT: A 417 VAL cc_start: 0.8511 (t) cc_final: 0.8302 (t) REVERT: A 424 ASP cc_start: 0.8233 (t0) cc_final: 0.8030 (t0) REVERT: A 433 VAL cc_start: 0.8472 (t) cc_final: 0.8262 (p) REVERT: A 434 ARG cc_start: 0.8299 (mmm160) cc_final: 0.7943 (tpt90) REVERT: A 455 CYS cc_start: 0.7887 (m) cc_final: 0.7649 (m) REVERT: A 457 TYR cc_start: 0.8523 (m-80) cc_final: 0.8283 (m-10) REVERT: A 467 MET cc_start: 0.8042 (ttp) cc_final: 0.7747 (ttm) REVERT: A 476 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7133 (tm-30) REVERT: A 511 LYS cc_start: 0.8653 (ptpp) cc_final: 0.8269 (ptpp) REVERT: A 527 MET cc_start: 0.8171 (mtt) cc_final: 0.7944 (mtm) REVERT: A 579 MET cc_start: 0.7975 (ttm) cc_final: 0.7655 (ttm) REVERT: A 597 LYS cc_start: 0.8137 (mmtm) cc_final: 0.7817 (tppp) REVERT: A 630 LYS cc_start: 0.8391 (mttt) cc_final: 0.8087 (mttp) REVERT: A 632 LYS cc_start: 0.8287 (tptt) cc_final: 0.7778 (ttmm) REVERT: A 636 ILE cc_start: 0.8465 (tt) cc_final: 0.8190 (tt) REVERT: A 644 GLU cc_start: 0.7607 (tp30) cc_final: 0.7103 (tp30) REVERT: A 647 ASN cc_start: 0.8335 (t0) cc_final: 0.7987 (t0) REVERT: A 678 ASN cc_start: 0.8461 (m-40) cc_final: 0.8208 (m-40) REVERT: A 690 SER cc_start: 0.8127 (t) cc_final: 0.7672 (m) REVERT: A 709 ASN cc_start: 0.8586 (m-40) cc_final: 0.8319 (m-40) REVERT: A 719 GLN cc_start: 0.8359 (tp40) cc_final: 0.7968 (tp-100) REVERT: A 721 CYS cc_start: 0.7985 (m) cc_final: 0.7577 (m) REVERT: A 729 MET cc_start: 0.8159 (ttm) cc_final: 0.7957 (mtp) REVERT: A 747 ASN cc_start: 0.8228 (p0) cc_final: 0.7872 (p0) REVERT: A 770 LYS cc_start: 0.7945 (mttp) cc_final: 0.7729 (mttp) REVERT: A 778 ASN cc_start: 0.8778 (m-40) cc_final: 0.8377 (m-40) REVERT: A 781 ASN cc_start: 0.8014 (t0) cc_final: 0.7566 (p0) REVERT: A 804 LYS cc_start: 0.8198 (mmtt) cc_final: 0.7886 (mmtt) REVERT: A 811 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7736 (mtt) REVERT: A 813 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7946 (mm-30) REVERT: A 819 ARG cc_start: 0.6659 (ttm-80) cc_final: 0.6202 (ttm110) REVERT: A 828 ILE cc_start: 0.8436 (pt) cc_final: 0.8100 (mt) REVERT: A 829 GLU cc_start: 0.8162 (tp30) cc_final: 0.7766 (tm-30) REVERT: A 842 MET cc_start: 0.7702 (ttt) cc_final: 0.7382 (tpp) REVERT: A 863 LYS cc_start: 0.8160 (mmmm) cc_final: 0.7870 (mmmm) REVERT: A 867 ILE cc_start: 0.7974 (mm) cc_final: 0.7630 (mm) REVERT: A 893 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6770 (mm-30) REVERT: A 897 ARG cc_start: 0.8221 (mtp85) cc_final: 0.7820 (ttm-80) REVERT: A 924 LYS cc_start: 0.7998 (mttp) cc_final: 0.7377 (mttm) REVERT: A 932 LYS cc_start: 0.8645 (mtmm) cc_final: 0.8278 (mtmm) REVERT: A 941 LEU cc_start: 0.8918 (mm) cc_final: 0.8488 (mp) REVERT: A 946 ASN cc_start: 0.8364 (m110) cc_final: 0.8123 (m110) REVERT: A 954 ARG cc_start: 0.8176 (mmt180) cc_final: 0.7884 (mmm-85) REVERT: A 978 ARG cc_start: 0.8367 (mtt180) cc_final: 0.8098 (mtt180) outliers start: 23 outliers final: 12 residues processed: 337 average time/residue: 0.2621 time to fit residues: 113.8098 Evaluate side-chains 333 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 319 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 811 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 4 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.148497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.122071 restraints weight = 12658.439| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.41 r_work: 0.3423 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8970 Z= 0.206 Angle : 0.565 9.576 12274 Z= 0.295 Chirality : 0.042 0.240 1332 Planarity : 0.004 0.049 1448 Dihedral : 17.954 137.192 1460 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.97 % Favored : 96.92 % Rotamer: Outliers : 2.05 % Allowed : 23.44 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.28), residues: 975 helix: 1.97 (0.24), residues: 446 sheet: 0.19 (0.37), residues: 166 loop : -0.28 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 241 HIS 0.004 0.001 HIS A 722 PHE 0.027 0.002 PHE A 558 TYR 0.016 0.001 TYR A 947 ARG 0.006 0.000 ARG A 13 *********************** 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 346 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 328 time to evaluate : 0.935 Fit side-chains REVERT: A 9 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7431 (tt0) REVERT: A 23 THR cc_start: 0.8706 (t) cc_final: 0.8422 (p) REVERT: A 27 GLN cc_start: 0.8555 (tp40) cc_final: 0.8145 (tp-100) REVERT: A 41 GLU cc_start: 0.7973 (pt0) cc_final: 0.7634 (pt0) REVERT: A 54 SER cc_start: 0.8494 (m) cc_final: 0.8173 (t) REVERT: A 56 GLU cc_start: 0.7729 (pt0) cc_final: 0.7186 (pt0) REVERT: A 62 GLU cc_start: 0.7663 (tt0) cc_final: 0.7418 (tt0) REVERT: A 75 GLN cc_start: 0.8433 (tm-30) cc_final: 0.7775 (tm-30) REVERT: A 85 PHE cc_start: 0.8935 (t80) cc_final: 0.8512 (t80) REVERT: A 126 PHE cc_start: 0.7965 (m-10) cc_final: 0.7676 (m-10) REVERT: A 127 LYS cc_start: 0.8584 (ttmm) cc_final: 0.8163 (ttmm) REVERT: A 134 LYS cc_start: 0.8129 (mmmm) cc_final: 0.7850 (mmmm) REVERT: A 142 MET cc_start: 0.8000 (mmm) cc_final: 0.7760 (tmm) REVERT: A 149 ASP cc_start: 0.7553 (p0) cc_final: 0.7104 (p0) REVERT: A 163 LYS cc_start: 0.8523 (tptt) cc_final: 0.8196 (tptt) REVERT: A 180 ARG cc_start: 0.7799 (mtm110) cc_final: 0.7391 (mtm110) REVERT: A 191 GLU cc_start: 0.7770 (mp0) cc_final: 0.7411 (mp0) REVERT: A 285 ARG cc_start: 0.8546 (tpp80) cc_final: 0.7841 (mmm-85) REVERT: A 289 ASP cc_start: 0.7880 (m-30) cc_final: 0.7533 (m-30) REVERT: A 307 LYS cc_start: 0.8616 (mmtt) cc_final: 0.7962 (mmmt) REVERT: A 320 LYS cc_start: 0.8718 (ttmm) cc_final: 0.8512 (ttmm) REVERT: A 321 MET cc_start: 0.8223 (ttp) cc_final: 0.7990 (ttm) REVERT: A 340 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7564 (mt-10) REVERT: A 349 LYS cc_start: 0.8373 (tttt) cc_final: 0.8114 (tttm) REVERT: A 369 MET cc_start: 0.7945 (mmp) cc_final: 0.7743 (mmt) REVERT: A 376 LYS cc_start: 0.8273 (mmtt) cc_final: 0.8004 (mmtm) REVERT: A 395 VAL cc_start: 0.7729 (m) cc_final: 0.7407 (p) REVERT: A 399 TYR cc_start: 0.7921 (m-80) cc_final: 0.6984 (m-80) REVERT: A 404 LYS cc_start: 0.8336 (tttm) cc_final: 0.8058 (tttm) REVERT: A 434 ARG cc_start: 0.8302 (mmm160) cc_final: 0.8046 (tpt90) REVERT: A 455 CYS cc_start: 0.7896 (m) cc_final: 0.7639 (m) REVERT: A 467 MET cc_start: 0.8093 (ttp) cc_final: 0.7778 (ttm) REVERT: A 476 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7362 (tm-30) REVERT: A 507 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7778 (tp) REVERT: A 511 LYS cc_start: 0.8691 (ptpp) cc_final: 0.8313 (ptpp) REVERT: A 579 MET cc_start: 0.8061 (ttm) cc_final: 0.7739 (ttm) REVERT: A 597 LYS cc_start: 0.8176 (mmtm) cc_final: 0.7810 (tppp) REVERT: A 630 LYS cc_start: 0.8410 (mttt) cc_final: 0.8084 (mttp) REVERT: A 632 LYS cc_start: 0.8303 (tptt) cc_final: 0.7786 (ttmm) REVERT: A 636 ILE cc_start: 0.8515 (tt) cc_final: 0.8225 (tt) REVERT: A 676 VAL cc_start: 0.8218 (OUTLIER) cc_final: 0.7962 (m) REVERT: A 678 ASN cc_start: 0.8535 (m-40) cc_final: 0.8318 (m-40) REVERT: A 690 SER cc_start: 0.8126 (t) cc_final: 0.7725 (m) REVERT: A 709 ASN cc_start: 0.8642 (m-40) cc_final: 0.8360 (m-40) REVERT: A 721 CYS cc_start: 0.8188 (m) cc_final: 0.7679 (m) REVERT: A 747 ASN cc_start: 0.8095 (p0) cc_final: 0.7793 (p0) REVERT: A 770 LYS cc_start: 0.7986 (mttp) cc_final: 0.7668 (mttp) REVERT: A 778 ASN cc_start: 0.8714 (m-40) cc_final: 0.8275 (m-40) REVERT: A 781 ASN cc_start: 0.8080 (t0) cc_final: 0.7601 (p0) REVERT: A 804 LYS cc_start: 0.8281 (mmtt) cc_final: 0.8002 (mmtt) REVERT: A 813 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7888 (mm-30) REVERT: A 818 ARG cc_start: 0.7901 (mtt90) cc_final: 0.7601 (mtt90) REVERT: A 819 ARG cc_start: 0.6936 (ttm-80) cc_final: 0.6360 (ttm110) REVERT: A 828 ILE cc_start: 0.8515 (pt) cc_final: 0.8286 (mt) REVERT: A 842 MET cc_start: 0.7837 (ttt) cc_final: 0.7519 (tpp) REVERT: A 851 ILE cc_start: 0.8685 (mt) cc_final: 0.8449 (mp) REVERT: A 863 LYS cc_start: 0.8220 (mmmm) cc_final: 0.7965 (mmmm) REVERT: A 869 MET cc_start: 0.7739 (mmm) cc_final: 0.7500 (mmm) REVERT: A 872 MET cc_start: 0.8036 (mmm) cc_final: 0.7716 (mmm) REVERT: A 932 LYS cc_start: 0.8588 (mtmm) cc_final: 0.8197 (mtmm) REVERT: A 954 ARG cc_start: 0.8150 (mmt180) cc_final: 0.7922 (mmm-85) outliers start: 18 outliers final: 13 residues processed: 333 average time/residue: 0.2635 time to fit residues: 113.0597 Evaluate side-chains 331 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 316 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 811 MET Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 888 GLN 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 17 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 HIS ** A 946 ASN ** 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 = 0.3932 r_free = 0.3932 target = 0.148279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.121710 restraints weight = 12528.051| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.39 r_work: 0.3416 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8970 Z= 0.206 Angle : 0.567 8.414 12274 Z= 0.298 Chirality : 0.042 0.241 1332 Planarity : 0.004 0.051 1448 Dihedral : 17.876 137.651 1460 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.77 % Favored : 97.13 % Rotamer: Outliers : 2.84 % Allowed : 24.23 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.28), residues: 975 helix: 1.96 (0.24), residues: 443 sheet: 0.28 (0.39), residues: 161 loop : -0.32 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 241 HIS 0.005 0.001 HIS A 722 PHE 0.024 0.002 PHE A 558 TYR 0.024 0.001 TYR A 772 ARG 0.005 0.001 ARG A 13 *********************** 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 352 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 327 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7420 (tt0) REVERT: A 23 THR cc_start: 0.8727 (t) cc_final: 0.8433 (p) REVERT: A 27 GLN cc_start: 0.8556 (tp40) cc_final: 0.8142 (tp-100) REVERT: A 41 GLU cc_start: 0.7973 (pt0) cc_final: 0.7636 (pt0) REVERT: A 54 SER cc_start: 0.8521 (m) cc_final: 0.8218 (t) REVERT: A 56 GLU cc_start: 0.7743 (pt0) cc_final: 0.7218 (pt0) REVERT: A 62 GLU cc_start: 0.7620 (tt0) cc_final: 0.7410 (tt0) REVERT: A 74 VAL cc_start: 0.8568 (t) cc_final: 0.8211 (m) REVERT: A 75 GLN cc_start: 0.8424 (tm-30) cc_final: 0.7728 (tm-30) REVERT: A 85 PHE cc_start: 0.8957 (t80) cc_final: 0.8538 (t80) REVERT: A 116 LYS cc_start: 0.8735 (mttm) cc_final: 0.8417 (mtpp) REVERT: A 127 LYS cc_start: 0.8590 (ttmm) cc_final: 0.8145 (ttmm) REVERT: A 134 LYS cc_start: 0.8117 (mmmm) cc_final: 0.7844 (mmmm) REVERT: A 142 MET cc_start: 0.7983 (mmm) cc_final: 0.7627 (tmm) REVERT: A 149 ASP cc_start: 0.7511 (p0) cc_final: 0.7009 (p0) REVERT: A 163 LYS cc_start: 0.8579 (tptt) cc_final: 0.8324 (tptt) REVERT: A 174 HIS cc_start: 0.7667 (t-90) cc_final: 0.7392 (t-90) REVERT: A 175 TYR cc_start: 0.8405 (p90) cc_final: 0.8169 (p90) REVERT: A 180 ARG cc_start: 0.7741 (mtm110) cc_final: 0.7302 (mtm110) REVERT: A 191 GLU cc_start: 0.7803 (mp0) cc_final: 0.7429 (mp0) REVERT: A 250 SER cc_start: 0.8627 (m) cc_final: 0.8256 (p) REVERT: A 255 MET cc_start: 0.8243 (mmt) cc_final: 0.7987 (mmt) REVERT: A 277 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8075 (mm) REVERT: A 285 ARG cc_start: 0.8527 (tpp80) cc_final: 0.7832 (mmm-85) REVERT: A 289 ASP cc_start: 0.8027 (m-30) cc_final: 0.7576 (m-30) REVERT: A 307 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8069 (mmmt) REVERT: A 320 LYS cc_start: 0.8741 (ttmm) cc_final: 0.8522 (ttmm) REVERT: A 321 MET cc_start: 0.8190 (ttp) cc_final: 0.7964 (ttm) REVERT: A 339 LYS cc_start: 0.8495 (mtmm) cc_final: 0.8155 (mtpp) REVERT: A 340 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7560 (mt-10) REVERT: A 349 LYS cc_start: 0.8324 (tttt) cc_final: 0.8076 (tttm) REVERT: A 369 MET cc_start: 0.7940 (mmp) cc_final: 0.7735 (mmt) REVERT: A 375 PRO cc_start: 0.8457 (Cg_endo) cc_final: 0.8134 (Cg_exo) REVERT: A 376 LYS cc_start: 0.8255 (mmtt) cc_final: 0.7934 (mmtm) REVERT: A 399 TYR cc_start: 0.7913 (m-80) cc_final: 0.6908 (m-80) REVERT: A 404 LYS cc_start: 0.8341 (tttm) cc_final: 0.8050 (tttm) REVERT: A 413 LYS cc_start: 0.8067 (tttm) cc_final: 0.7857 (tttm) REVERT: A 434 ARG cc_start: 0.8330 (mmm160) cc_final: 0.8075 (tpt90) REVERT: A 455 CYS cc_start: 0.7902 (m) cc_final: 0.7671 (m) REVERT: A 467 MET cc_start: 0.8090 (ttp) cc_final: 0.7750 (ttm) REVERT: A 475 ASP cc_start: 0.7791 (t0) cc_final: 0.7578 (t0) REVERT: A 476 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7420 (tm-30) REVERT: A 485 ILE cc_start: 0.8373 (pt) cc_final: 0.8141 (pt) REVERT: A 507 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7796 (tp) REVERT: A 511 LYS cc_start: 0.8636 (ptpp) cc_final: 0.8067 (ptpp) REVERT: A 579 MET cc_start: 0.8051 (ttm) cc_final: 0.7665 (mtp) REVERT: A 597 LYS cc_start: 0.8157 (mmtm) cc_final: 0.7777 (tppp) REVERT: A 632 LYS cc_start: 0.8339 (tptt) cc_final: 0.7828 (ttmm) REVERT: A 636 ILE cc_start: 0.8517 (tt) cc_final: 0.8131 (tp) REVERT: A 676 VAL cc_start: 0.8302 (OUTLIER) cc_final: 0.8083 (m) REVERT: A 690 SER cc_start: 0.8111 (t) cc_final: 0.7759 (m) REVERT: A 704 THR cc_start: 0.8220 (p) cc_final: 0.7714 (t) REVERT: A 709 ASN cc_start: 0.8614 (m-40) cc_final: 0.8352 (m-40) REVERT: A 711 GLN cc_start: 0.8261 (tp40) cc_final: 0.7854 (tp40) REVERT: A 721 CYS cc_start: 0.8296 (m) cc_final: 0.7849 (m) REVERT: A 742 TYR cc_start: 0.8930 (t80) cc_final: 0.8726 (t80) REVERT: A 747 ASN cc_start: 0.8145 (p0) cc_final: 0.7832 (p0) REVERT: A 756 TYR cc_start: 0.7405 (t80) cc_final: 0.7101 (t80) REVERT: A 770 LYS cc_start: 0.8031 (mttp) cc_final: 0.7722 (mttp) REVERT: A 778 ASN cc_start: 0.8652 (m-40) cc_final: 0.8252 (m-40) REVERT: A 781 ASN cc_start: 0.8191 (t0) cc_final: 0.7697 (p0) REVERT: A 782 PHE cc_start: 0.8808 (m-80) cc_final: 0.8430 (m-10) REVERT: A 804 LYS cc_start: 0.8278 (mmtt) cc_final: 0.8024 (mmtt) REVERT: A 812 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8133 (mt-10) REVERT: A 813 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7986 (mm-30) REVERT: A 816 LYS cc_start: 0.8581 (ptpp) cc_final: 0.7930 (ptpp) REVERT: A 818 ARG cc_start: 0.8047 (mtt90) cc_final: 0.7384 (mtt90) REVERT: A 819 ARG cc_start: 0.7107 (ttm-80) cc_final: 0.6649 (ttm110) REVERT: A 828 ILE cc_start: 0.8565 (pt) cc_final: 0.8356 (mt) REVERT: A 834 VAL cc_start: 0.8788 (t) cc_final: 0.8546 (p) REVERT: A 842 MET cc_start: 0.7827 (ttt) cc_final: 0.7419 (tpp) REVERT: A 851 ILE cc_start: 0.8710 (mt) cc_final: 0.8493 (mp) REVERT: A 863 LYS cc_start: 0.8330 (mmmm) cc_final: 0.7676 (mmmm) REVERT: A 869 MET cc_start: 0.7719 (mmm) cc_final: 0.7504 (mmm) REVERT: A 872 MET cc_start: 0.8043 (mmm) cc_final: 0.7739 (mmm) REVERT: A 932 LYS cc_start: 0.8572 (mtmm) cc_final: 0.8185 (mtmm) REVERT: A 954 ARG cc_start: 0.8287 (mmt180) cc_final: 0.8022 (mmm-85) outliers start: 25 outliers final: 14 residues processed: 337 average time/residue: 0.2727 time to fit residues: 118.0110 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 : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 943 TYR 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 47 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 63 optimal weight: 0.2980 chunk 69 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.144046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.117211 restraints weight = 12734.416| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.43 r_work: 0.3416 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8970 Z= 0.198 Angle : 0.575 8.605 12274 Z= 0.301 Chirality : 0.041 0.236 1332 Planarity : 0.004 0.064 1448 Dihedral : 17.855 137.998 1458 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.87 % Favored : 97.03 % Rotamer: Outliers : 2.39 % Allowed : 25.26 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.28), residues: 975 helix: 1.94 (0.25), residues: 444 sheet: 0.18 (0.38), residues: 166 loop : -0.28 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 325 HIS 0.016 0.001 HIS A 823 PHE 0.031 0.002 PHE A 126 TYR 0.023 0.001 TYR A 772 ARG 0.013 0.001 ARG A 99 *********************** 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 345 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 324 time to evaluate : 0.925 Fit side-chains REVERT: A 21 ARG cc_start: 0.8315 (ttp80) cc_final: 0.8098 (ttp80) REVERT: A 22 VAL cc_start: 0.8695 (t) cc_final: 0.8462 (t) REVERT: A 23 THR cc_start: 0.8727 (t) cc_final: 0.8448 (p) REVERT: A 27 GLN cc_start: 0.8583 (tp40) cc_final: 0.8147 (tp-100) REVERT: A 41 GLU cc_start: 0.7974 (pt0) cc_final: 0.7643 (pt0) REVERT: A 54 SER cc_start: 0.8523 (m) cc_final: 0.8225 (t) REVERT: A 56 GLU cc_start: 0.7716 (pt0) cc_final: 0.7327 (pt0) REVERT: A 62 GLU cc_start: 0.7635 (tt0) cc_final: 0.7409 (tt0) REVERT: A 74 VAL cc_start: 0.8578 (t) cc_final: 0.8223 (m) REVERT: A 75 GLN cc_start: 0.8425 (tm-30) cc_final: 0.7979 (tm-30) REVERT: A 85 PHE cc_start: 0.8950 (t80) cc_final: 0.8538 (t80) REVERT: A 127 LYS cc_start: 0.8581 (ttmm) cc_final: 0.8158 (ttmm) REVERT: A 134 LYS cc_start: 0.8052 (mmmm) cc_final: 0.7798 (mmmm) REVERT: A 142 MET cc_start: 0.7996 (mmm) cc_final: 0.7637 (tmm) REVERT: A 149 ASP cc_start: 0.7543 (p0) cc_final: 0.7044 (p0) REVERT: A 150 ASP cc_start: 0.8301 (m-30) cc_final: 0.8041 (m-30) REVERT: A 163 LYS cc_start: 0.8512 (tptt) cc_final: 0.8297 (tptt) REVERT: A 174 HIS cc_start: 0.7745 (t-90) cc_final: 0.7544 (t70) REVERT: A 175 TYR cc_start: 0.8452 (p90) cc_final: 0.8176 (p90) REVERT: A 180 ARG cc_start: 0.7742 (mtm110) cc_final: 0.7263 (mtm110) REVERT: A 191 GLU cc_start: 0.7791 (mp0) cc_final: 0.7417 (mp0) REVERT: A 250 SER cc_start: 0.8641 (m) cc_final: 0.8262 (p) REVERT: A 255 MET cc_start: 0.8267 (mmt) cc_final: 0.7963 (mmt) REVERT: A 277 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8058 (mm) REVERT: A 285 ARG cc_start: 0.8543 (tpp80) cc_final: 0.7894 (mmm-85) REVERT: A 289 ASP cc_start: 0.8037 (m-30) cc_final: 0.7583 (m-30) REVERT: A 307 LYS cc_start: 0.8550 (mmtt) cc_final: 0.8022 (mmmt) REVERT: A 320 LYS cc_start: 0.8766 (ttmm) cc_final: 0.8546 (ttmm) REVERT: A 321 MET cc_start: 0.8209 (ttp) cc_final: 0.7984 (ttm) REVERT: A 340 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7549 (mt-10) REVERT: A 349 LYS cc_start: 0.8292 (tttt) cc_final: 0.8038 (tttm) REVERT: A 369 MET cc_start: 0.7852 (mmp) cc_final: 0.7631 (mmt) REVERT: A 375 PRO cc_start: 0.8410 (Cg_endo) cc_final: 0.8082 (Cg_exo) REVERT: A 376 LYS cc_start: 0.8270 (mmtt) cc_final: 0.7948 (mmtm) REVERT: A 399 TYR cc_start: 0.7865 (m-80) cc_final: 0.6783 (m-80) REVERT: A 404 LYS cc_start: 0.8337 (tttm) cc_final: 0.8052 (tttm) REVERT: A 413 LYS cc_start: 0.8194 (tttm) cc_final: 0.7882 (tttt) REVERT: A 434 ARG cc_start: 0.8315 (mmm160) cc_final: 0.8075 (tpt90) REVERT: A 455 CYS cc_start: 0.7931 (m) cc_final: 0.7691 (m) REVERT: A 467 MET cc_start: 0.8088 (ttp) cc_final: 0.7740 (ttm) REVERT: A 476 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7404 (tm-30) REVERT: A 507 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7925 (tp) REVERT: A 511 LYS cc_start: 0.8589 (ptpp) cc_final: 0.8326 (pttm) REVERT: A 527 MET cc_start: 0.7972 (mtm) cc_final: 0.7738 (mtp) REVERT: A 529 TYR cc_start: 0.8247 (m-80) cc_final: 0.8029 (m-80) REVERT: A 547 MET cc_start: 0.7792 (tpp) cc_final: 0.7315 (mmm) REVERT: A 579 MET cc_start: 0.8080 (ttm) cc_final: 0.7761 (ttm) REVERT: A 597 LYS cc_start: 0.8155 (mmtm) cc_final: 0.7772 (tppp) REVERT: A 630 LYS cc_start: 0.8431 (mttt) cc_final: 0.8102 (mttp) REVERT: A 632 LYS cc_start: 0.8340 (tptt) cc_final: 0.7783 (ttmm) REVERT: A 636 ILE cc_start: 0.8491 (tt) cc_final: 0.8113 (tp) REVERT: A 670 LYS cc_start: 0.8409 (ttmm) cc_final: 0.8190 (tttm) REVERT: A 690 SER cc_start: 0.8139 (t) cc_final: 0.7784 (m) REVERT: A 704 THR cc_start: 0.8176 (p) cc_final: 0.7721 (t) REVERT: A 711 GLN cc_start: 0.8330 (tp40) cc_final: 0.7899 (tp40) REVERT: A 721 CYS cc_start: 0.8321 (m) cc_final: 0.7923 (m) REVERT: A 726 LEU cc_start: 0.8624 (mt) cc_final: 0.8373 (mm) REVERT: A 742 TYR cc_start: 0.8939 (t80) cc_final: 0.8652 (t80) REVERT: A 747 ASN cc_start: 0.8114 (p0) cc_final: 0.7846 (p0) REVERT: A 756 TYR cc_start: 0.7388 (t80) cc_final: 0.7028 (t80) REVERT: A 770 LYS cc_start: 0.8064 (mttp) cc_final: 0.7742 (mttp) REVERT: A 778 ASN cc_start: 0.8648 (m-40) cc_final: 0.8215 (m-40) REVERT: A 781 ASN cc_start: 0.8171 (t0) cc_final: 0.7652 (p0) REVERT: A 782 PHE cc_start: 0.8809 (m-80) cc_final: 0.8400 (m-10) REVERT: A 804 LYS cc_start: 0.8284 (mmtt) cc_final: 0.8022 (mmtt) REVERT: A 812 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8148 (mt-10) REVERT: A 813 GLU cc_start: 0.8268 (mm-30) cc_final: 0.8058 (mm-30) REVERT: A 816 LYS cc_start: 0.8571 (ptpp) cc_final: 0.8151 (ptpp) REVERT: A 818 ARG cc_start: 0.8074 (mtt90) cc_final: 0.7685 (mtt90) REVERT: A 819 ARG cc_start: 0.7167 (ttm-80) cc_final: 0.6744 (ttm110) REVERT: A 828 ILE cc_start: 0.8575 (pt) cc_final: 0.8374 (mt) REVERT: A 834 VAL cc_start: 0.8791 (t) cc_final: 0.8560 (p) REVERT: A 842 MET cc_start: 0.7953 (ttt) cc_final: 0.7537 (tpp) REVERT: A 851 ILE cc_start: 0.8725 (mt) cc_final: 0.8478 (mp) REVERT: A 863 LYS cc_start: 0.8384 (mmmm) cc_final: 0.7727 (mmmm) REVERT: A 869 MET cc_start: 0.7766 (mmm) cc_final: 0.7547 (mmm) REVERT: A 932 LYS cc_start: 0.8595 (mtmm) cc_final: 0.8184 (mtmm) outliers start: 21 outliers final: 13 residues processed: 332 average time/residue: 0.2757 time to fit residues: 117.6882 Evaluate side-chains 334 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 319 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 888 GLN 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 20 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 95 optimal weight: 0.3980 chunk 27 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 0.4980 chunk 11 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3872 r_free = 0.3872 target = 0.141387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.114759 restraints weight = 12827.209| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.37 r_work: 0.3376 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8970 Z= 0.276 Angle : 0.628 9.717 12274 Z= 0.331 Chirality : 0.044 0.266 1332 Planarity : 0.004 0.058 1448 Dihedral : 17.927 138.515 1458 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.28 % Favored : 96.62 % Rotamer: Outliers : 2.39 % Allowed : 25.71 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.28), residues: 975 helix: 1.86 (0.25), residues: 442 sheet: 0.23 (0.39), residues: 161 loop : -0.35 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 169 HIS 0.005 0.001 HIS A 722 PHE 0.026 0.002 PHE A 558 TYR 0.023 0.002 TYR A 772 ARG 0.010 0.001 ARG A 99 *********************** 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 345 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 324 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: A 18 ILE cc_start: 0.8875 (mm) cc_final: 0.8552 (mm) REVERT: A 19 THR cc_start: 0.8499 (p) cc_final: 0.8234 (t) REVERT: A 21 ARG cc_start: 0.8343 (ttp80) cc_final: 0.8125 (ttp80) REVERT: A 22 VAL cc_start: 0.8765 (t) cc_final: 0.8550 (t) REVERT: A 23 THR cc_start: 0.8741 (t) cc_final: 0.8458 (p) REVERT: A 41 GLU cc_start: 0.7999 (pt0) cc_final: 0.7659 (pt0) REVERT: A 54 SER cc_start: 0.8580 (m) cc_final: 0.8238 (p) REVERT: A 56 GLU cc_start: 0.7792 (pt0) cc_final: 0.7408 (pt0) REVERT: A 66 GLU cc_start: 0.8097 (tt0) cc_final: 0.7783 (tp30) REVERT: A 74 VAL cc_start: 0.8602 (t) cc_final: 0.8214 (m) REVERT: A 75 GLN cc_start: 0.8425 (tm-30) cc_final: 0.8032 (tm-30) REVERT: A 85 PHE cc_start: 0.8980 (t80) cc_final: 0.8574 (t80) REVERT: A 126 PHE cc_start: 0.7943 (m-10) cc_final: 0.7621 (m-10) REVERT: A 127 LYS cc_start: 0.8600 (ttmm) cc_final: 0.8173 (ttmm) REVERT: A 134 LYS cc_start: 0.8199 (mmmm) cc_final: 0.7946 (mmmm) REVERT: A 142 MET cc_start: 0.7995 (mmm) cc_final: 0.7640 (tmm) REVERT: A 149 ASP cc_start: 0.7500 (p0) cc_final: 0.7089 (p0) REVERT: A 175 TYR cc_start: 0.8496 (p90) cc_final: 0.8187 (p90) REVERT: A 180 ARG cc_start: 0.7861 (mtm110) cc_final: 0.7377 (mtm110) REVERT: A 191 GLU cc_start: 0.7820 (mp0) cc_final: 0.7483 (mp0) REVERT: A 250 SER cc_start: 0.8595 (m) cc_final: 0.8231 (p) REVERT: A 255 MET cc_start: 0.8295 (mmt) cc_final: 0.7963 (mmt) REVERT: A 277 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8090 (mm) REVERT: A 289 ASP cc_start: 0.8095 (m-30) cc_final: 0.7757 (m-30) REVERT: A 307 LYS cc_start: 0.8599 (mmtt) cc_final: 0.8133 (mmmt) REVERT: A 320 LYS cc_start: 0.8789 (ttmm) cc_final: 0.8560 (ttmm) REVERT: A 321 MET cc_start: 0.8229 (ttp) cc_final: 0.8007 (ttm) REVERT: A 340 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7528 (mt-10) REVERT: A 349 LYS cc_start: 0.8302 (tttt) cc_final: 0.8055 (tttm) REVERT: A 375 PRO cc_start: 0.8433 (Cg_endo) cc_final: 0.8118 (Cg_exo) REVERT: A 376 LYS cc_start: 0.8246 (mmtt) cc_final: 0.7917 (mmtm) REVERT: A 399 TYR cc_start: 0.7856 (m-80) cc_final: 0.6873 (m-80) REVERT: A 404 LYS cc_start: 0.8407 (tttm) cc_final: 0.8146 (tttm) REVERT: A 434 ARG cc_start: 0.8327 (mmm160) cc_final: 0.8094 (tpt90) REVERT: A 455 CYS cc_start: 0.7953 (m) cc_final: 0.7751 (m) REVERT: A 467 MET cc_start: 0.8098 (ttp) cc_final: 0.7758 (ttm) REVERT: A 476 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7180 (tm-30) REVERT: A 507 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7802 (tp) REVERT: A 563 ARG cc_start: 0.8620 (ptm-80) cc_final: 0.8193 (ptt-90) REVERT: A 579 MET cc_start: 0.8072 (ttm) cc_final: 0.7779 (ttm) REVERT: A 599 GLU cc_start: 0.8085 (tt0) cc_final: 0.7765 (tt0) REVERT: A 630 LYS cc_start: 0.8478 (mttt) cc_final: 0.8180 (mttp) REVERT: A 632 LYS cc_start: 0.8341 (tptt) cc_final: 0.7833 (ttmm) REVERT: A 636 ILE cc_start: 0.8516 (tt) cc_final: 0.8060 (tp) REVERT: A 670 LYS cc_start: 0.8504 (ttmm) cc_final: 0.8264 (ttmm) REVERT: A 690 SER cc_start: 0.8214 (t) cc_final: 0.7838 (m) REVERT: A 704 THR cc_start: 0.8321 (p) cc_final: 0.7842 (t) REVERT: A 711 GLN cc_start: 0.8370 (tp40) cc_final: 0.7884 (tp40) REVERT: A 716 HIS cc_start: 0.8365 (m170) cc_final: 0.7979 (m170) REVERT: A 721 CYS cc_start: 0.8410 (m) cc_final: 0.8072 (m) REVERT: A 741 GLU cc_start: 0.8213 (tp30) cc_final: 0.7878 (tp30) REVERT: A 756 TYR cc_start: 0.7540 (t80) cc_final: 0.7068 (t80) REVERT: A 770 LYS cc_start: 0.8066 (mttp) cc_final: 0.7721 (mttp) REVERT: A 778 ASN cc_start: 0.8670 (m-40) cc_final: 0.8232 (m-40) REVERT: A 781 ASN cc_start: 0.8168 (t0) cc_final: 0.7708 (p0) REVERT: A 782 PHE cc_start: 0.8832 (m-80) cc_final: 0.8551 (m-80) REVERT: A 804 LYS cc_start: 0.8327 (mmtt) cc_final: 0.8031 (mmtt) REVERT: A 813 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8094 (mm-30) REVERT: A 816 LYS cc_start: 0.8637 (ptpp) cc_final: 0.8304 (ptpp) REVERT: A 818 ARG cc_start: 0.8195 (mtt90) cc_final: 0.7972 (mtt90) REVERT: A 819 ARG cc_start: 0.7519 (ttm-80) cc_final: 0.7118 (ttm110) REVERT: A 828 ILE cc_start: 0.8603 (pt) cc_final: 0.8393 (mt) REVERT: A 834 VAL cc_start: 0.8838 (t) cc_final: 0.8617 (p) REVERT: A 841 ASN cc_start: 0.7610 (t0) cc_final: 0.7269 (t0) REVERT: A 842 MET cc_start: 0.7971 (ttt) cc_final: 0.7654 (tpp) REVERT: A 851 ILE cc_start: 0.8751 (mt) cc_final: 0.8485 (mp) REVERT: A 863 LYS cc_start: 0.8510 (mmmm) cc_final: 0.7831 (mmmm) REVERT: A 869 MET cc_start: 0.7823 (mmm) cc_final: 0.7595 (mmm) REVERT: A 902 ILE cc_start: 0.8266 (mt) cc_final: 0.8027 (mm) REVERT: A 925 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7366 (mmm) REVERT: A 932 LYS cc_start: 0.8636 (mtmm) cc_final: 0.8175 (mtmm) REVERT: A 954 ARG cc_start: 0.8487 (mmt180) cc_final: 0.8259 (mmm-85) REVERT: A 958 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6982 (mp0) outliers start: 21 outliers final: 9 residues processed: 334 average time/residue: 0.2738 time to fit residues: 117.4728 Evaluate side-chains 330 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 317 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 943 TYR 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 43 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 79 optimal weight: 0.0970 chunk 66 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 12 optimal weight: 0.0370 chunk 87 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS ** A 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.144138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.117351 restraints weight = 12713.619| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.38 r_work: 0.3419 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.5598 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= 0.177 Angle : 0.610 10.036 12274 Z= 0.314 Chirality : 0.043 0.333 1332 Planarity : 0.004 0.044 1448 Dihedral : 17.817 138.560 1458 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.77 % Favored : 97.13 % Rotamer: Outliers : 2.05 % Allowed : 25.71 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.28), residues: 975 helix: 1.89 (0.25), residues: 442 sheet: 0.07 (0.38), residues: 171 loop : -0.25 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 325 HIS 0.004 0.001 HIS A 722 PHE 0.027 0.002 PHE A 558 TYR 0.020 0.001 TYR A 97 ARG 0.010 0.001 ARG A 99 *********************** 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 337 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 319 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7764 (tt0) cc_final: 0.7249 (tt0) REVERT: A 11 VAL cc_start: 0.8613 (t) cc_final: 0.8308 (p) REVERT: A 19 THR cc_start: 0.8392 (p) cc_final: 0.8072 (t) REVERT: A 22 VAL cc_start: 0.8704 (t) cc_final: 0.8475 (t) REVERT: A 23 THR cc_start: 0.8722 (t) cc_final: 0.8446 (p) REVERT: A 41 GLU cc_start: 0.8003 (pt0) cc_final: 0.7634 (pt0) REVERT: A 54 SER cc_start: 0.8542 (m) cc_final: 0.8213 (t) REVERT: A 56 GLU cc_start: 0.7756 (pt0) cc_final: 0.7361 (pt0) REVERT: A 74 VAL cc_start: 0.8489 (t) cc_final: 0.8178 (m) REVERT: A 75 GLN cc_start: 0.8378 (tm-30) cc_final: 0.7991 (tm-30) REVERT: A 85 PHE cc_start: 0.8944 (t80) cc_final: 0.8510 (t80) REVERT: A 127 LYS cc_start: 0.8616 (ttmm) cc_final: 0.8192 (ttmm) REVERT: A 134 LYS cc_start: 0.8051 (mmmm) cc_final: 0.7794 (mmmm) REVERT: A 142 MET cc_start: 0.7970 (mmm) cc_final: 0.7596 (tmm) REVERT: A 149 ASP cc_start: 0.7517 (p0) cc_final: 0.7095 (p0) REVERT: A 150 ASP cc_start: 0.8289 (m-30) cc_final: 0.8041 (m-30) REVERT: A 163 LYS cc_start: 0.8565 (tptt) cc_final: 0.8278 (tptt) REVERT: A 175 TYR cc_start: 0.8486 (p90) cc_final: 0.8197 (p90) REVERT: A 180 ARG cc_start: 0.7751 (mtm110) cc_final: 0.7549 (mtm110) REVERT: A 191 GLU cc_start: 0.7785 (mp0) cc_final: 0.7450 (mp0) REVERT: A 255 MET cc_start: 0.8275 (mmt) cc_final: 0.8037 (mmt) REVERT: A 277 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8056 (mm) REVERT: A 285 ARG cc_start: 0.8519 (tpp80) cc_final: 0.7819 (mmm-85) REVERT: A 289 ASP cc_start: 0.8021 (m-30) cc_final: 0.7558 (m-30) REVERT: A 307 LYS cc_start: 0.8529 (mmtt) cc_final: 0.7992 (mmmt) REVERT: A 320 LYS cc_start: 0.8772 (ttmm) cc_final: 0.8552 (ttmm) REVERT: A 321 MET cc_start: 0.8200 (ttp) cc_final: 0.7975 (ttm) REVERT: A 340 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7469 (mt-10) REVERT: A 349 LYS cc_start: 0.8273 (tttt) cc_final: 0.8015 (tttm) REVERT: A 351 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8354 (mt) REVERT: A 375 PRO cc_start: 0.8423 (Cg_endo) cc_final: 0.8080 (Cg_exo) REVERT: A 376 LYS cc_start: 0.8251 (mmtt) cc_final: 0.7920 (mmtm) REVERT: A 399 TYR cc_start: 0.7773 (m-80) cc_final: 0.6695 (m-80) REVERT: A 404 LYS cc_start: 0.8369 (tttm) cc_final: 0.8101 (tttm) REVERT: A 434 ARG cc_start: 0.8325 (mmm160) cc_final: 0.8087 (tpt90) REVERT: A 455 CYS cc_start: 0.7959 (m) cc_final: 0.7722 (m) REVERT: A 467 MET cc_start: 0.8066 (ttp) cc_final: 0.7693 (ttm) REVERT: A 476 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7166 (tm-30) REVERT: A 507 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7876 (tp) REVERT: A 527 MET cc_start: 0.7960 (mtm) cc_final: 0.7695 (mtp) REVERT: A 529 TYR cc_start: 0.8137 (m-80) cc_final: 0.7806 (m-80) REVERT: A 547 MET cc_start: 0.7779 (tpp) cc_final: 0.7282 (mmm) REVERT: A 563 ARG cc_start: 0.8597 (ptm-80) cc_final: 0.8185 (ptt-90) REVERT: A 579 MET cc_start: 0.8086 (ttm) cc_final: 0.7756 (ttm) REVERT: A 630 LYS cc_start: 0.8442 (mttt) cc_final: 0.8125 (mttp) REVERT: A 632 LYS cc_start: 0.8398 (tptt) cc_final: 0.7893 (ttmm) REVERT: A 636 ILE cc_start: 0.8488 (tt) cc_final: 0.8103 (tp) REVERT: A 666 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7998 (mm-40) REVERT: A 689 ASP cc_start: 0.7623 (p0) cc_final: 0.7318 (p0) REVERT: A 690 SER cc_start: 0.8084 (t) cc_final: 0.7607 (m) REVERT: A 704 THR cc_start: 0.8269 (p) cc_final: 0.7939 (t) REVERT: A 711 GLN cc_start: 0.8366 (tp40) cc_final: 0.7975 (tp40) REVERT: A 716 HIS cc_start: 0.8323 (m170) cc_final: 0.7973 (m170) REVERT: A 718 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: A 741 GLU cc_start: 0.8153 (tp30) cc_final: 0.7798 (tp30) REVERT: A 756 TYR cc_start: 0.7346 (t80) cc_final: 0.6953 (t80) REVERT: A 770 LYS cc_start: 0.8048 (mttp) cc_final: 0.7697 (mttp) REVERT: A 778 ASN cc_start: 0.8666 (m-40) cc_final: 0.8223 (m-40) REVERT: A 781 ASN cc_start: 0.8172 (t0) cc_final: 0.7693 (p0) REVERT: A 782 PHE cc_start: 0.8819 (m-80) cc_final: 0.8523 (m-80) REVERT: A 804 LYS cc_start: 0.8270 (mmtt) cc_final: 0.7963 (mmtt) REVERT: A 816 LYS cc_start: 0.8539 (ptpp) cc_final: 0.8099 (ptpp) REVERT: A 818 ARG cc_start: 0.8089 (mtt90) cc_final: 0.7695 (mtt90) REVERT: A 819 ARG cc_start: 0.7290 (ttm-80) cc_final: 0.6851 (ttm110) REVERT: A 834 VAL cc_start: 0.8795 (t) cc_final: 0.8572 (p) REVERT: A 842 MET cc_start: 0.7946 (ttt) cc_final: 0.7596 (tpp) REVERT: A 851 ILE cc_start: 0.8746 (mt) cc_final: 0.8454 (mp) REVERT: A 863 LYS cc_start: 0.8479 (mmmm) cc_final: 0.7843 (mmmm) REVERT: A 932 LYS cc_start: 0.8597 (mtmm) cc_final: 0.8136 (mtmm) REVERT: A 954 ARG cc_start: 0.8437 (mmt180) cc_final: 0.8199 (mmm-85) REVERT: A 958 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6924 (mp0) outliers start: 18 outliers final: 12 residues processed: 327 average time/residue: 0.2782 time to fit residues: 116.7785 Evaluate side-chains 327 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 310 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 507 LEU 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 664 SER Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 943 TYR 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 24 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 83 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 69 optimal weight: 0.0980 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 HIS ** 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 = 0.3913 r_free = 0.3913 target = 0.146916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.120376 restraints weight = 12882.079| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.43 r_work: 0.3413 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.5690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8970 Z= 0.197 Angle : 0.628 9.897 12274 Z= 0.324 Chirality : 0.043 0.316 1332 Planarity : 0.004 0.056 1448 Dihedral : 17.719 138.768 1458 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.97 % Favored : 96.92 % Rotamer: Outliers : 1.93 % Allowed : 26.85 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.28), residues: 975 helix: 1.90 (0.25), residues: 442 sheet: 0.02 (0.38), residues: 171 loop : -0.22 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 241 HIS 0.008 0.001 HIS A 174 PHE 0.033 0.002 PHE A 126 TYR 0.022 0.001 TYR A 772 ARG 0.013 0.001 ARG A 99 ********************** 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 325 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 308 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7811 (tt0) cc_final: 0.7265 (tt0) REVERT: A 11 VAL cc_start: 0.8603 (t) cc_final: 0.8286 (p) REVERT: A 19 THR cc_start: 0.8414 (p) cc_final: 0.8105 (t) REVERT: A 22 VAL cc_start: 0.8699 (t) cc_final: 0.8460 (t) REVERT: A 23 THR cc_start: 0.8695 (t) cc_final: 0.8419 (p) REVERT: A 41 GLU cc_start: 0.8082 (pt0) cc_final: 0.7680 (pt0) REVERT: A 54 SER cc_start: 0.8540 (m) cc_final: 0.8230 (t) REVERT: A 56 GLU cc_start: 0.7874 (pt0) cc_final: 0.7356 (pt0) REVERT: A 74 VAL cc_start: 0.8461 (t) cc_final: 0.8115 (m) REVERT: A 75 GLN cc_start: 0.8399 (tm-30) cc_final: 0.8008 (tm-30) REVERT: A 85 PHE cc_start: 0.8934 (t80) cc_final: 0.8520 (t80) REVERT: A 125 PHE cc_start: 0.7866 (m-80) cc_final: 0.7600 (m-80) REVERT: A 127 LYS cc_start: 0.8577 (ttmm) cc_final: 0.8133 (ttmm) REVERT: A 134 LYS cc_start: 0.8022 (mmmm) cc_final: 0.7780 (mmmm) REVERT: A 142 MET cc_start: 0.7967 (mmm) cc_final: 0.7589 (tmm) REVERT: A 149 ASP cc_start: 0.7519 (p0) cc_final: 0.7102 (p0) REVERT: A 163 LYS cc_start: 0.8606 (tptt) cc_final: 0.8325 (tppt) REVERT: A 175 TYR cc_start: 0.8475 (p90) cc_final: 0.8166 (p90) REVERT: A 180 ARG cc_start: 0.7707 (mtm110) cc_final: 0.7474 (mtm110) REVERT: A 191 GLU cc_start: 0.7818 (mp0) cc_final: 0.7472 (mp0) REVERT: A 255 MET cc_start: 0.8252 (mmt) cc_final: 0.8006 (mmt) REVERT: A 277 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8027 (mm) REVERT: A 285 ARG cc_start: 0.8533 (tpp80) cc_final: 0.7782 (mmm-85) REVERT: A 289 ASP cc_start: 0.8042 (m-30) cc_final: 0.7562 (m-30) REVERT: A 295 ASN cc_start: 0.8751 (t0) cc_final: 0.8537 (t0) REVERT: A 307 LYS cc_start: 0.8573 (mmtt) cc_final: 0.8104 (mmmt) REVERT: A 320 LYS cc_start: 0.8802 (ttmm) cc_final: 0.8586 (ttmm) REVERT: A 321 MET cc_start: 0.8196 (ttp) cc_final: 0.7963 (ttm) REVERT: A 340 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7485 (mt-10) REVERT: A 349 LYS cc_start: 0.8264 (tttt) cc_final: 0.8022 (tttm) REVERT: A 375 PRO cc_start: 0.8385 (Cg_endo) cc_final: 0.8058 (Cg_exo) REVERT: A 376 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7839 (mmtm) REVERT: A 399 TYR cc_start: 0.7810 (m-80) cc_final: 0.6731 (m-80) REVERT: A 404 LYS cc_start: 0.8351 (tttm) cc_final: 0.8086 (tttm) REVERT: A 434 ARG cc_start: 0.8313 (mmm160) cc_final: 0.8072 (tpt90) REVERT: A 455 CYS cc_start: 0.8004 (m) cc_final: 0.7765 (m) REVERT: A 467 MET cc_start: 0.8072 (ttp) cc_final: 0.7689 (ttm) REVERT: A 476 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7164 (tm-30) REVERT: A 507 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7862 (tp) REVERT: A 527 MET cc_start: 0.8013 (mtm) cc_final: 0.7770 (mtp) REVERT: A 529 TYR cc_start: 0.8178 (m-80) cc_final: 0.7831 (m-80) REVERT: A 563 ARG cc_start: 0.8587 (ptm-80) cc_final: 0.8184 (ptt-90) REVERT: A 579 MET cc_start: 0.8053 (ttm) cc_final: 0.7724 (ttm) REVERT: A 599 GLU cc_start: 0.8046 (tt0) cc_final: 0.7756 (tt0) REVERT: A 630 LYS cc_start: 0.8440 (mttt) cc_final: 0.8143 (mttp) REVERT: A 632 LYS cc_start: 0.8390 (tptt) cc_final: 0.7894 (ttmm) REVERT: A 636 ILE cc_start: 0.8444 (tt) cc_final: 0.8066 (tp) REVERT: A 666 GLN cc_start: 0.8235 (mm-40) cc_final: 0.8015 (mm-40) REVERT: A 690 SER cc_start: 0.8127 (t) cc_final: 0.7752 (m) REVERT: A 704 THR cc_start: 0.8281 (p) cc_final: 0.7972 (t) REVERT: A 711 GLN cc_start: 0.8473 (tp40) cc_final: 0.8067 (tp40) REVERT: A 716 HIS cc_start: 0.8411 (m170) cc_final: 0.8026 (m170) REVERT: A 718 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: A 741 GLU cc_start: 0.8211 (tp30) cc_final: 0.7811 (tp30) REVERT: A 756 TYR cc_start: 0.7537 (t80) cc_final: 0.7044 (t80) REVERT: A 770 LYS cc_start: 0.8088 (mttp) cc_final: 0.7729 (mttp) REVERT: A 778 ASN cc_start: 0.8710 (m-40) cc_final: 0.8256 (m-40) REVERT: A 781 ASN cc_start: 0.8199 (t0) cc_final: 0.7694 (p0) REVERT: A 782 PHE cc_start: 0.8745 (m-80) cc_final: 0.8488 (m-80) REVERT: A 804 LYS cc_start: 0.8285 (mmtt) cc_final: 0.8004 (mmtt) REVERT: A 813 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7946 (mm-30) REVERT: A 818 ARG cc_start: 0.8068 (mtt90) cc_final: 0.7709 (mtt90) REVERT: A 819 ARG cc_start: 0.7316 (ttm-80) cc_final: 0.6894 (ttm110) REVERT: A 834 VAL cc_start: 0.8828 (t) cc_final: 0.8599 (p) REVERT: A 842 MET cc_start: 0.7967 (ttt) cc_final: 0.7595 (tpp) REVERT: A 851 ILE cc_start: 0.8734 (mt) cc_final: 0.8440 (mp) REVERT: A 863 LYS cc_start: 0.8482 (mmmm) cc_final: 0.7875 (mmmm) REVERT: A 925 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7391 (mmm) REVERT: A 932 LYS cc_start: 0.8605 (mtmm) cc_final: 0.8107 (mtmm) REVERT: A 954 ARG cc_start: 0.8432 (mmt180) cc_final: 0.8186 (mmm-85) outliers start: 17 outliers final: 12 residues processed: 316 average time/residue: 0.2667 time to fit residues: 108.1852 Evaluate side-chains 319 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 303 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 925 MET 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 6 optimal weight: 0.6980 chunk 33 optimal weight: 0.0770 chunk 49 optimal weight: 0.0770 chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3924 r_free = 0.3924 target = 0.148157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.121654 restraints weight = 12913.536| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.45 r_work: 0.3422 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.5780 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= 0.182 Angle : 0.618 9.735 12274 Z= 0.315 Chirality : 0.043 0.308 1332 Planarity : 0.004 0.057 1448 Dihedral : 17.662 138.853 1458 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.67 % Favored : 97.23 % Rotamer: Outliers : 2.39 % Allowed : 26.62 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.28), residues: 975 helix: 1.96 (0.25), residues: 443 sheet: 0.04 (0.38), residues: 171 loop : -0.22 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 241 HIS 0.004 0.000 HIS A 722 PHE 0.027 0.002 PHE A 986 TYR 0.025 0.001 TYR A 772 ARG 0.013 0.001 ARG A 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4282.36 seconds wall clock time: 76 minutes 47.82 seconds (4607.82 seconds total)