Starting phenix.real_space_refine on Sat Jun 7 07:48:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ywm_39638/06_2025/8ywm_39638.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ywm_39638/06_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_39638/06_2025/8ywm_39638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ywm_39638/06_2025/8ywm_39638.map" model { file = "/net/cci-nas-00/data/ceres_data/8ywm_39638/06_2025/8ywm_39638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ywm_39638/06_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-5710/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: 5.38, per 1000 atoms: 0.62 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: 2.40 Conformation dependent library (CDL) restraints added in 918.4 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: 3.12 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: 3.52 Time building geometry restraints manager: 2.80 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: 0.580 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.110 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.250 ------------------------------------------------------------------------------- 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= 0.189 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 Details of bonding type rmsd hydrogen bonds : bond 0.15361 ( 452) hydrogen bonds : angle 6.55321 ( 1274) covalent geometry : bond 0.00396 ( 8970) covalent geometry : angle 0.70869 (12274) *********************** 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 : 0.855 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: 0.2517 time to fit residues: 114.3448 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 : 0.841 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.127789 restraints weight = 12777.893| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.54 r_work: 0.3525 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 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= 0.139 Angle : 0.590 10.518 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 Details of bonding type rmsd hydrogen bonds : bond 0.04870 ( 452) hydrogen bonds : angle 4.30864 ( 1274) covalent geometry : bond 0.00310 ( 8970) covalent geometry : angle 0.58994 (12274) *********************** 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 : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8546 (tp40) cc_final: 0.8236 (tp-100) REVERT: A 41 GLU cc_start: 0.8039 (pt0) cc_final: 0.7597 (pt0) REVERT: A 54 SER cc_start: 0.8280 (m) cc_final: 0.7961 (p) REVERT: A 59 TYR cc_start: 0.8121 (m-10) cc_final: 0.7591 (m-80) REVERT: A 75 GLN cc_start: 0.8480 (tm-30) cc_final: 0.8172 (tm-30) REVERT: A 127 LYS cc_start: 0.8555 (ttmm) cc_final: 0.8244 (ttmm) REVERT: A 132 ARG cc_start: 0.7658 (ttt-90) cc_final: 0.7412 (ttt180) REVERT: A 134 LYS cc_start: 0.8062 (mmmm) cc_final: 0.7789 (mmmm) REVERT: A 149 ASP cc_start: 0.7493 (p0) cc_final: 0.6964 (p0) REVERT: A 163 LYS cc_start: 0.8487 (mmtm) cc_final: 0.8262 (mmtm) REVERT: A 180 ARG cc_start: 0.7747 (mtm110) cc_final: 0.7459 (mtm110) REVERT: A 191 GLU cc_start: 0.7666 (mp0) cc_final: 0.7345 (mp0) REVERT: A 207 VAL cc_start: 0.8335 (t) cc_final: 0.8073 (m) REVERT: A 237 MET cc_start: 0.7897 (ptt) cc_final: 0.7491 (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: 0.8279 (mmtt) cc_final: 0.8001 (mmtm) REVERT: A 397 LEU cc_start: 0.8440 (tp) cc_final: 0.8238 (tp) REVERT: A 399 TYR cc_start: 0.7832 (m-80) cc_final: 0.6839 (m-80) REVERT: A 476 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7225 (tm-30) REVERT: A 484 THR cc_start: 0.7831 (m) cc_final: 0.7504 (p) REVERT: A 507 LEU cc_start: 0.7915 (mt) cc_final: 0.7714 (mt) REVERT: A 513 THR cc_start: 0.7301 (t) cc_final: 0.6984 (p) REVERT: A 527 MET cc_start: 0.8145 (mtt) cc_final: 0.7898 (mtp) REVERT: A 530 ASN cc_start: 0.7981 (t0) cc_final: 0.7771 (t0) REVERT: A 549 LYS cc_start: 0.8513 (ptmt) cc_final: 0.8116 (ptmt) REVERT: A 579 MET cc_start: 0.7648 (ttm) cc_final: 0.7302 (ttm) REVERT: A 593 ARG cc_start: 0.8260 (ttt90) cc_final: 0.8046 (ttt90) REVERT: A 630 LYS cc_start: 0.8264 (mttt) cc_final: 0.8034 (mtpp) REVERT: A 632 LYS cc_start: 0.8200 (tptt) cc_final: 0.7839 (ttmm) REVERT: A 636 ILE cc_start: 0.8379 (tt) cc_final: 0.7976 (tp) REVERT: A 687 ASP cc_start: 0.7065 (t0) cc_final: 0.6808 (t0) REVERT: A 719 GLN cc_start: 0.8256 (tp40) cc_final: 0.8021 (tp40) REVERT: A 738 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8126 (mt-10) REVERT: A 794 ILE cc_start: 0.7499 (tp) cc_final: 0.7289 (tp) REVERT: A 810 ILE cc_start: 0.8640 (mt) cc_final: 0.8284 (tp) REVERT: A 824 ARG cc_start: 0.7017 (mtt-85) cc_final: 0.6739 (mtt-85) REVERT: A 829 GLU cc_start: 0.7291 (tp30) cc_final: 0.7050 (tp30) REVERT: A 839 VAL cc_start: 0.8500 (t) cc_final: 0.8281 (m) REVERT: A 842 MET cc_start: 0.7317 (ttt) cc_final: 0.6892 (tpp) REVERT: A 846 ASN cc_start: 0.7390 (p0) cc_final: 0.6763 (p0) REVERT: A 848 GLU cc_start: 0.7591 (mp0) cc_final: 0.7362 (mp0) REVERT: A 863 LYS cc_start: 0.7708 (mmmm) cc_final: 0.7456 (mmmm) REVERT: A 876 ARG cc_start: 0.7748 (ttm110) cc_final: 0.7485 (ttm110) REVERT: A 897 ARG cc_start: 0.7912 (mtp85) cc_final: 0.7597 (ttm-80) REVERT: A 900 TYR cc_start: 0.7899 (p90) cc_final: 0.7136 (p90) REVERT: A 924 LYS cc_start: 0.7949 (mttp) cc_final: 0.7310 (mttm) REVERT: A 947 TYR cc_start: 0.8187 (m-80) cc_final: 0.7958 (m-10) outliers start: 13 outliers final: 5 residues processed: 326 average time/residue: 0.2570 time to fit residues: 108.5814 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 : 0.870 ------------------------------------------------------------------------------- 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: 4.9990 chunk 84 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 chunk 70 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 78 optimal weight: 0.0270 chunk 36 optimal weight: 0.8980 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.151319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.125396 restraints weight = 12950.842| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.51 r_work: 0.3494 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8970 Z= 0.128 Angle : 0.561 8.578 12274 Z= 0.296 Chirality : 0.042 0.218 1332 Planarity : 0.004 0.038 1448 Dihedral : 18.157 136.620 1460 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.97 % Favored : 96.92 % Rotamer: Outliers : 2.50 % Allowed : 18.43 % Favored : 79.07 % 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: 1.04 (0.27), residues: 975 helix: 1.83 (0.24), residues: 444 sheet: 0.24 (0.38), residues: 164 loop : -0.47 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 325 HIS 0.004 0.001 HIS A 722 PHE 0.019 0.002 PHE A 85 TYR 0.021 0.001 TYR A 772 ARG 0.010 0.001 ARG A 824 Details of bonding type rmsd hydrogen bonds : bond 0.04101 ( 452) hydrogen bonds : angle 4.09202 ( 1274) covalent geometry : bond 0.00294 ( 8970) covalent geometry : angle 0.56074 (12274) *********************** 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 344 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 322 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 27 GLN cc_start: 0.8591 (tp40) cc_final: 0.8323 (tp-100) REVERT: A 41 GLU cc_start: 0.8070 (pt0) cc_final: 0.7691 (pt0) REVERT: A 54 SER cc_start: 0.8354 (m) cc_final: 0.7980 (t) REVERT: A 56 GLU cc_start: 0.7604 (pt0) cc_final: 0.7123 (pt0) REVERT: A 59 TYR cc_start: 0.8243 (m-10) cc_final: 0.7925 (m-80) REVERT: A 62 GLU cc_start: 0.7631 (tt0) cc_final: 0.7360 (tt0) REVERT: A 75 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8195 (tm-30) REVERT: A 85 PHE cc_start: 0.8870 (t80) cc_final: 0.8412 (t80) REVERT: A 116 LYS cc_start: 0.8529 (mttm) cc_final: 0.8061 (mtmm) REVERT: A 126 PHE cc_start: 0.8175 (m-10) cc_final: 0.7806 (m-10) REVERT: A 127 LYS cc_start: 0.8560 (ttmm) cc_final: 0.8137 (ttmm) REVERT: A 134 LYS cc_start: 0.8091 (mmmm) cc_final: 0.7768 (mmmm) REVERT: A 137 THR cc_start: 0.8409 (m) cc_final: 0.8182 (m) REVERT: A 138 TYR cc_start: 0.8488 (t80) cc_final: 0.8181 (t80) REVERT: A 142 MET cc_start: 0.7838 (mmm) cc_final: 0.7618 (tmm) REVERT: A 149 ASP cc_start: 0.7551 (p0) cc_final: 0.6932 (p0) REVERT: A 180 ARG cc_start: 0.7735 (mtm110) cc_final: 0.7318 (mtm110) REVERT: A 191 GLU cc_start: 0.7725 (mp0) cc_final: 0.7341 (mp0) REVERT: A 307 LYS cc_start: 0.8389 (mmtt) cc_final: 0.7654 (mmmt) REVERT: A 321 MET cc_start: 0.8365 (ttp) cc_final: 0.8105 (ttm) REVERT: A 334 LYS cc_start: 0.8411 (tppp) cc_final: 0.7993 (tppp) REVERT: A 349 LYS cc_start: 0.8258 (tttt) cc_final: 0.8017 (mttm) REVERT: A 376 LYS cc_start: 0.8273 (mmtt) cc_final: 0.8010 (mmtm) REVERT: A 399 TYR cc_start: 0.7867 (m-80) cc_final: 0.6814 (m-80) REVERT: A 424 ASP cc_start: 0.8191 (t0) cc_final: 0.7715 (t0) REVERT: A 433 VAL cc_start: 0.8295 (t) cc_final: 0.8089 (p) REVERT: A 434 ARG cc_start: 0.8203 (mmm160) cc_final: 0.7985 (mmm160) REVERT: A 455 CYS cc_start: 0.7843 (m) cc_final: 0.7618 (m) REVERT: A 469 ILE cc_start: 0.8643 (mt) cc_final: 0.8227 (tt) REVERT: A 476 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7343 (tm-30) REVERT: A 482 CYS cc_start: 0.6818 (p) cc_final: 0.6469 (p) REVERT: A 484 THR cc_start: 0.7792 (m) cc_final: 0.7475 (p) REVERT: A 511 LYS cc_start: 0.8172 (ptpp) cc_final: 0.7537 (ptpp) REVERT: A 513 THR cc_start: 0.7699 (t) cc_final: 0.7421 (p) REVERT: A 527 MET cc_start: 0.8156 (mtt) cc_final: 0.7918 (mtp) REVERT: A 530 ASN cc_start: 0.8189 (t0) cc_final: 0.7928 (t0) REVERT: A 579 MET cc_start: 0.7889 (ttm) cc_final: 0.7551 (ttm) REVERT: A 597 LYS cc_start: 0.8035 (mmtm) cc_final: 0.7780 (tppp) REVERT: A 630 LYS cc_start: 0.8346 (mttt) cc_final: 0.8072 (mttp) REVERT: A 632 LYS cc_start: 0.8252 (tptt) cc_final: 0.7770 (ttmm) REVERT: A 636 ILE cc_start: 0.8412 (tt) cc_final: 0.8139 (tt) REVERT: A 644 GLU cc_start: 0.7384 (tp30) cc_final: 0.6796 (tp30) REVERT: A 647 ASN cc_start: 0.8162 (t0) cc_final: 0.7844 (t0) REVERT: A 672 VAL cc_start: 0.8663 (t) cc_final: 0.8448 (t) REVERT: A 678 ASN cc_start: 0.8532 (m-40) cc_final: 0.8265 (m-40) REVERT: A 687 ASP cc_start: 0.7249 (t0) cc_final: 0.6958 (t0) REVERT: A 719 GLN cc_start: 0.8376 (tp40) cc_final: 0.7985 (tp-100) REVERT: A 721 CYS cc_start: 0.7837 (m) cc_final: 0.7328 (m) REVERT: A 804 LYS cc_start: 0.8180 (mmtt) cc_final: 0.7906 (mmtt) REVERT: A 810 ILE cc_start: 0.8663 (mt) cc_final: 0.8382 (tp) REVERT: A 829 GLU cc_start: 0.7831 (tp30) cc_final: 0.7339 (tp30) REVERT: A 859 ASP cc_start: 0.7367 (p0) cc_final: 0.7051 (p0) REVERT: A 863 LYS cc_start: 0.7805 (mmmm) cc_final: 0.7440 (mmmm) REVERT: A 897 ARG cc_start: 0.8016 (mtp85) cc_final: 0.7755 (ttm-80) REVERT: A 900 TYR cc_start: 0.7953 (p90) cc_final: 0.7289 (p90) REVERT: A 924 LYS cc_start: 0.7963 (mttp) cc_final: 0.7278 (mttm) REVERT: A 947 TYR cc_start: 0.8272 (m-80) cc_final: 0.8050 (m-10) outliers start: 22 outliers final: 13 residues processed: 326 average time/residue: 0.2592 time to fit residues: 109.5156 Evaluate side-chains 322 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 309 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 494 LYS Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 800 THR 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: 0.9980 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 40 optimal weight: 0.0980 chunk 73 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.150310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.124307 restraints weight = 12806.970| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.46 r_work: 0.3465 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3991 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= 0.127 Angle : 0.547 9.574 12274 Z= 0.287 Chirality : 0.041 0.235 1332 Planarity : 0.004 0.068 1448 Dihedral : 18.105 136.402 1460 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.87 % Favored : 97.03 % Rotamer: Outliers : 1.71 % Allowed : 22.53 % Favored : 75.77 % 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: 1.27 (0.28), residues: 975 helix: 2.04 (0.25), residues: 443 sheet: 0.16 (0.37), residues: 171 loop : -0.26 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 325 HIS 0.004 0.001 HIS A 474 PHE 0.030 0.002 PHE A 72 TYR 0.017 0.001 TYR A 772 ARG 0.011 0.001 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 452) hydrogen bonds : angle 4.02530 ( 1274) covalent geometry : bond 0.00290 ( 8970) covalent geometry : angle 0.54735 (12274) *********************** 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 347 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 332 time to evaluate : 0.841 Fit side-chains REVERT: A 27 GLN cc_start: 0.8568 (tp40) cc_final: 0.8295 (tp-100) REVERT: A 41 GLU cc_start: 0.8060 (pt0) cc_final: 0.7680 (pt0) REVERT: A 54 SER cc_start: 0.8360 (m) cc_final: 0.8074 (t) REVERT: A 56 GLU cc_start: 0.7684 (pt0) cc_final: 0.7132 (pt0) REVERT: A 62 GLU cc_start: 0.7591 (tt0) cc_final: 0.7318 (tt0) REVERT: A 75 GLN cc_start: 0.8467 (tm-30) cc_final: 0.7828 (tm-30) REVERT: A 85 PHE cc_start: 0.8897 (t80) cc_final: 0.8465 (t80) REVERT: A 126 PHE cc_start: 0.8210 (m-10) cc_final: 0.7924 (m-10) REVERT: A 127 LYS cc_start: 0.8611 (ttmm) cc_final: 0.8190 (ttmm) REVERT: A 134 LYS cc_start: 0.8101 (mmmm) cc_final: 0.7818 (mmmm) REVERT: A 142 MET cc_start: 0.7889 (mmm) cc_final: 0.7634 (tmm) REVERT: A 149 ASP cc_start: 0.7597 (p0) cc_final: 0.7172 (p0) REVERT: A 180 ARG cc_start: 0.7720 (mtm110) cc_final: 0.7390 (mtm110) REVERT: A 191 GLU cc_start: 0.7741 (mp0) cc_final: 0.7360 (mp0) REVERT: A 255 MET cc_start: 0.8187 (mmt) cc_final: 0.7752 (mmt) REVERT: A 285 ARG cc_start: 0.8459 (tpp80) cc_final: 0.7830 (mmm-85) REVERT: A 289 ASP cc_start: 0.7741 (m-30) cc_final: 0.7400 (m-30) REVERT: A 307 LYS cc_start: 0.8482 (mmtt) cc_final: 0.7872 (mmmt) REVERT: A 321 MET cc_start: 0.8257 (ttp) cc_final: 0.8023 (ttm) REVERT: A 334 LYS cc_start: 0.8441 (tppp) cc_final: 0.8036 (tppp) REVERT: A 349 LYS cc_start: 0.8285 (tttt) cc_final: 0.8068 (tttm) REVERT: A 375 PRO cc_start: 0.8446 (Cg_endo) cc_final: 0.8137 (Cg_exo) REVERT: A 376 LYS cc_start: 0.8290 (mmtt) cc_final: 0.7984 (mmtm) REVERT: A 395 VAL cc_start: 0.7353 (m) cc_final: 0.6991 (p) REVERT: A 399 TYR cc_start: 0.7854 (m-80) cc_final: 0.6962 (m-80) REVERT: A 404 LYS cc_start: 0.8207 (tttm) cc_final: 0.7922 (tttm) REVERT: A 424 ASP cc_start: 0.8159 (t0) cc_final: 0.7780 (t0) REVERT: A 433 VAL cc_start: 0.8374 (t) cc_final: 0.8159 (p) REVERT: A 434 ARG cc_start: 0.8264 (mmm160) cc_final: 0.7917 (tpt90) REVERT: A 476 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7233 (tm-30) REVERT: A 511 LYS cc_start: 0.8563 (ptpp) cc_final: 0.8014 (ptpp) REVERT: A 513 THR cc_start: 0.7889 (t) cc_final: 0.7684 (p) REVERT: A 527 MET cc_start: 0.8176 (mtt) cc_final: 0.7969 (mtm) REVERT: A 530 ASN cc_start: 0.8335 (t0) cc_final: 0.8064 (t0) REVERT: A 579 MET cc_start: 0.7912 (ttm) cc_final: 0.7590 (ttm) REVERT: A 597 LYS cc_start: 0.8087 (mmtm) cc_final: 0.7767 (tppp) REVERT: A 630 LYS cc_start: 0.8372 (mttt) cc_final: 0.8087 (mttp) REVERT: A 632 LYS cc_start: 0.8230 (tptt) cc_final: 0.7718 (ttmm) REVERT: A 636 ILE cc_start: 0.8444 (tt) cc_final: 0.8217 (tt) REVERT: A 637 PHE cc_start: 0.7796 (m-80) cc_final: 0.7045 (t80) REVERT: A 644 GLU cc_start: 0.7532 (tp30) cc_final: 0.7019 (tp30) REVERT: A 647 ASN cc_start: 0.8278 (t0) cc_final: 0.7953 (t0) REVERT: A 678 ASN cc_start: 0.8413 (m-40) cc_final: 0.8121 (m-40) REVERT: A 687 ASP cc_start: 0.7212 (t0) cc_final: 0.6997 (t0) REVERT: A 690 SER cc_start: 0.8095 (t) cc_final: 0.7700 (m) REVERT: A 719 GLN cc_start: 0.8281 (tp40) cc_final: 0.7825 (tp-100) REVERT: A 721 CYS cc_start: 0.7861 (m) cc_final: 0.7387 (m) REVERT: A 739 VAL cc_start: 0.8940 (t) cc_final: 0.8689 (p) REVERT: A 778 ASN cc_start: 0.8694 (m-40) cc_final: 0.8293 (m-40) REVERT: A 801 LYS cc_start: 0.7504 (ptmm) cc_final: 0.7238 (ptmm) REVERT: A 804 LYS cc_start: 0.8202 (mmtt) cc_final: 0.7933 (mmtt) REVERT: A 810 ILE cc_start: 0.8628 (mt) cc_final: 0.8371 (tp) REVERT: A 813 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7803 (mm-30) REVERT: A 829 GLU cc_start: 0.8015 (tp30) cc_final: 0.7782 (tm-30) REVERT: A 842 MET cc_start: 0.7471 (ttt) cc_final: 0.7194 (tpp) REVERT: A 847 PHE cc_start: 0.8434 (t80) cc_final: 0.7953 (t80) REVERT: A 863 LYS cc_start: 0.7995 (mmmm) cc_final: 0.7456 (mmmm) REVERT: A 867 ILE cc_start: 0.7743 (mm) cc_final: 0.7512 (mm) REVERT: A 893 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6776 (mm-30) REVERT: A 897 ARG cc_start: 0.8116 (mtp85) cc_final: 0.7811 (ttm-80) REVERT: A 900 TYR cc_start: 0.7991 (p90) cc_final: 0.7245 (p90) REVERT: A 924 LYS cc_start: 0.8006 (mttp) cc_final: 0.7210 (mttm) REVERT: A 946 ASN cc_start: 0.8414 (m110) cc_final: 0.8099 (m110) REVERT: A 978 ARG cc_start: 0.8265 (mtt180) cc_final: 0.8007 (mtt180) outliers start: 15 outliers final: 9 residues processed: 337 average time/residue: 0.2478 time to fit residues: 108.3483 Evaluate side-chains 323 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 314 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 676 VAL 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: 4.9990 chunk 66 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 37 optimal weight: 0.0670 chunk 46 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.149437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.122661 restraints weight = 12861.560| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.50 r_work: 0.3436 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8970 Z= 0.136 Angle : 0.567 9.938 12274 Z= 0.296 Chirality : 0.042 0.242 1332 Planarity : 0.004 0.044 1448 Dihedral : 17.903 137.083 1460 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.97 % Favored : 96.92 % Rotamer: Outliers : 2.39 % Allowed : 23.21 % Favored : 74.40 % 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: 1.27 (0.28), residues: 975 helix: 2.02 (0.25), residues: 445 sheet: 0.17 (0.38), residues: 166 loop : -0.26 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 325 HIS 0.004 0.001 HIS A 722 PHE 0.024 0.002 PHE A 72 TYR 0.032 0.001 TYR A 772 ARG 0.006 0.000 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 452) hydrogen bonds : angle 4.00579 ( 1274) covalent geometry : bond 0.00308 ( 8970) covalent geometry : angle 0.56727 (12274) *********************** 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 344 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 323 time to evaluate : 0.911 Fit side-chains REVERT: A 5 MET cc_start: 0.7383 (ttp) cc_final: 0.7149 (ttp) REVERT: A 23 THR cc_start: 0.8753 (t) cc_final: 0.8437 (p) REVERT: A 27 GLN cc_start: 0.8621 (tp40) cc_final: 0.8193 (tp-100) REVERT: A 41 GLU cc_start: 0.7965 (pt0) cc_final: 0.7635 (pt0) REVERT: A 54 SER cc_start: 0.8401 (m) cc_final: 0.8086 (p) REVERT: A 62 GLU cc_start: 0.7689 (tt0) cc_final: 0.7219 (tt0) REVERT: A 75 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8047 (tm-30) REVERT: A 85 PHE cc_start: 0.8939 (t80) cc_final: 0.8513 (t80) REVERT: A 127 LYS cc_start: 0.8619 (ttmm) cc_final: 0.8186 (ttmm) REVERT: A 134 LYS cc_start: 0.8123 (mmmm) cc_final: 0.7840 (mmmm) REVERT: A 142 MET cc_start: 0.7976 (mmm) cc_final: 0.7750 (tmm) REVERT: A 149 ASP cc_start: 0.7563 (p0) cc_final: 0.7140 (p0) REVERT: A 163 LYS cc_start: 0.8528 (tptt) cc_final: 0.8121 (mptt) REVERT: A 180 ARG cc_start: 0.7729 (mtm110) cc_final: 0.5616 (mtm110) REVERT: A 191 GLU cc_start: 0.7724 (mp0) cc_final: 0.7379 (mp0) REVERT: A 277 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8105 (mm) REVERT: A 285 ARG cc_start: 0.8500 (tpp80) cc_final: 0.7828 (mmm-85) REVERT: A 289 ASP cc_start: 0.7859 (m-30) cc_final: 0.7517 (m-30) REVERT: A 307 LYS cc_start: 0.8490 (mmtt) cc_final: 0.7908 (mmmt) REVERT: A 321 MET cc_start: 0.8326 (ttp) cc_final: 0.8069 (ttm) REVERT: A 349 LYS cc_start: 0.8316 (tttt) cc_final: 0.8080 (tttm) REVERT: A 369 MET cc_start: 0.7998 (mmp) cc_final: 0.7769 (mmt) REVERT: A 375 PRO cc_start: 0.8444 (Cg_endo) cc_final: 0.8133 (Cg_exo) REVERT: A 376 LYS cc_start: 0.8292 (mmtt) cc_final: 0.7986 (mmtm) REVERT: A 395 VAL cc_start: 0.7480 (m) cc_final: 0.7112 (p) REVERT: A 399 TYR cc_start: 0.7917 (m-80) cc_final: 0.7009 (m-80) REVERT: A 404 LYS cc_start: 0.8262 (tttm) cc_final: 0.7979 (tttm) REVERT: A 417 VAL cc_start: 0.8500 (t) cc_final: 0.8300 (t) REVERT: A 424 ASP cc_start: 0.8205 (t0) cc_final: 0.7780 (t0) REVERT: A 433 VAL cc_start: 0.8432 (t) cc_final: 0.8231 (p) REVERT: A 434 ARG cc_start: 0.8287 (mmm160) cc_final: 0.8020 (tpt90) REVERT: A 476 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7235 (tm-30) REVERT: A 510 ASP cc_start: 0.7990 (m-30) cc_final: 0.7706 (t0) REVERT: A 511 LYS cc_start: 0.8600 (ptpp) cc_final: 0.8132 (ptpp) REVERT: A 530 ASN cc_start: 0.8414 (t0) cc_final: 0.8188 (t0) REVERT: A 547 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7726 (tpp) REVERT: A 566 GLU cc_start: 0.8009 (pt0) cc_final: 0.7786 (pt0) REVERT: A 579 MET cc_start: 0.7990 (ttm) cc_final: 0.7675 (ttm) REVERT: A 597 LYS cc_start: 0.8128 (mmtm) cc_final: 0.7544 (tppp) REVERT: A 630 LYS cc_start: 0.8390 (mttt) cc_final: 0.8057 (mttp) REVERT: A 632 LYS cc_start: 0.8295 (tptt) cc_final: 0.7779 (ttmm) REVERT: A 636 ILE cc_start: 0.8495 (tt) cc_final: 0.8216 (tt) REVERT: A 647 ASN cc_start: 0.8339 (t0) cc_final: 0.8004 (t0) REVERT: A 678 ASN cc_start: 0.8436 (m-40) cc_final: 0.8184 (m-40) REVERT: A 690 SER cc_start: 0.8039 (t) cc_final: 0.7619 (m) REVERT: A 694 THR cc_start: 0.8405 (t) cc_final: 0.8198 (p) REVERT: A 709 ASN cc_start: 0.8535 (m-40) cc_final: 0.8299 (m-40) REVERT: A 719 GLN cc_start: 0.8311 (tp40) cc_final: 0.8086 (tp-100) REVERT: A 721 CYS cc_start: 0.8045 (m) cc_final: 0.7579 (m) REVERT: A 742 TYR cc_start: 0.8952 (t80) cc_final: 0.8723 (t80) REVERT: A 778 ASN cc_start: 0.8779 (m-40) cc_final: 0.8354 (m-40) REVERT: A 800 THR cc_start: 0.7727 (p) cc_final: 0.7524 (m) REVERT: A 801 LYS cc_start: 0.7548 (ptmm) cc_final: 0.7287 (ptpp) REVERT: A 804 LYS cc_start: 0.8222 (mmtt) cc_final: 0.7956 (mmtt) REVERT: A 810 ILE cc_start: 0.8596 (mt) cc_final: 0.8390 (tt) REVERT: A 813 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7976 (mm-30) REVERT: A 819 ARG cc_start: 0.6771 (ttm-80) cc_final: 0.6454 (ttm-80) REVERT: A 828 ILE cc_start: 0.8443 (pt) cc_final: 0.8160 (mt) REVERT: A 829 GLU cc_start: 0.8181 (tp30) cc_final: 0.7790 (tm-30) REVERT: A 842 MET cc_start: 0.7603 (ttt) cc_final: 0.7372 (tpp) REVERT: A 847 PHE cc_start: 0.8349 (t80) cc_final: 0.8020 (t80) REVERT: A 863 LYS cc_start: 0.8112 (mmmm) cc_final: 0.7808 (mmmm) REVERT: A 867 ILE cc_start: 0.7809 (mm) cc_final: 0.7447 (mm) REVERT: A 893 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6809 (mm-30) REVERT: A 897 ARG cc_start: 0.8209 (mtp85) cc_final: 0.7911 (ttm-80) REVERT: A 900 TYR cc_start: 0.7980 (p90) cc_final: 0.7266 (p90) REVERT: A 924 LYS cc_start: 0.8074 (mttp) cc_final: 0.7337 (mtpp) REVERT: A 932 LYS cc_start: 0.8706 (mmtt) cc_final: 0.8506 (mmtt) REVERT: A 946 ASN cc_start: 0.8460 (m110) cc_final: 0.8192 (m110) REVERT: A 978 ARG cc_start: 0.8294 (mtt180) cc_final: 0.7868 (mtt180) outliers start: 21 outliers final: 11 residues processed: 331 average time/residue: 0.2696 time to fit residues: 114.6149 Evaluate side-chains 327 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 314 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 927 TYR 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: 0.9990 chunk 76 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** 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 = 0.147063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.119831 restraints weight = 12686.053| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.48 r_work: 0.3404 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4892 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= 0.153 Angle : 0.585 9.965 12274 Z= 0.305 Chirality : 0.042 0.243 1332 Planarity : 0.004 0.045 1448 Dihedral : 17.814 137.514 1460 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.49 % Favored : 96.41 % Rotamer: Outliers : 2.16 % Allowed : 24.35 % Favored : 73.49 % 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: 1.36 (0.28), residues: 975 helix: 2.14 (0.25), residues: 444 sheet: 0.21 (0.38), residues: 161 loop : -0.26 (0.35), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 325 HIS 0.005 0.001 HIS A 722 PHE 0.026 0.002 PHE A 126 TYR 0.028 0.001 TYR A 772 ARG 0.007 0.001 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 452) hydrogen bonds : angle 4.00850 ( 1274) covalent geometry : bond 0.00348 ( 8970) covalent geometry : angle 0.58464 (12274) *********************** 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 344 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 325 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 18 ILE cc_start: 0.8800 (mm) cc_final: 0.8580 (mm) REVERT: A 19 THR cc_start: 0.8474 (p) cc_final: 0.8214 (t) REVERT: A 22 VAL cc_start: 0.8676 (t) cc_final: 0.8435 (t) REVERT: A 23 THR cc_start: 0.8787 (t) cc_final: 0.8469 (p) REVERT: A 27 GLN cc_start: 0.8574 (tp40) cc_final: 0.8153 (tp-100) REVERT: A 41 GLU cc_start: 0.7955 (pt0) cc_final: 0.7623 (pt0) REVERT: A 54 SER cc_start: 0.8480 (m) cc_final: 0.8150 (p) REVERT: A 56 GLU cc_start: 0.7656 (pt0) cc_final: 0.7126 (pt0) REVERT: A 62 GLU cc_start: 0.7412 (tt0) cc_final: 0.7185 (tt0) REVERT: A 75 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8043 (tm-30) REVERT: A 85 PHE cc_start: 0.8963 (t80) cc_final: 0.8523 (t80) REVERT: A 127 LYS cc_start: 0.8579 (ttmm) cc_final: 0.8140 (ttmm) REVERT: A 134 LYS cc_start: 0.8106 (mmmm) cc_final: 0.7819 (mmmm) REVERT: A 142 MET cc_start: 0.8042 (mmm) cc_final: 0.7685 (tmm) REVERT: A 149 ASP cc_start: 0.7573 (p0) cc_final: 0.7162 (p0) REVERT: A 174 HIS cc_start: 0.7627 (t-90) cc_final: 0.7363 (t-90) REVERT: A 191 GLU cc_start: 0.7776 (mp0) cc_final: 0.7409 (mp0) REVERT: A 255 MET cc_start: 0.8290 (mmt) cc_final: 0.7759 (mmt) REVERT: A 285 ARG cc_start: 0.8510 (tpp80) cc_final: 0.7835 (mmm-85) REVERT: A 289 ASP cc_start: 0.7987 (m-30) cc_final: 0.7630 (m-30) REVERT: A 307 LYS cc_start: 0.8531 (mmtt) cc_final: 0.7956 (mmmt) REVERT: A 321 MET cc_start: 0.8314 (ttp) cc_final: 0.8054 (ttm) REVERT: A 349 LYS cc_start: 0.8368 (tttt) cc_final: 0.8109 (tttm) REVERT: A 369 MET cc_start: 0.7992 (mmp) cc_final: 0.7775 (mmt) REVERT: A 375 PRO cc_start: 0.8475 (Cg_endo) cc_final: 0.8161 (Cg_exo) REVERT: A 376 LYS cc_start: 0.8308 (mmtt) cc_final: 0.7986 (mmtm) REVERT: A 395 VAL cc_start: 0.7737 (m) cc_final: 0.7387 (p) REVERT: A 399 TYR cc_start: 0.7918 (m-80) cc_final: 0.6911 (m-80) REVERT: A 404 LYS cc_start: 0.8338 (tttm) cc_final: 0.8062 (tttm) REVERT: A 433 VAL cc_start: 0.8474 (t) cc_final: 0.8272 (p) REVERT: A 434 ARG cc_start: 0.8307 (mmm160) cc_final: 0.8053 (tpt90) REVERT: A 467 MET cc_start: 0.8090 (ttp) cc_final: 0.7807 (ttt) REVERT: A 476 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7211 (tm-30) REVERT: A 511 LYS cc_start: 0.8700 (ptpp) cc_final: 0.8487 (pttm) REVERT: A 547 MET cc_start: 0.7880 (tpp) cc_final: 0.7663 (tpp) REVERT: A 566 GLU cc_start: 0.8069 (pt0) cc_final: 0.7852 (pt0) REVERT: A 579 MET cc_start: 0.8079 (ttm) cc_final: 0.7762 (ttm) REVERT: A 632 LYS cc_start: 0.8287 (tptt) cc_final: 0.7778 (ttmm) REVERT: A 636 ILE cc_start: 0.8501 (tt) cc_final: 0.8230 (tt) REVERT: A 676 VAL cc_start: 0.8246 (t) cc_final: 0.7985 (m) REVERT: A 678 ASN cc_start: 0.8517 (m-40) cc_final: 0.8291 (m-40) REVERT: A 690 SER cc_start: 0.8071 (t) cc_final: 0.7726 (m) REVERT: A 709 ASN cc_start: 0.8618 (m-40) cc_final: 0.8362 (m-40) REVERT: A 711 GLN cc_start: 0.8242 (tp40) cc_final: 0.7833 (tp40) REVERT: A 719 GLN cc_start: 0.8390 (tp40) cc_final: 0.8129 (tp-100) REVERT: A 721 CYS cc_start: 0.8240 (m) cc_final: 0.7832 (m) REVERT: A 742 TYR cc_start: 0.8942 (t80) cc_final: 0.8692 (t80) REVERT: A 778 ASN cc_start: 0.8790 (m-40) cc_final: 0.8391 (m-40) REVERT: A 801 LYS cc_start: 0.7476 (ptmm) cc_final: 0.7215 (ptmm) REVERT: A 804 LYS cc_start: 0.8212 (mmtt) cc_final: 0.7967 (mmtt) REVERT: A 816 LYS cc_start: 0.8637 (ptpp) cc_final: 0.8219 (ptpp) REVERT: A 818 ARG cc_start: 0.7929 (mtt90) cc_final: 0.7673 (mtt90) REVERT: A 819 ARG cc_start: 0.7041 (ttm-80) cc_final: 0.6707 (ttm-80) REVERT: A 828 ILE cc_start: 0.8538 (pt) cc_final: 0.8324 (mt) REVERT: A 842 MET cc_start: 0.7698 (ttt) cc_final: 0.7405 (tpp) REVERT: A 847 PHE cc_start: 0.8453 (t80) cc_final: 0.8064 (t80) REVERT: A 863 LYS cc_start: 0.8218 (mmmm) cc_final: 0.7922 (mmmm) REVERT: A 900 TYR cc_start: 0.8008 (p90) cc_final: 0.7381 (p90) REVERT: A 924 LYS cc_start: 0.8037 (mttp) cc_final: 0.7535 (mttm) REVERT: A 946 ASN cc_start: 0.8578 (m110) cc_final: 0.8224 (m110) REVERT: A 954 ARG cc_start: 0.8211 (mmt180) cc_final: 0.8002 (mmm-85) REVERT: A 978 ARG cc_start: 0.8327 (mtt180) cc_final: 0.8070 (mtt180) outliers start: 19 outliers final: 13 residues processed: 333 average time/residue: 0.2733 time to fit residues: 117.7296 Evaluate side-chains 329 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 316 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 254 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 952 CYS 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: 0.2980 chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 63 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 49 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.148873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.121931 restraints weight = 12905.492| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.51 r_work: 0.3419 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.5126 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= 0.129 Angle : 0.572 8.679 12274 Z= 0.298 Chirality : 0.041 0.239 1332 Planarity : 0.004 0.046 1448 Dihedral : 17.796 137.886 1458 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.18 % Favored : 96.72 % Rotamer: Outliers : 2.62 % Allowed : 24.46 % 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: 1.25 (0.28), residues: 975 helix: 2.07 (0.24), residues: 445 sheet: 0.06 (0.37), residues: 160 loop : -0.30 (0.35), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 325 HIS 0.005 0.001 HIS A 722 PHE 0.025 0.002 PHE A 986 TYR 0.021 0.001 TYR A 772 ARG 0.007 0.001 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 452) hydrogen bonds : angle 3.97562 ( 1274) covalent geometry : bond 0.00298 ( 8970) covalent geometry : angle 0.57171 (12274) *********************** 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 343 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 320 time to evaluate : 0.883 Fit side-chains REVERT: A 9 GLU cc_start: 0.7804 (tt0) cc_final: 0.7286 (tt0) REVERT: A 18 ILE cc_start: 0.8794 (mm) cc_final: 0.8541 (mm) REVERT: A 19 THR cc_start: 0.8494 (p) cc_final: 0.8198 (t) REVERT: A 22 VAL cc_start: 0.8718 (t) cc_final: 0.8479 (t) REVERT: A 23 THR cc_start: 0.8790 (t) cc_final: 0.8471 (p) REVERT: A 27 GLN cc_start: 0.8586 (tp40) cc_final: 0.8153 (tp-100) REVERT: A 41 GLU cc_start: 0.7964 (pt0) cc_final: 0.7618 (pt0) REVERT: A 54 SER cc_start: 0.8463 (m) cc_final: 0.8158 (p) REVERT: A 66 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7707 (mt-10) REVERT: A 74 VAL cc_start: 0.8544 (t) cc_final: 0.8180 (m) REVERT: A 75 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8008 (tm-30) REVERT: A 85 PHE cc_start: 0.8935 (t80) cc_final: 0.8498 (t80) REVERT: A 87 LYS cc_start: 0.8826 (mmmt) cc_final: 0.8600 (mmmt) REVERT: A 126 PHE cc_start: 0.7865 (m-10) cc_final: 0.7644 (m-10) REVERT: A 127 LYS cc_start: 0.8582 (ttmm) cc_final: 0.8160 (ttmm) REVERT: A 134 LYS cc_start: 0.8043 (mmmm) cc_final: 0.7764 (mmmm) REVERT: A 142 MET cc_start: 0.8012 (mmm) cc_final: 0.7706 (tmm) REVERT: A 149 ASP cc_start: 0.7561 (p0) cc_final: 0.7162 (p0) REVERT: A 191 GLU cc_start: 0.7799 (mp0) cc_final: 0.7430 (mp0) REVERT: A 255 MET cc_start: 0.8296 (mmt) cc_final: 0.7837 (mmt) REVERT: A 277 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8062 (mm) REVERT: A 285 ARG cc_start: 0.8508 (tpp80) cc_final: 0.7822 (mmm-85) REVERT: A 289 ASP cc_start: 0.8004 (m-30) cc_final: 0.7554 (m-30) REVERT: A 307 LYS cc_start: 0.8510 (mmtt) cc_final: 0.7966 (mmmt) REVERT: A 321 MET cc_start: 0.8210 (ttp) cc_final: 0.7974 (ttm) REVERT: A 349 LYS cc_start: 0.8307 (tttt) cc_final: 0.8095 (tttm) REVERT: A 369 MET cc_start: 0.7901 (mmp) cc_final: 0.7670 (mmt) REVERT: A 375 PRO cc_start: 0.8438 (Cg_endo) cc_final: 0.8109 (Cg_exo) REVERT: A 376 LYS cc_start: 0.8298 (mmtt) cc_final: 0.7975 (mmtm) REVERT: A 395 VAL cc_start: 0.7733 (m) cc_final: 0.7352 (p) REVERT: A 399 TYR cc_start: 0.7893 (m-80) cc_final: 0.6877 (m-80) REVERT: A 404 LYS cc_start: 0.8343 (tttm) cc_final: 0.8054 (tttm) REVERT: A 434 ARG cc_start: 0.8267 (mmm160) cc_final: 0.8010 (tpt90) REVERT: A 467 MET cc_start: 0.8072 (ttp) cc_final: 0.7724 (ttm) REVERT: A 475 ASP cc_start: 0.7701 (t0) cc_final: 0.7487 (t0) REVERT: A 476 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7422 (tm-30) REVERT: A 511 LYS cc_start: 0.8645 (ptpp) cc_final: 0.8399 (ptpp) REVERT: A 527 MET cc_start: 0.7960 (mtm) cc_final: 0.7726 (mtp) REVERT: A 547 MET cc_start: 0.7878 (tpp) cc_final: 0.7355 (mmm) REVERT: A 579 MET cc_start: 0.8042 (ttm) cc_final: 0.7718 (ttm) REVERT: A 630 LYS cc_start: 0.8400 (mttt) cc_final: 0.8109 (mttp) REVERT: A 632 LYS cc_start: 0.8302 (tptt) cc_final: 0.7792 (ttmm) REVERT: A 635 LYS cc_start: 0.8306 (ttpp) cc_final: 0.8074 (ttpp) REVERT: A 636 ILE cc_start: 0.8497 (tt) cc_final: 0.8196 (tt) REVERT: A 678 ASN cc_start: 0.8505 (m-40) cc_final: 0.8268 (m-40) REVERT: A 690 SER cc_start: 0.8077 (t) cc_final: 0.7696 (m) REVERT: A 711 GLN cc_start: 0.8245 (tp40) cc_final: 0.7823 (tp40) REVERT: A 719 GLN cc_start: 0.8368 (tp40) cc_final: 0.8122 (tp-100) REVERT: A 721 CYS cc_start: 0.8200 (m) cc_final: 0.7843 (m) REVERT: A 729 MET cc_start: 0.8168 (ttm) cc_final: 0.7917 (mtp) REVERT: A 742 TYR cc_start: 0.8925 (t80) cc_final: 0.8700 (t80) REVERT: A 756 TYR cc_start: 0.7335 (t80) cc_final: 0.7042 (t80) REVERT: A 778 ASN cc_start: 0.8794 (m-40) cc_final: 0.8304 (m-40) REVERT: A 801 LYS cc_start: 0.7322 (ptmm) cc_final: 0.7114 (ptpp) REVERT: A 804 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7972 (mmtt) REVERT: A 813 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7816 (mm-30) REVERT: A 816 LYS cc_start: 0.8649 (ptpp) cc_final: 0.7897 (ptpp) REVERT: A 819 ARG cc_start: 0.7088 (ttm-80) cc_final: 0.6791 (ttm-80) REVERT: A 828 ILE cc_start: 0.8549 (pt) cc_final: 0.8302 (mt) REVERT: A 842 MET cc_start: 0.7866 (ttt) cc_final: 0.7485 (tpp) REVERT: A 847 PHE cc_start: 0.8625 (t80) cc_final: 0.8139 (t80) REVERT: A 851 ILE cc_start: 0.8727 (mt) cc_final: 0.8490 (mp) REVERT: A 863 LYS cc_start: 0.8300 (mmmm) cc_final: 0.7891 (mmmm) REVERT: A 900 TYR cc_start: 0.7995 (p90) cc_final: 0.7214 (p90) REVERT: A 924 LYS cc_start: 0.8024 (mttp) cc_final: 0.7476 (mttm) REVERT: A 946 ASN cc_start: 0.8499 (m110) cc_final: 0.8157 (m110) REVERT: A 954 ARG cc_start: 0.8218 (mmt180) cc_final: 0.7959 (mmm-85) REVERT: A 978 ARG cc_start: 0.8363 (mtt180) cc_final: 0.8101 (mtt180) outliers start: 23 outliers final: 14 residues processed: 328 average time/residue: 0.2634 time to fit residues: 111.2162 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 : 0.848 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 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: 0.6980 chunk 0 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.147588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.121022 restraints weight = 12827.423| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.43 r_work: 0.3415 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.5364 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= 0.142 Angle : 0.592 11.417 12274 Z= 0.307 Chirality : 0.041 0.232 1332 Planarity : 0.004 0.042 1448 Dihedral : 17.783 138.339 1458 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.08 % Favored : 96.82 % Rotamer: Outliers : 2.16 % Allowed : 25.94 % 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: 1.18 (0.27), residues: 975 helix: 2.01 (0.24), residues: 444 sheet: 0.01 (0.37), residues: 161 loop : -0.32 (0.35), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 241 HIS 0.005 0.001 HIS A 722 PHE 0.024 0.002 PHE A 986 TYR 0.021 0.001 TYR A 772 ARG 0.008 0.001 ARG A 185 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 452) hydrogen bonds : angle 3.98943 ( 1274) covalent geometry : bond 0.00329 ( 8970) covalent geometry : angle 0.59157 (12274) *********************** 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 348 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 329 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7772 (tt0) cc_final: 0.7277 (tt0) REVERT: A 18 ILE cc_start: 0.8839 (mm) cc_final: 0.8592 (mm) REVERT: A 19 THR cc_start: 0.8514 (p) cc_final: 0.8230 (t) REVERT: A 22 VAL cc_start: 0.8749 (t) cc_final: 0.8492 (t) REVERT: A 23 THR cc_start: 0.8793 (t) cc_final: 0.8482 (p) REVERT: A 41 GLU cc_start: 0.7953 (pt0) cc_final: 0.7613 (pt0) REVERT: A 54 SER cc_start: 0.8491 (m) cc_final: 0.8163 (p) REVERT: A 56 GLU cc_start: 0.7637 (pt0) cc_final: 0.7111 (pt0) REVERT: A 66 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7742 (mt-10) REVERT: A 74 VAL cc_start: 0.8535 (t) cc_final: 0.8186 (m) REVERT: A 75 GLN cc_start: 0.8404 (tm-30) cc_final: 0.7970 (tm-30) REVERT: A 85 PHE cc_start: 0.8943 (t80) cc_final: 0.8517 (t80) REVERT: A 87 LYS cc_start: 0.8894 (mmmt) cc_final: 0.8610 (mmmt) REVERT: A 91 THR cc_start: 0.8523 (m) cc_final: 0.8316 (p) REVERT: A 109 MET cc_start: 0.7912 (mmm) cc_final: 0.7688 (mmt) REVERT: A 125 PHE cc_start: 0.8286 (m-80) cc_final: 0.7765 (m-80) REVERT: A 127 LYS cc_start: 0.8578 (ttmm) cc_final: 0.8174 (ttmm) REVERT: A 134 LYS cc_start: 0.8056 (mmmm) cc_final: 0.7792 (mmmm) REVERT: A 142 MET cc_start: 0.8031 (mmm) cc_final: 0.7705 (tmm) REVERT: A 149 ASP cc_start: 0.7542 (p0) cc_final: 0.7122 (p0) REVERT: A 180 ARG cc_start: 0.7477 (mtm180) cc_final: 0.6994 (mtm-85) REVERT: A 185 ARG cc_start: 0.7259 (ttm170) cc_final: 0.6989 (ttm170) REVERT: A 191 GLU cc_start: 0.7841 (mp0) cc_final: 0.7465 (mp0) REVERT: A 250 SER cc_start: 0.8626 (m) cc_final: 0.8242 (p) REVERT: A 255 MET cc_start: 0.8261 (mmt) cc_final: 0.7862 (mmt) REVERT: A 277 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8076 (mm) REVERT: A 285 ARG cc_start: 0.8485 (tpp80) cc_final: 0.7863 (mmm-85) REVERT: A 289 ASP cc_start: 0.7999 (m-30) cc_final: 0.7555 (m-30) REVERT: A 307 LYS cc_start: 0.8531 (mmtt) cc_final: 0.7997 (mmmt) REVERT: A 321 MET cc_start: 0.8193 (ttp) cc_final: 0.7969 (ttm) REVERT: A 369 MET cc_start: 0.7970 (mmp) cc_final: 0.7761 (mmt) REVERT: A 375 PRO cc_start: 0.8485 (Cg_endo) cc_final: 0.8154 (Cg_exo) REVERT: A 376 LYS cc_start: 0.8268 (mmtt) cc_final: 0.7933 (mmtm) REVERT: A 395 VAL cc_start: 0.7796 (m) cc_final: 0.7419 (p) REVERT: A 399 TYR cc_start: 0.7812 (m-80) cc_final: 0.6773 (m-80) REVERT: A 404 LYS cc_start: 0.8363 (tttm) cc_final: 0.8086 (tttm) REVERT: A 434 ARG cc_start: 0.8297 (mmm160) cc_final: 0.8049 (tpt90) REVERT: A 467 MET cc_start: 0.8100 (ttp) cc_final: 0.7753 (ttm) REVERT: A 476 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7190 (tm-30) REVERT: A 499 PHE cc_start: 0.7625 (t80) cc_final: 0.7412 (t80) REVERT: A 525 LEU cc_start: 0.8097 (mt) cc_final: 0.7889 (mm) REVERT: A 527 MET cc_start: 0.7972 (mtm) cc_final: 0.7742 (mtp) REVERT: A 529 TYR cc_start: 0.8276 (m-80) cc_final: 0.7993 (m-80) REVERT: A 547 MET cc_start: 0.7868 (tpp) cc_final: 0.7547 (tpp) REVERT: A 579 MET cc_start: 0.8101 (ttm) cc_final: 0.7782 (ttm) REVERT: A 630 LYS cc_start: 0.8401 (mttt) cc_final: 0.8107 (mttp) REVERT: A 632 LYS cc_start: 0.8305 (tptt) cc_final: 0.7759 (ttmm) REVERT: A 636 ILE cc_start: 0.8493 (tt) cc_final: 0.8111 (tp) REVERT: A 678 ASN cc_start: 0.8514 (m-40) cc_final: 0.8294 (m-40) REVERT: A 690 SER cc_start: 0.8101 (t) cc_final: 0.7731 (m) REVERT: A 711 GLN cc_start: 0.8260 (tp40) cc_final: 0.7743 (tp40) REVERT: A 716 HIS cc_start: 0.8326 (m170) cc_final: 0.8106 (m-70) REVERT: A 719 GLN cc_start: 0.8346 (tp40) cc_final: 0.8031 (tp40) REVERT: A 721 CYS cc_start: 0.8303 (m) cc_final: 0.7893 (m) REVERT: A 742 TYR cc_start: 0.8928 (t80) cc_final: 0.8695 (t80) REVERT: A 756 TYR cc_start: 0.7385 (t80) cc_final: 0.7053 (t80) REVERT: A 778 ASN cc_start: 0.8751 (m-40) cc_final: 0.8340 (m-40) REVERT: A 801 LYS cc_start: 0.7377 (ptmm) cc_final: 0.7177 (ptpp) REVERT: A 804 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7943 (mmtt) REVERT: A 812 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7986 (tt0) REVERT: A 813 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7925 (mm-30) REVERT: A 819 ARG cc_start: 0.7296 (ttm-80) cc_final: 0.6816 (ttm110) REVERT: A 842 MET cc_start: 0.7859 (ttt) cc_final: 0.7460 (tpp) REVERT: A 847 PHE cc_start: 0.8669 (t80) cc_final: 0.8029 (t80) REVERT: A 851 ILE cc_start: 0.8747 (mt) cc_final: 0.8469 (mm) REVERT: A 863 LYS cc_start: 0.8337 (mmmm) cc_final: 0.7675 (mmmm) REVERT: A 946 ASN cc_start: 0.8526 (m110) cc_final: 0.8236 (m110) REVERT: A 978 ARG cc_start: 0.8412 (mtt180) cc_final: 0.8123 (mtt180) outliers start: 19 outliers final: 16 residues processed: 336 average time/residue: 0.2693 time to fit residues: 116.6767 Evaluate side-chains 337 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 320 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 266 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 597 LYS Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 952 CYS 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: 0.0270 chunk 6 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.147695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.121403 restraints weight = 12754.960| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.39 r_work: 0.3425 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.5558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8970 Z= 0.140 Angle : 0.595 10.397 12274 Z= 0.312 Chirality : 0.042 0.241 1332 Planarity : 0.004 0.041 1448 Dihedral : 17.810 138.575 1458 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.18 % Favored : 96.72 % Rotamer: Outliers : 2.16 % Allowed : 27.19 % Favored : 70.65 % 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: 1.17 (0.28), residues: 975 helix: 1.99 (0.25), residues: 444 sheet: -0.05 (0.37), residues: 165 loop : -0.27 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 325 HIS 0.017 0.001 HIS A 823 PHE 0.033 0.002 PHE A 126 TYR 0.024 0.001 TYR A 947 ARG 0.012 0.001 ARG A 185 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 452) hydrogen bonds : angle 4.02626 ( 1274) covalent geometry : bond 0.00328 ( 8970) covalent geometry : angle 0.59479 (12274) *********************** 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 339 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 320 time to evaluate : 0.932 Fit side-chains REVERT: A 5 MET cc_start: 0.7286 (ttp) cc_final: 0.6261 (ttm) REVERT: A 9 GLU cc_start: 0.7733 (tt0) cc_final: 0.7204 (tt0) REVERT: A 18 ILE cc_start: 0.8837 (mm) cc_final: 0.8575 (mm) REVERT: A 19 THR cc_start: 0.8510 (p) cc_final: 0.8216 (t) REVERT: A 22 VAL cc_start: 0.8774 (t) cc_final: 0.8526 (t) REVERT: A 23 THR cc_start: 0.8824 (t) cc_final: 0.8494 (p) REVERT: A 41 GLU cc_start: 0.7982 (pt0) cc_final: 0.7635 (pt0) REVERT: A 54 SER cc_start: 0.8473 (m) cc_final: 0.8197 (p) REVERT: A 66 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7726 (mt-10) REVERT: A 74 VAL cc_start: 0.8538 (t) cc_final: 0.8200 (m) REVERT: A 75 GLN cc_start: 0.8387 (tm-30) cc_final: 0.7992 (tm-30) REVERT: A 85 PHE cc_start: 0.8929 (t80) cc_final: 0.8512 (t80) REVERT: A 87 LYS cc_start: 0.8818 (mmmt) cc_final: 0.8494 (mmmt) REVERT: A 91 THR cc_start: 0.8582 (m) cc_final: 0.8362 (p) REVERT: A 125 PHE cc_start: 0.8181 (m-80) cc_final: 0.7800 (m-80) REVERT: A 127 LYS cc_start: 0.8570 (ttmm) cc_final: 0.8157 (ttmm) REVERT: A 134 LYS cc_start: 0.7986 (mmmm) cc_final: 0.7732 (mmmm) REVERT: A 142 MET cc_start: 0.8021 (mmm) cc_final: 0.7683 (tmm) REVERT: A 149 ASP cc_start: 0.7520 (p0) cc_final: 0.7114 (p0) REVERT: A 163 LYS cc_start: 0.8401 (tppt) cc_final: 0.8046 (mmtp) REVERT: A 183 VAL cc_start: 0.8356 (p) cc_final: 0.8098 (m) REVERT: A 191 GLU cc_start: 0.7829 (mp0) cc_final: 0.7469 (mp0) REVERT: A 250 SER cc_start: 0.8590 (m) cc_final: 0.8202 (p) REVERT: A 255 MET cc_start: 0.8287 (mmt) cc_final: 0.7906 (mmt) REVERT: A 277 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8051 (mm) REVERT: A 285 ARG cc_start: 0.8474 (tpp80) cc_final: 0.7872 (mmm-85) REVERT: A 289 ASP cc_start: 0.8025 (m-30) cc_final: 0.7696 (m-30) REVERT: A 307 LYS cc_start: 0.8525 (mmtt) cc_final: 0.7983 (mmmt) REVERT: A 321 MET cc_start: 0.8184 (ttp) cc_final: 0.7958 (ttm) REVERT: A 369 MET cc_start: 0.7937 (mmp) cc_final: 0.7707 (mmt) REVERT: A 375 PRO cc_start: 0.8426 (Cg_endo) cc_final: 0.8088 (Cg_exo) REVERT: A 376 LYS cc_start: 0.8296 (mmtt) cc_final: 0.7939 (mmtp) REVERT: A 399 TYR cc_start: 0.7792 (m-80) cc_final: 0.6752 (m-80) REVERT: A 404 LYS cc_start: 0.8366 (tttm) cc_final: 0.8137 (tttm) REVERT: A 434 ARG cc_start: 0.8273 (mmm160) cc_final: 0.8015 (tpt90) REVERT: A 467 MET cc_start: 0.8094 (ttp) cc_final: 0.7748 (ttm) REVERT: A 476 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7501 (tm-30) REVERT: A 511 LYS cc_start: 0.8629 (ptpp) cc_final: 0.8342 (ptpp) REVERT: A 527 MET cc_start: 0.7946 (mtm) cc_final: 0.7723 (mtp) REVERT: A 529 TYR cc_start: 0.8308 (m-80) cc_final: 0.7995 (m-80) REVERT: A 547 MET cc_start: 0.7871 (tpp) cc_final: 0.7555 (tpp) REVERT: A 579 MET cc_start: 0.8082 (ttm) cc_final: 0.7765 (ttm) REVERT: A 632 LYS cc_start: 0.8303 (tptt) cc_final: 0.7755 (ttmm) REVERT: A 636 ILE cc_start: 0.8515 (tt) cc_final: 0.8124 (tp) REVERT: A 670 LYS cc_start: 0.8386 (tttm) cc_final: 0.7868 (ttmm) REVERT: A 678 ASN cc_start: 0.8521 (m-40) cc_final: 0.8303 (m-40) REVERT: A 690 SER cc_start: 0.8093 (t) cc_final: 0.7721 (m) REVERT: A 711 GLN cc_start: 0.8277 (tp40) cc_final: 0.7862 (tp40) REVERT: A 716 HIS cc_start: 0.8347 (m170) cc_final: 0.8016 (m170) REVERT: A 718 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: A 719 GLN cc_start: 0.8294 (tp40) cc_final: 0.7973 (tp40) REVERT: A 729 MET cc_start: 0.8164 (ttm) cc_final: 0.7913 (mtp) REVERT: A 756 TYR cc_start: 0.7332 (t80) cc_final: 0.7000 (t80) REVERT: A 778 ASN cc_start: 0.8728 (m-40) cc_final: 0.8257 (m-40) REVERT: A 804 LYS cc_start: 0.8259 (mmtt) cc_final: 0.7992 (mmtt) REVERT: A 812 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7993 (tt0) REVERT: A 813 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7919 (mm-30) REVERT: A 819 ARG cc_start: 0.7327 (ttm-80) cc_final: 0.6855 (ttm110) REVERT: A 841 ASN cc_start: 0.7398 (t0) cc_final: 0.6970 (t0) REVERT: A 842 MET cc_start: 0.7832 (ttt) cc_final: 0.7486 (tpp) REVERT: A 847 PHE cc_start: 0.8645 (t80) cc_final: 0.8201 (t80) REVERT: A 851 ILE cc_start: 0.8735 (mt) cc_final: 0.8454 (mp) REVERT: A 863 LYS cc_start: 0.8385 (mmmm) cc_final: 0.7686 (mmmm) REVERT: A 946 ASN cc_start: 0.8539 (m110) cc_final: 0.8214 (m110) REVERT: A 958 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: A 978 ARG cc_start: 0.8333 (mtt180) cc_final: 0.8057 (mtt180) outliers start: 19 outliers final: 12 residues processed: 327 average time/residue: 0.2659 time to fit residues: 111.7876 Evaluate side-chains 332 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 317 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 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 626 MET Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 958 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 24 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 0.0070 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.148516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.122550 restraints weight = 12955.298| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.46 r_work: 0.3416 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8970 Z= 0.145 Angle : 0.628 12.082 12274 Z= 0.329 Chirality : 0.042 0.256 1332 Planarity : 0.005 0.072 1448 Dihedral : 17.806 138.770 1458 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.38 % Favored : 96.51 % Rotamer: Outliers : 2.16 % Allowed : 28.10 % Favored : 69.74 % 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: 1.15 (0.28), residues: 975 helix: 1.96 (0.25), residues: 444 sheet: -0.09 (0.37), residues: 170 loop : -0.26 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 325 HIS 0.009 0.001 HIS A 174 PHE 0.041 0.002 PHE A 126 TYR 0.031 0.001 TYR A 772 ARG 0.015 0.001 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 452) hydrogen bonds : angle 4.02757 ( 1274) covalent geometry : bond 0.00339 ( 8970) covalent geometry : angle 0.62795 (12274) ********************** 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 338 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 319 time to evaluate : 0.837 Fit side-chains REVERT: A 5 MET cc_start: 0.7337 (ttp) cc_final: 0.6250 (ttm) REVERT: A 9 GLU cc_start: 0.7760 (tt0) cc_final: 0.7194 (tt0) REVERT: A 18 ILE cc_start: 0.8850 (mm) cc_final: 0.8585 (mm) REVERT: A 19 THR cc_start: 0.8536 (p) cc_final: 0.8247 (t) REVERT: A 22 VAL cc_start: 0.8762 (t) cc_final: 0.8501 (t) REVERT: A 23 THR cc_start: 0.8813 (t) cc_final: 0.8481 (p) REVERT: A 41 GLU cc_start: 0.8038 (pt0) cc_final: 0.7675 (pt0) REVERT: A 54 SER cc_start: 0.8455 (m) cc_final: 0.8171 (p) REVERT: A 66 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7784 (mt-10) REVERT: A 74 VAL cc_start: 0.8500 (t) cc_final: 0.8172 (m) REVERT: A 75 GLN cc_start: 0.8379 (tm-30) cc_final: 0.7977 (tm-30) REVERT: A 85 PHE cc_start: 0.8937 (t80) cc_final: 0.8506 (t80) REVERT: A 87 LYS cc_start: 0.8909 (mmmt) cc_final: 0.8621 (mmmt) REVERT: A 91 THR cc_start: 0.8586 (m) cc_final: 0.8327 (p) REVERT: A 109 MET cc_start: 0.7968 (mmm) cc_final: 0.7703 (mmt) REVERT: A 127 LYS cc_start: 0.8549 (ttmm) cc_final: 0.8119 (ttmm) REVERT: A 134 LYS cc_start: 0.8027 (mmmm) cc_final: 0.7799 (mmmm) REVERT: A 142 MET cc_start: 0.8021 (mmm) cc_final: 0.7682 (tmm) REVERT: A 149 ASP cc_start: 0.7538 (p0) cc_final: 0.7139 (p0) REVERT: A 180 ARG cc_start: 0.7744 (mtm-85) cc_final: 0.7254 (mtm-85) REVERT: A 183 VAL cc_start: 0.8517 (p) cc_final: 0.8241 (m) REVERT: A 185 ARG cc_start: 0.7340 (ttm170) cc_final: 0.7130 (ttm170) REVERT: A 191 GLU cc_start: 0.7835 (mp0) cc_final: 0.7462 (mp0) REVERT: A 250 SER cc_start: 0.8613 (m) cc_final: 0.8227 (p) REVERT: A 255 MET cc_start: 0.8268 (mmt) cc_final: 0.7883 (mmt) REVERT: A 277 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8026 (mm) REVERT: A 285 ARG cc_start: 0.8482 (tpp80) cc_final: 0.7884 (mmm-85) REVERT: A 289 ASP cc_start: 0.8115 (m-30) cc_final: 0.7642 (m-30) REVERT: A 295 ASN cc_start: 0.8748 (t0) cc_final: 0.8543 (t0) REVERT: A 307 LYS cc_start: 0.8562 (mmtt) cc_final: 0.8042 (mmmt) REVERT: A 321 MET cc_start: 0.8170 (ttp) cc_final: 0.7941 (ttm) REVERT: A 369 MET cc_start: 0.7886 (mmp) cc_final: 0.7664 (mmt) REVERT: A 375 PRO cc_start: 0.8415 (Cg_endo) cc_final: 0.8081 (Cg_exo) REVERT: A 376 LYS cc_start: 0.8295 (mmtt) cc_final: 0.7879 (mmtm) REVERT: A 399 TYR cc_start: 0.7800 (m-80) cc_final: 0.6777 (m-80) REVERT: A 404 LYS cc_start: 0.8361 (tttm) cc_final: 0.8071 (tttm) REVERT: A 434 ARG cc_start: 0.8290 (mmm160) cc_final: 0.8032 (tpt90) REVERT: A 467 MET cc_start: 0.8107 (ttp) cc_final: 0.7729 (ttm) REVERT: A 476 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7155 (tm-30) REVERT: A 499 PHE cc_start: 0.7737 (t80) cc_final: 0.7278 (t80) REVERT: A 527 MET cc_start: 0.7995 (mtm) cc_final: 0.7770 (mtp) REVERT: A 529 TYR cc_start: 0.8321 (m-80) cc_final: 0.8026 (m-80) REVERT: A 547 MET cc_start: 0.7909 (tpp) cc_final: 0.7584 (tpp) REVERT: A 579 MET cc_start: 0.8026 (ttm) cc_final: 0.7694 (ttm) REVERT: A 630 LYS cc_start: 0.8413 (mttt) cc_final: 0.8159 (mttp) REVERT: A 632 LYS cc_start: 0.8333 (tptt) cc_final: 0.7802 (ttmm) REVERT: A 636 ILE cc_start: 0.8480 (tt) cc_final: 0.8088 (tp) REVERT: A 666 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7834 (mm-40) REVERT: A 670 LYS cc_start: 0.8327 (tttm) cc_final: 0.7873 (ttmm) REVERT: A 678 ASN cc_start: 0.8476 (m-40) cc_final: 0.8255 (m-40) REVERT: A 690 SER cc_start: 0.8090 (t) cc_final: 0.7707 (m) REVERT: A 711 GLN cc_start: 0.8416 (tp40) cc_final: 0.7977 (tp40) REVERT: A 716 HIS cc_start: 0.8398 (m170) cc_final: 0.8036 (m170) REVERT: A 718 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: A 741 GLU cc_start: 0.8206 (tp30) cc_final: 0.7860 (tp30) REVERT: A 756 TYR cc_start: 0.7356 (t80) cc_final: 0.7027 (t80) REVERT: A 778 ASN cc_start: 0.8736 (m-40) cc_final: 0.8324 (m-40) REVERT: A 804 LYS cc_start: 0.8290 (mmtt) cc_final: 0.8003 (mmtt) REVERT: A 813 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7929 (mm-30) REVERT: A 819 ARG cc_start: 0.7368 (ttm-80) cc_final: 0.6877 (ttm110) REVERT: A 841 ASN cc_start: 0.7397 (t0) cc_final: 0.6930 (t0) REVERT: A 842 MET cc_start: 0.7856 (ttt) cc_final: 0.7471 (tpp) REVERT: A 847 PHE cc_start: 0.8601 (t80) cc_final: 0.8216 (t80) REVERT: A 851 ILE cc_start: 0.8725 (mt) cc_final: 0.8466 (mp) REVERT: A 863 LYS cc_start: 0.8390 (mmmm) cc_final: 0.7706 (mmmm) REVERT: A 902 ILE cc_start: 0.8122 (mt) cc_final: 0.7918 (mm) REVERT: A 946 ASN cc_start: 0.8560 (m110) cc_final: 0.8238 (m110) REVERT: A 958 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: A 978 ARG cc_start: 0.8344 (mtt180) cc_final: 0.8056 (mtt180) outliers start: 19 outliers final: 12 residues processed: 326 average time/residue: 0.2642 time to fit residues: 111.9298 Evaluate side-chains 336 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 321 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU 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 266 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 597 LYS Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LYS 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: 0.8980 chunk 33 optimal weight: 0.2980 chunk 49 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.148706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.122771 restraints weight = 12964.518| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.46 r_work: 0.3425 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8970 Z= 0.134 Angle : 0.623 11.581 12274 Z= 0.324 Chirality : 0.043 0.282 1332 Planarity : 0.005 0.055 1448 Dihedral : 17.708 138.856 1458 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.28 % Favored : 96.62 % Rotamer: Outliers : 2.05 % Allowed : 28.56 % Favored : 69.40 % 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: 1.17 (0.28), residues: 975 helix: 1.95 (0.25), residues: 445 sheet: 0.16 (0.39), residues: 157 loop : -0.34 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 325 HIS 0.005 0.001 HIS A 722 PHE 0.040 0.002 PHE A 126 TYR 0.026 0.001 TYR A 947 ARG 0.012 0.001 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.03432 ( 452) hydrogen bonds : angle 4.02107 ( 1274) covalent geometry : bond 0.00310 ( 8970) covalent geometry : angle 0.62347 (12274) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4916.07 seconds wall clock time: 85 minutes 11.54 seconds (5111.54 seconds total)