Starting phenix.real_space_refine on Wed Sep 17 12:07:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ywm_39638/09_2025/8ywm_39638.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ywm_39638/09_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_39638/09_2025/8ywm_39638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ywm_39638/09_2025/8ywm_39638.map" model { file = "/net/cci-nas-00/data/ceres_data/8ywm_39638/09_2025/8ywm_39638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ywm_39638/09_2025/8ywm_39638.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 34 5.49 5 S 51 5.16 5 C 5455 2.51 5 N 1478 2.21 5 O 1675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8693 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 979, 7980 Classifications: {'peptide': 979} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 934} Chain breaks: 1 Chain: "D" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 339 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "E" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 374 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Time building chain proxies: 1.97, per 1000 atoms: 0.23 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: 0.84 Conformation dependent library (CDL) restraints added in 284.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1870 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 48.5% alpha, 16.6% beta 16 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 6 through 15 Processing helix chain 'A' and resid 15 through 28 Processing helix chain 'A' and resid 79 through 93 removed outlier: 3.780A pdb=" N GLU A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 142 Processing helix chain 'A' and resid 154 through 163 removed outlier: 3.590A pdb=" N LYS A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 191 No H-bonds generated for 'chain 'A' and resid 189 through 191' Processing helix chain 'A' and resid 271 through 287 Processing helix chain 'A' and resid 299 through 311 removed outlier: 3.650A pdb=" N PHE A 303 " --> pdb=" O TYR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 322 Processing helix chain 'A' and resid 328 through 336 removed outlier: 3.562A pdb=" N TYR A 336 " --> pdb=" O ILE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 374 Processing helix chain 'A' and resid 381 through 389 Processing helix chain 'A' and resid 398 through 409 removed outlier: 3.550A pdb=" N ARG A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 436 removed outlier: 3.607A pdb=" N VAL A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 449 removed outlier: 3.531A pdb=" N ASP A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 458 Processing helix chain 'A' and resid 459 through 475 removed outlier: 4.044A pdb=" N LYS A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 529 Processing helix chain 'A' and resid 532 through 534 No H-bonds generated for 'chain 'A' and resid 532 through 534' Processing helix chain 'A' and resid 539 through 549 Processing helix chain 'A' and resid 575 through 579 Processing helix chain 'A' and resid 580 through 610 Processing helix chain 'A' and resid 616 through 639 Processing helix chain 'A' and resid 640 through 647 Processing helix chain 'A' and resid 654 through 679 Processing helix chain 'A' and resid 697 through 699 No H-bonds generated for 'chain 'A' and resid 697 through 699' Processing helix chain 'A' and resid 700 through 709 removed outlier: 3.973A pdb=" N TYR A 707 " --> pdb=" O VAL A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 748 removed outlier: 3.871A pdb=" N THR A 734 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 815 Processing helix chain 'A' and resid 826 through 841 Processing helix chain 'A' and resid 847 through 851 removed outlier: 3.710A pdb=" N ILE A 851 " --> pdb=" O GLU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 882 Processing helix chain 'A' and resid 921 through 923 No H-bonds generated for 'chain 'A' and resid 921 through 923' Processing helix chain 'A' and resid 928 through 935 Processing helix chain 'A' and resid 939 through 953 removed outlier: 3.616A pdb=" N TYR A 943 " --> pdb=" O ASP A 939 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLY A 950 " --> pdb=" O ASN A 946 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU A 951 " --> pdb=" O TYR A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 990 Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 179 removed outlier: 6.992A pdb=" N PHE A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILE A 39 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N TYR A 52 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 194 " --> pdb=" O GLN A 171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 105 removed outlier: 4.356A pdb=" N VAL A 70 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 268 removed outlier: 3.616A pdb=" N ALA A 249 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N VAL A 232 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR A 215 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY A 293 " --> pdb=" O ILE A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 344 Processing sheet with id=AA5, first strand: chain 'A' and resid 506 through 508 removed outlier: 3.502A pdb=" N PHE A 765 " --> pdb=" O GLY A 506 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TYR A 756 " --> pdb=" O ASP A 517 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASP A 517 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLU A 758 " --> pdb=" O GLY A 515 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 515 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY A 686 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TYR A 692 " --> pdb=" O LYS A 684 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 506 through 508 removed outlier: 3.502A pdb=" N PHE A 765 " --> pdb=" O GLY A 506 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU A 760 " --> pdb=" O HIS A 776 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N HIS A 776 " --> pdb=" O LEU A 760 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LYS A 770 " --> pdb=" O THR A 766 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 536 through 537 Processing sheet with id=AA8, first strand: chain 'A' and resid 852 through 855 418 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 1.63 Time building geometry restraints manager: 1.05 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: 0.800 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 9.640 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.070 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.26), residues: 975 helix: 0.90 (0.24), residues: 442 sheet: 0.28 (0.42), residues: 151 loop : -0.72 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 99 TYR 0.031 0.002 TYR A 177 PHE 0.037 0.002 PHE A 303 TRP 0.025 0.002 TRP A 325 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8970) covalent geometry : angle 0.70869 (12274) hydrogen bonds : bond 0.15361 ( 452) hydrogen bonds : angle 6.55321 ( 1274) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 348 time to evaluate : 0.302 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: 0.1062 time to fit residues: 48.5695 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 : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 938 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 GLN A 319 ASN ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.150446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.124514 restraints weight = 13029.777| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.47 r_work: 0.3450 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 8970 Z= 0.186 Angle : 0.635 11.054 12274 Z= 0.337 Chirality : 0.045 0.223 1332 Planarity : 0.005 0.045 1448 Dihedral : 18.492 136.936 1464 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.08 % Favored : 96.82 % Rotamer: Outliers : 1.82 % Allowed : 16.04 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.27), residues: 975 helix: 1.51 (0.24), residues: 443 sheet: 0.31 (0.40), residues: 164 loop : -0.66 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 13 TYR 0.028 0.002 TYR A 405 PHE 0.023 0.002 PHE A 294 TRP 0.022 0.002 TRP A 325 HIS 0.004 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 8970) covalent geometry : angle 0.63537 (12274) hydrogen bonds : bond 0.05244 ( 452) hydrogen bonds : angle 4.38628 ( 1274) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 334 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.8550 (ttp80) cc_final: 0.8346 (ttp80) REVERT: A 27 GLN cc_start: 0.8592 (tp40) cc_final: 0.8254 (tp-100) REVERT: A 38 ASP cc_start: 0.7495 (t0) cc_final: 0.7286 (t0) REVERT: A 41 GLU cc_start: 0.8061 (pt0) cc_final: 0.7680 (pt0) REVERT: A 54 SER cc_start: 0.8388 (m) cc_final: 0.8042 (p) REVERT: A 56 GLU cc_start: 0.7628 (pt0) cc_final: 0.7195 (pt0) REVERT: A 59 TYR cc_start: 0.8301 (m-10) cc_final: 0.7979 (m-80) REVERT: A 75 GLN cc_start: 0.8450 (tm-30) cc_final: 0.8112 (tm-30) REVERT: A 127 LYS cc_start: 0.8546 (ttmm) cc_final: 0.8151 (ttmm) REVERT: A 134 LYS cc_start: 0.8161 (mmmm) cc_final: 0.7903 (mmmm) REVERT: A 149 ASP cc_start: 0.7471 (p0) cc_final: 0.6967 (p0) REVERT: A 157 MET cc_start: 0.8174 (mmm) cc_final: 0.7969 (tpp) REVERT: A 180 ARG cc_start: 0.7914 (mtm110) cc_final: 0.7527 (mtm110) REVERT: A 191 GLU cc_start: 0.7763 (mp0) cc_final: 0.7465 (mp0) REVERT: A 192 ASP cc_start: 0.7636 (m-30) cc_final: 0.7363 (m-30) REVERT: A 285 ARG cc_start: 0.8506 (ttm-80) cc_final: 0.7949 (mmm-85) REVERT: A 307 LYS cc_start: 0.8444 (mmtt) cc_final: 0.7786 (mmmm) REVERT: A 321 MET cc_start: 0.8343 (ttp) cc_final: 0.8079 (ttm) REVERT: A 334 LYS cc_start: 0.8531 (tppp) cc_final: 0.8164 (tppp) REVERT: A 349 LYS cc_start: 0.8321 (tttt) cc_final: 0.8084 (tttm) REVERT: A 376 LYS cc_start: 0.8293 (mmtt) cc_final: 0.8014 (mmtm) REVERT: A 397 LEU cc_start: 0.8575 (tp) cc_final: 0.8334 (tp) REVERT: A 399 TYR cc_start: 0.7938 (m-80) cc_final: 0.7000 (m-80) REVERT: A 404 LYS cc_start: 0.8234 (tttm) cc_final: 0.7957 (tttm) REVERT: A 455 CYS cc_start: 0.7870 (m) cc_final: 0.7669 (m) REVERT: A 476 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7397 (tm-30) REVERT: A 484 THR cc_start: 0.7835 (m) cc_final: 0.7505 (p) REVERT: A 511 LYS cc_start: 0.8250 (ptpp) cc_final: 0.7596 (ptpp) REVERT: A 513 THR cc_start: 0.7732 (t) cc_final: 0.7447 (p) REVERT: A 549 LYS cc_start: 0.8544 (ptmt) cc_final: 0.8156 (ptmt) REVERT: A 579 MET cc_start: 0.7859 (ttm) cc_final: 0.7531 (ttm) REVERT: A 597 LYS cc_start: 0.8031 (mmtm) cc_final: 0.7813 (tppp) REVERT: A 630 LYS cc_start: 0.8378 (mttt) cc_final: 0.8099 (mttp) REVERT: A 632 LYS cc_start: 0.8287 (tptt) cc_final: 0.7883 (ttmm) REVERT: A 644 GLU cc_start: 0.7455 (tp30) cc_final: 0.7004 (tp30) REVERT: A 647 ASN cc_start: 0.8245 (t0) cc_final: 0.7933 (t0) REVERT: A 687 ASP cc_start: 0.7190 (t0) cc_final: 0.6950 (t0) REVERT: A 693 ILE cc_start: 0.8508 (mm) cc_final: 0.8305 (mm) REVERT: A 719 GLN cc_start: 0.8307 (tp40) cc_final: 0.7925 (tp40) REVERT: A 721 CYS cc_start: 0.7816 (m) cc_final: 0.7323 (m) REVERT: A 738 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8273 (mt-10) REVERT: A 778 ASN cc_start: 0.8669 (m-40) cc_final: 0.8196 (m-40) REVERT: A 787 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8120 (mp) REVERT: A 794 ILE cc_start: 0.7528 (tp) cc_final: 0.7274 (tp) REVERT: A 810 ILE cc_start: 0.8699 (mt) cc_final: 0.8408 (tp) REVERT: A 813 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7759 (mm-30) REVERT: A 824 ARG cc_start: 0.7632 (mtt-85) cc_final: 0.7377 (mtt-85) REVERT: A 829 GLU cc_start: 0.7874 (tp30) cc_final: 0.7495 (tp30) REVERT: A 846 ASN cc_start: 0.7652 (p0) cc_final: 0.7109 (p0) REVERT: A 863 LYS cc_start: 0.8007 (mmmm) cc_final: 0.7512 (mmmm) REVERT: A 900 TYR cc_start: 0.8094 (p90) cc_final: 0.7607 (p90) REVERT: A 924 LYS cc_start: 0.8093 (mttp) cc_final: 0.7483 (mttm) REVERT: A 947 TYR cc_start: 0.8245 (m-80) cc_final: 0.8030 (m-10) outliers start: 16 outliers final: 9 residues processed: 341 average time/residue: 0.1095 time to fit residues: 48.9573 Evaluate side-chains 327 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 317 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 787 LEU Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 952 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 71 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 37 optimal weight: 0.0270 chunk 76 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN A 963 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.149261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.122953 restraints weight = 12686.377| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.45 r_work: 0.3451 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8970 Z= 0.132 Angle : 0.563 9.062 12274 Z= 0.298 Chirality : 0.042 0.215 1332 Planarity : 0.004 0.045 1448 Dihedral : 18.277 136.757 1460 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.67 % Favored : 97.23 % Rotamer: Outliers : 1.82 % Allowed : 20.71 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.27), residues: 975 helix: 1.84 (0.24), residues: 444 sheet: 0.26 (0.39), residues: 164 loop : -0.55 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 824 TYR 0.020 0.001 TYR A 772 PHE 0.027 0.002 PHE A 72 TRP 0.013 0.001 TRP A 325 HIS 0.004 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8970) covalent geometry : angle 0.56332 (12274) hydrogen bonds : bond 0.04224 ( 452) hydrogen bonds : angle 4.13943 ( 1274) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 319 time to evaluate : 0.357 Fit side-chains REVERT: A 27 GLN cc_start: 0.8539 (tp40) cc_final: 0.8284 (tp-100) REVERT: A 38 ASP cc_start: 0.7469 (t0) cc_final: 0.7231 (t0) REVERT: A 41 GLU cc_start: 0.8038 (pt0) cc_final: 0.7653 (pt0) REVERT: A 54 SER cc_start: 0.8378 (m) cc_final: 0.8090 (t) REVERT: A 56 GLU cc_start: 0.7677 (pt0) cc_final: 0.7188 (pt0) REVERT: A 59 TYR cc_start: 0.8278 (m-10) cc_final: 0.8049 (m-80) REVERT: A 62 GLU cc_start: 0.7645 (tt0) cc_final: 0.7395 (tt0) REVERT: A 75 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8106 (tm-30) REVERT: A 85 PHE cc_start: 0.8900 (t80) cc_final: 0.8489 (t80) REVERT: A 126 PHE cc_start: 0.8276 (m-10) cc_final: 0.7951 (m-10) REVERT: A 127 LYS cc_start: 0.8582 (ttmm) cc_final: 0.8163 (ttmm) REVERT: A 134 LYS cc_start: 0.8126 (mmmm) cc_final: 0.7851 (mmmm) REVERT: A 142 MET cc_start: 0.7979 (mmm) cc_final: 0.7712 (tmm) REVERT: A 149 ASP cc_start: 0.7517 (p0) cc_final: 0.7066 (p0) REVERT: A 157 MET cc_start: 0.8247 (mmm) cc_final: 0.8040 (tpp) REVERT: A 180 ARG cc_start: 0.7872 (mtm110) cc_final: 0.7406 (mtm110) REVERT: A 191 GLU cc_start: 0.7737 (mp0) cc_final: 0.7388 (mp0) REVERT: A 194 VAL cc_start: 0.8588 (p) cc_final: 0.8230 (m) REVERT: A 285 ARG cc_start: 0.8555 (ttm-80) cc_final: 0.8004 (mmm-85) REVERT: A 289 ASP cc_start: 0.7752 (m-30) cc_final: 0.7400 (m-30) REVERT: A 307 LYS cc_start: 0.8473 (mmtt) cc_final: 0.7738 (mmmt) REVERT: A 320 LYS cc_start: 0.8695 (ttmm) cc_final: 0.8460 (ttmm) REVERT: A 321 MET cc_start: 0.8400 (ttp) cc_final: 0.8119 (ttm) REVERT: A 334 LYS cc_start: 0.8517 (tppp) cc_final: 0.8107 (tppp) REVERT: A 349 LYS cc_start: 0.8267 (tttt) cc_final: 0.8063 (tttm) REVERT: A 376 LYS cc_start: 0.8297 (mmtt) cc_final: 0.8044 (mmtm) REVERT: A 395 VAL cc_start: 0.7375 (m) cc_final: 0.7033 (p) REVERT: A 397 LEU cc_start: 0.8574 (tp) cc_final: 0.8326 (tp) REVERT: A 399 TYR cc_start: 0.7934 (m-80) cc_final: 0.6909 (m-80) REVERT: A 404 LYS cc_start: 0.8241 (tttm) cc_final: 0.7962 (tttm) REVERT: A 424 ASP cc_start: 0.8225 (t0) cc_final: 0.7771 (t0) REVERT: A 455 CYS cc_start: 0.7860 (m) cc_final: 0.7648 (m) REVERT: A 475 ASP cc_start: 0.7306 (t0) cc_final: 0.7078 (t0) REVERT: A 476 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7345 (tm-30) REVERT: A 507 LEU cc_start: 0.8369 (tp) cc_final: 0.7933 (tp) REVERT: A 511 LYS cc_start: 0.8474 (ptpp) cc_final: 0.7776 (ptpp) REVERT: A 513 THR cc_start: 0.7925 (t) cc_final: 0.7655 (p) REVERT: A 530 ASN cc_start: 0.8354 (t0) cc_final: 0.8113 (t0) REVERT: A 555 TYR cc_start: 0.8353 (t80) cc_final: 0.8102 (t80) REVERT: A 579 MET cc_start: 0.7948 (ttm) cc_final: 0.7608 (ttm) REVERT: A 593 ARG cc_start: 0.8276 (ttt90) cc_final: 0.8050 (ttt90) REVERT: A 597 LYS cc_start: 0.8018 (mmtm) cc_final: 0.7716 (tppp) REVERT: A 630 LYS cc_start: 0.8385 (mttt) cc_final: 0.8075 (mttp) REVERT: A 632 LYS cc_start: 0.8284 (tptt) cc_final: 0.7803 (ttmm) REVERT: A 635 LYS cc_start: 0.8365 (ttpt) cc_final: 0.7785 (ttmm) REVERT: A 636 ILE cc_start: 0.8410 (tt) cc_final: 0.8117 (tp) REVERT: A 644 GLU cc_start: 0.7427 (tp30) cc_final: 0.6845 (tp30) REVERT: A 647 ASN cc_start: 0.8311 (t0) cc_final: 0.7982 (t0) REVERT: A 689 ASP cc_start: 0.8149 (p0) cc_final: 0.7915 (p0) REVERT: A 715 LYS cc_start: 0.8269 (mmtt) cc_final: 0.8054 (mmtt) REVERT: A 719 GLN cc_start: 0.8341 (tp40) cc_final: 0.7893 (tp-100) REVERT: A 721 CYS cc_start: 0.7861 (m) cc_final: 0.7414 (m) REVERT: A 744 ARG cc_start: 0.8235 (tmm-80) cc_final: 0.7996 (tmm-80) REVERT: A 747 ASN cc_start: 0.8141 (p0) cc_final: 0.7814 (p0) REVERT: A 778 ASN cc_start: 0.8798 (m-40) cc_final: 0.8331 (m-40) REVERT: A 794 ILE cc_start: 0.7507 (tp) cc_final: 0.7243 (tp) REVERT: A 810 ILE cc_start: 0.8637 (mt) cc_final: 0.8358 (tp) REVERT: A 813 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7906 (mm-30) REVERT: A 819 ARG cc_start: 0.6426 (ttm-80) cc_final: 0.6134 (ttm-80) REVERT: A 842 MET cc_start: 0.7526 (ttt) cc_final: 0.7238 (tpp) REVERT: A 893 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6800 (mm-30) REVERT: A 897 ARG cc_start: 0.8094 (mtp85) cc_final: 0.7681 (ttm-80) REVERT: A 900 TYR cc_start: 0.8055 (p90) cc_final: 0.7555 (p90) REVERT: A 924 LYS cc_start: 0.7980 (mttp) cc_final: 0.7289 (mttm) REVERT: A 947 TYR cc_start: 0.8243 (m-80) cc_final: 0.8021 (m-10) REVERT: A 954 ARG cc_start: 0.8110 (mmt180) cc_final: 0.7763 (mmm160) outliers start: 16 outliers final: 11 residues processed: 324 average time/residue: 0.1203 time to fit residues: 50.4159 Evaluate side-chains 317 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 306 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 811 MET Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 949 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 60 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 90 optimal weight: 0.0470 chunk 51 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.148329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.121332 restraints weight = 12974.785| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.50 r_work: 0.3425 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8970 Z= 0.133 Angle : 0.557 9.656 12274 Z= 0.294 Chirality : 0.042 0.229 1332 Planarity : 0.004 0.046 1448 Dihedral : 18.235 136.244 1460 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.97 % Favored : 96.92 % Rotamer: Outliers : 2.16 % Allowed : 21.84 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.27), residues: 975 helix: 2.03 (0.24), residues: 443 sheet: 0.27 (0.38), residues: 164 loop : -0.47 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 13 TYR 0.016 0.001 TYR A 138 PHE 0.031 0.002 PHE A 294 TRP 0.012 0.001 TRP A 325 HIS 0.005 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8970) covalent geometry : angle 0.55745 (12274) hydrogen bonds : bond 0.04032 ( 452) hydrogen bonds : angle 4.06966 ( 1274) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 327 time to evaluate : 0.330 Fit side-chains REVERT: A 9 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7396 (tt0) REVERT: A 27 GLN cc_start: 0.8529 (tp40) cc_final: 0.8267 (tp-100) REVERT: A 38 ASP cc_start: 0.7520 (t0) cc_final: 0.7227 (t0) REVERT: A 41 GLU cc_start: 0.8041 (pt0) cc_final: 0.7671 (pt0) REVERT: A 54 SER cc_start: 0.8380 (m) cc_final: 0.8093 (t) REVERT: A 56 GLU cc_start: 0.7713 (pt0) cc_final: 0.7196 (pt0) REVERT: A 62 GLU cc_start: 0.7618 (tt0) cc_final: 0.7355 (tt0) REVERT: A 75 GLN cc_start: 0.8448 (tm-30) cc_final: 0.7817 (tm-30) REVERT: A 85 PHE cc_start: 0.8939 (t80) cc_final: 0.8512 (t80) REVERT: A 115 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7846 (mt-10) REVERT: A 127 LYS cc_start: 0.8590 (ttmm) cc_final: 0.8167 (ttmm) REVERT: A 134 LYS cc_start: 0.8141 (mmmm) cc_final: 0.7855 (mmmm) REVERT: A 142 MET cc_start: 0.8009 (mmm) cc_final: 0.7765 (tmm) REVERT: A 149 ASP cc_start: 0.7517 (p0) cc_final: 0.7074 (p0) REVERT: A 157 MET cc_start: 0.8258 (mmm) cc_final: 0.8046 (tpp) REVERT: A 180 ARG cc_start: 0.7888 (mtm110) cc_final: 0.7325 (mtm110) REVERT: A 191 GLU cc_start: 0.7786 (mp0) cc_final: 0.7451 (mp0) REVERT: A 194 VAL cc_start: 0.8587 (p) cc_final: 0.8268 (m) REVERT: A 260 LYS cc_start: 0.8476 (mmmt) cc_final: 0.8155 (mmmt) REVERT: A 277 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8115 (mm) REVERT: A 285 ARG cc_start: 0.8572 (ttm-80) cc_final: 0.8004 (mmm-85) REVERT: A 288 PRO cc_start: 0.8588 (Cg_exo) cc_final: 0.8373 (Cg_endo) REVERT: A 289 ASP cc_start: 0.7872 (m-30) cc_final: 0.7526 (m-30) REVERT: A 307 LYS cc_start: 0.8523 (mmtt) cc_final: 0.7879 (mmmt) REVERT: A 320 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8200 (ttpp) REVERT: A 321 MET cc_start: 0.8362 (ttp) cc_final: 0.8087 (ttm) REVERT: A 334 LYS cc_start: 0.8479 (tppp) cc_final: 0.8060 (tppp) REVERT: A 349 LYS cc_start: 0.8341 (tttt) cc_final: 0.8125 (tttm) REVERT: A 369 MET cc_start: 0.7900 (mmp) cc_final: 0.7678 (mmt) REVERT: A 375 PRO cc_start: 0.8461 (Cg_endo) cc_final: 0.8180 (Cg_exo) REVERT: A 376 LYS cc_start: 0.8318 (mmtt) cc_final: 0.8006 (mmtm) REVERT: A 395 VAL cc_start: 0.7519 (m) cc_final: 0.7183 (p) REVERT: A 399 TYR cc_start: 0.7920 (m-80) cc_final: 0.6970 (m-80) REVERT: A 404 LYS cc_start: 0.8286 (tttm) cc_final: 0.8010 (tttm) REVERT: A 417 VAL cc_start: 0.8479 (t) cc_final: 0.8259 (t) REVERT: A 434 ARG cc_start: 0.8280 (mmm160) cc_final: 0.7935 (tpt90) REVERT: A 455 CYS cc_start: 0.7871 (m) cc_final: 0.7595 (m) REVERT: A 467 MET cc_start: 0.8060 (ttp) cc_final: 0.7790 (ttt) REVERT: A 476 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7244 (tm-30) REVERT: A 510 ASP cc_start: 0.8141 (m-30) cc_final: 0.7892 (t0) REVERT: A 511 LYS cc_start: 0.8615 (ptpp) cc_final: 0.8275 (ptpp) REVERT: A 517 ASP cc_start: 0.7727 (t0) cc_final: 0.7477 (t0) REVERT: A 579 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7534 (mtp) REVERT: A 593 ARG cc_start: 0.8269 (ttt90) cc_final: 0.8011 (ttt90) REVERT: A 597 LYS cc_start: 0.8098 (mmtm) cc_final: 0.7751 (tppp) REVERT: A 630 LYS cc_start: 0.8376 (mttt) cc_final: 0.8060 (mttp) REVERT: A 632 LYS cc_start: 0.8280 (tptt) cc_final: 0.7780 (ttmm) REVERT: A 635 LYS cc_start: 0.8301 (ttpt) cc_final: 0.7741 (ttmm) REVERT: A 636 ILE cc_start: 0.8471 (tt) cc_final: 0.8123 (tp) REVERT: A 644 GLU cc_start: 0.7582 (tp30) cc_final: 0.7083 (tp30) REVERT: A 647 ASN cc_start: 0.8316 (t0) cc_final: 0.7968 (t0) REVERT: A 670 LYS cc_start: 0.8516 (ttmm) cc_final: 0.8225 (ttmm) REVERT: A 676 VAL cc_start: 0.8331 (t) cc_final: 0.8086 (m) REVERT: A 678 ASN cc_start: 0.8480 (m110) cc_final: 0.8279 (m-40) REVERT: A 689 ASP cc_start: 0.8139 (p0) cc_final: 0.7835 (p0) REVERT: A 690 SER cc_start: 0.8233 (t) cc_final: 0.7885 (p) REVERT: A 719 GLN cc_start: 0.8344 (tp40) cc_final: 0.8126 (tp-100) REVERT: A 721 CYS cc_start: 0.8054 (m) cc_final: 0.7576 (m) REVERT: A 744 ARG cc_start: 0.8226 (tmm-80) cc_final: 0.7988 (tmm-80) REVERT: A 747 ASN cc_start: 0.8048 (p0) cc_final: 0.7750 (p0) REVERT: A 770 LYS cc_start: 0.7938 (mttp) cc_final: 0.7628 (mttp) REVERT: A 778 ASN cc_start: 0.8834 (m-40) cc_final: 0.8369 (m-40) REVERT: A 804 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7884 (mmtt) REVERT: A 810 ILE cc_start: 0.8561 (mt) cc_final: 0.8329 (tp) REVERT: A 813 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7928 (mm-30) REVERT: A 816 LYS cc_start: 0.8498 (ptpp) cc_final: 0.7830 (ptpp) REVERT: A 828 ILE cc_start: 0.8445 (pt) cc_final: 0.8131 (mt) REVERT: A 842 MET cc_start: 0.7612 (ttt) cc_final: 0.7370 (tpp) REVERT: A 847 PHE cc_start: 0.8568 (t80) cc_final: 0.8257 (t80) REVERT: A 867 ILE cc_start: 0.7650 (mm) cc_final: 0.7390 (mm) REVERT: A 893 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6794 (mm-30) REVERT: A 897 ARG cc_start: 0.8212 (mtp85) cc_final: 0.7819 (ttm-80) REVERT: A 900 TYR cc_start: 0.7972 (p90) cc_final: 0.7376 (p90) REVERT: A 924 LYS cc_start: 0.7976 (mttp) cc_final: 0.7373 (mttm) REVERT: A 932 LYS cc_start: 0.8811 (mmtp) cc_final: 0.8560 (mmtp) REVERT: A 942 PHE cc_start: 0.7746 (t80) cc_final: 0.7412 (t80) REVERT: A 946 ASN cc_start: 0.8384 (m110) cc_final: 0.7913 (m110) REVERT: A 978 ARG cc_start: 0.8366 (mtt180) cc_final: 0.8091 (mtt180) outliers start: 19 outliers final: 13 residues processed: 332 average time/residue: 0.1169 time to fit residues: 50.2881 Evaluate side-chains 327 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 312 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 811 MET Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 958 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 82 optimal weight: 0.1980 chunk 22 optimal weight: 0.3980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 204 HIS ** A 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.146214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.119339 restraints weight = 12801.377| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.44 r_work: 0.3403 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4774 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= 0.170 Angle : 0.576 9.850 12274 Z= 0.304 Chirality : 0.043 0.250 1332 Planarity : 0.004 0.045 1448 Dihedral : 18.168 136.880 1460 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.18 % Favored : 96.72 % Rotamer: Outliers : 2.73 % Allowed : 22.98 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.28), residues: 975 helix: 2.05 (0.25), residues: 443 sheet: 0.26 (0.39), residues: 161 loop : -0.47 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 824 TYR 0.021 0.001 TYR A 947 PHE 0.024 0.002 PHE A 126 TRP 0.009 0.001 TRP A 241 HIS 0.005 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 8970) covalent geometry : angle 0.57630 (12274) hydrogen bonds : bond 0.04234 ( 452) hydrogen bonds : angle 4.11240 ( 1274) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 318 time to evaluate : 0.298 Fit side-chains REVERT: A 9 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7430 (tt0) REVERT: A 23 THR cc_start: 0.8718 (t) cc_final: 0.8429 (p) REVERT: A 27 GLN cc_start: 0.8579 (tp40) cc_final: 0.8167 (tp-100) REVERT: A 38 ASP cc_start: 0.7616 (t0) cc_final: 0.7335 (t0) REVERT: A 41 GLU cc_start: 0.7972 (pt0) cc_final: 0.7610 (pt0) REVERT: A 54 SER cc_start: 0.8519 (m) cc_final: 0.8192 (p) REVERT: A 56 GLU cc_start: 0.7767 (pt0) cc_final: 0.7254 (pt0) REVERT: A 62 GLU cc_start: 0.7616 (tt0) cc_final: 0.7366 (tt0) REVERT: A 75 GLN cc_start: 0.8416 (tm-30) cc_final: 0.7772 (tm-30) REVERT: A 85 PHE cc_start: 0.8953 (t80) cc_final: 0.8536 (t80) REVERT: A 91 THR cc_start: 0.8538 (m) cc_final: 0.8330 (p) REVERT: A 109 MET cc_start: 0.7887 (mmm) cc_final: 0.7659 (mmt) REVERT: A 127 LYS cc_start: 0.8570 (ttmm) cc_final: 0.8142 (ttmm) REVERT: A 134 LYS cc_start: 0.8159 (mmmm) cc_final: 0.7841 (mmmm) REVERT: A 142 MET cc_start: 0.8052 (mmm) cc_final: 0.7774 (tmm) REVERT: A 149 ASP cc_start: 0.7489 (p0) cc_final: 0.7049 (p0) REVERT: A 157 MET cc_start: 0.8348 (mmm) cc_final: 0.8110 (tpp) REVERT: A 180 ARG cc_start: 0.7848 (mtm110) cc_final: 0.7431 (mtm110) REVERT: A 183 VAL cc_start: 0.8480 (p) cc_final: 0.8242 (m) REVERT: A 191 GLU cc_start: 0.7846 (mp0) cc_final: 0.7494 (mp0) REVERT: A 194 VAL cc_start: 0.8629 (p) cc_final: 0.8318 (m) REVERT: A 208 MET cc_start: 0.8215 (ttm) cc_final: 0.7980 (ttp) REVERT: A 242 ILE cc_start: 0.8285 (tp) cc_final: 0.8038 (mm) REVERT: A 255 MET cc_start: 0.8317 (mmt) cc_final: 0.7779 (mmt) REVERT: A 277 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8130 (mm) REVERT: A 285 ARG cc_start: 0.8571 (ttm-80) cc_final: 0.8118 (mmm-85) REVERT: A 289 ASP cc_start: 0.8022 (m-30) cc_final: 0.7818 (m-30) REVERT: A 307 LYS cc_start: 0.8549 (mmtt) cc_final: 0.7976 (mmmt) REVERT: A 321 MET cc_start: 0.8351 (ttp) cc_final: 0.8105 (ttm) REVERT: A 349 LYS cc_start: 0.8365 (tttt) cc_final: 0.8141 (tttm) REVERT: A 376 LYS cc_start: 0.8285 (mmtt) cc_final: 0.8014 (mmtm) REVERT: A 399 TYR cc_start: 0.7953 (m-80) cc_final: 0.7001 (m-80) REVERT: A 404 LYS cc_start: 0.8385 (tttm) cc_final: 0.8115 (tttm) REVERT: A 417 VAL cc_start: 0.8522 (t) cc_final: 0.8310 (t) REVERT: A 434 ARG cc_start: 0.8365 (mmm160) cc_final: 0.8059 (tpt90) REVERT: A 455 CYS cc_start: 0.7831 (m) cc_final: 0.7596 (m) REVERT: A 476 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7301 (tm-30) REVERT: A 511 LYS cc_start: 0.8646 (ptpp) cc_final: 0.8283 (ptpp) REVERT: A 579 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7632 (ttm) REVERT: A 588 ASP cc_start: 0.8039 (t70) cc_final: 0.7587 (t0) REVERT: A 599 GLU cc_start: 0.7989 (tt0) cc_final: 0.7763 (tt0) REVERT: A 630 LYS cc_start: 0.8440 (mttt) cc_final: 0.8111 (mttp) REVERT: A 632 LYS cc_start: 0.8342 (tptt) cc_final: 0.7834 (ttmm) REVERT: A 635 LYS cc_start: 0.8359 (ttpt) cc_final: 0.7757 (ttmm) REVERT: A 636 ILE cc_start: 0.8502 (tt) cc_final: 0.8241 (tt) REVERT: A 670 LYS cc_start: 0.8487 (ttmm) cc_final: 0.8174 (ttmm) REVERT: A 676 VAL cc_start: 0.8366 (t) cc_final: 0.8139 (m) REVERT: A 690 SER cc_start: 0.8261 (t) cc_final: 0.7953 (p) REVERT: A 711 GLN cc_start: 0.8239 (tp40) cc_final: 0.7814 (tp40) REVERT: A 721 CYS cc_start: 0.8169 (m) cc_final: 0.7720 (m) REVERT: A 742 TYR cc_start: 0.8979 (t80) cc_final: 0.8772 (t80) REVERT: A 747 ASN cc_start: 0.8069 (p0) cc_final: 0.7780 (p0) REVERT: A 770 LYS cc_start: 0.8084 (mttp) cc_final: 0.7746 (mttp) REVERT: A 778 ASN cc_start: 0.8800 (m-40) cc_final: 0.8367 (m-40) REVERT: A 787 LEU cc_start: 0.8707 (mm) cc_final: 0.8431 (mt) REVERT: A 793 ASP cc_start: 0.7759 (t0) cc_final: 0.7480 (t0) REVERT: A 804 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7872 (mmtt) REVERT: A 810 ILE cc_start: 0.8531 (mt) cc_final: 0.8245 (tp) REVERT: A 811 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7666 (mtt) REVERT: A 813 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8034 (mm-30) REVERT: A 816 LYS cc_start: 0.8594 (ptpp) cc_final: 0.8056 (ptpp) REVERT: A 818 ARG cc_start: 0.7983 (mtt90) cc_final: 0.7454 (mtt90) REVERT: A 819 ARG cc_start: 0.6975 (ttm-80) cc_final: 0.6545 (ttm110) REVERT: A 842 MET cc_start: 0.7826 (ttt) cc_final: 0.7443 (tpp) REVERT: A 847 PHE cc_start: 0.8595 (t80) cc_final: 0.8057 (t80) REVERT: A 851 ILE cc_start: 0.8710 (mt) cc_final: 0.8479 (mp) REVERT: A 869 MET cc_start: 0.7757 (mmm) cc_final: 0.7518 (mmm) REVERT: A 872 MET cc_start: 0.8086 (mmm) cc_final: 0.7784 (mmm) REVERT: A 942 PHE cc_start: 0.7817 (t80) cc_final: 0.7331 (t80) REVERT: A 946 ASN cc_start: 0.8357 (m110) cc_final: 0.7878 (m110) REVERT: A 952 CYS cc_start: 0.8327 (t) cc_final: 0.7861 (t) REVERT: A 954 ARG cc_start: 0.8192 (mmt180) cc_final: 0.7983 (mmt180) REVERT: A 976 GLN cc_start: 0.7608 (tt0) cc_final: 0.7196 (tt0) outliers start: 24 outliers final: 12 residues processed: 323 average time/residue: 0.1128 time to fit residues: 46.9811 Evaluate side-chains 330 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 314 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 189 THR Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 638 MET Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 811 MET Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 958 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 90 optimal weight: 0.0370 chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 overall best weight: 0.5060 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.147841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.121014 restraints weight = 12807.449| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.46 r_work: 0.3423 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4953 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= 0.124 Angle : 0.559 9.759 12274 Z= 0.292 Chirality : 0.041 0.241 1332 Planarity : 0.004 0.045 1448 Dihedral : 17.991 137.266 1460 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.08 % Favored : 96.82 % Rotamer: Outliers : 2.73 % Allowed : 23.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.28), residues: 975 helix: 2.06 (0.25), residues: 443 sheet: 0.10 (0.38), residues: 171 loop : -0.31 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 13 TYR 0.015 0.001 TYR A 97 PHE 0.025 0.002 PHE A 558 TRP 0.007 0.001 TRP A 325 HIS 0.004 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8970) covalent geometry : angle 0.55875 (12274) hydrogen bonds : bond 0.03769 ( 452) hydrogen bonds : angle 4.04233 ( 1274) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 319 time to evaluate : 0.322 Fit side-chains REVERT: A 9 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7410 (tt0) REVERT: A 23 THR cc_start: 0.8713 (t) cc_final: 0.8413 (p) REVERT: A 27 GLN cc_start: 0.8545 (tp40) cc_final: 0.8132 (tp-100) REVERT: A 38 ASP cc_start: 0.7626 (t0) cc_final: 0.7325 (t0) REVERT: A 39 ILE cc_start: 0.8496 (mm) cc_final: 0.8140 (mm) REVERT: A 41 GLU cc_start: 0.7960 (pt0) cc_final: 0.7602 (pt0) REVERT: A 54 SER cc_start: 0.8506 (m) cc_final: 0.8032 (t) REVERT: A 56 GLU cc_start: 0.7727 (pt0) cc_final: 0.7219 (pt0) REVERT: A 62 GLU cc_start: 0.7641 (tt0) cc_final: 0.7398 (tt0) REVERT: A 74 VAL cc_start: 0.8587 (t) cc_final: 0.8236 (m) REVERT: A 75 GLN cc_start: 0.8425 (tm-30) cc_final: 0.7723 (tm-30) REVERT: A 85 PHE cc_start: 0.8975 (t80) cc_final: 0.8541 (t80) REVERT: A 91 THR cc_start: 0.8513 (m) cc_final: 0.8301 (p) REVERT: A 127 LYS cc_start: 0.8591 (ttmm) cc_final: 0.8157 (ttmm) REVERT: A 134 LYS cc_start: 0.8062 (mmmm) cc_final: 0.7773 (mmmm) REVERT: A 142 MET cc_start: 0.8023 (mmm) cc_final: 0.7764 (tmm) REVERT: A 149 ASP cc_start: 0.7548 (p0) cc_final: 0.7075 (p0) REVERT: A 157 MET cc_start: 0.8320 (mmm) cc_final: 0.8110 (tpp) REVERT: A 163 LYS cc_start: 0.8466 (mmtm) cc_final: 0.8246 (tppt) REVERT: A 174 HIS cc_start: 0.7735 (t-90) cc_final: 0.7464 (t-90) REVERT: A 175 TYR cc_start: 0.8363 (p90) cc_final: 0.8140 (p90) REVERT: A 180 ARG cc_start: 0.7729 (mtm110) cc_final: 0.7345 (mtm110) REVERT: A 183 VAL cc_start: 0.8435 (p) cc_final: 0.8218 (m) REVERT: A 191 GLU cc_start: 0.7833 (mp0) cc_final: 0.7483 (mp0) REVERT: A 194 VAL cc_start: 0.8602 (p) cc_final: 0.8309 (m) REVERT: A 208 MET cc_start: 0.8215 (ttm) cc_final: 0.8010 (ttp) REVERT: A 255 MET cc_start: 0.8301 (mmt) cc_final: 0.7966 (mmt) REVERT: A 277 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8059 (mm) REVERT: A 285 ARG cc_start: 0.8472 (ttm-80) cc_final: 0.7961 (mmm-85) REVERT: A 307 LYS cc_start: 0.8516 (mmtt) cc_final: 0.7956 (mmmt) REVERT: A 321 MET cc_start: 0.8248 (ttp) cc_final: 0.7996 (ttm) REVERT: A 339 LYS cc_start: 0.8470 (mtmm) cc_final: 0.8242 (mtmm) REVERT: A 349 LYS cc_start: 0.8328 (tttt) cc_final: 0.8077 (tttm) REVERT: A 375 PRO cc_start: 0.8485 (Cg_endo) cc_final: 0.8165 (Cg_exo) REVERT: A 376 LYS cc_start: 0.8283 (mmtt) cc_final: 0.7953 (mmtm) REVERT: A 399 TYR cc_start: 0.7905 (m-80) cc_final: 0.6907 (m-80) REVERT: A 404 LYS cc_start: 0.8373 (tttm) cc_final: 0.8095 (tttm) REVERT: A 434 ARG cc_start: 0.8307 (mmm160) cc_final: 0.8032 (tpt90) REVERT: A 475 ASP cc_start: 0.7661 (t0) cc_final: 0.7459 (t0) REVERT: A 476 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7422 (tm-30) REVERT: A 579 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7561 (ttm) REVERT: A 588 ASP cc_start: 0.8030 (t70) cc_final: 0.7570 (t0) REVERT: A 630 LYS cc_start: 0.8455 (mttt) cc_final: 0.8123 (mttp) REVERT: A 632 LYS cc_start: 0.8354 (tptt) cc_final: 0.7841 (ttmm) REVERT: A 635 LYS cc_start: 0.8368 (ttpt) cc_final: 0.7975 (ttpp) REVERT: A 636 ILE cc_start: 0.8487 (tt) cc_final: 0.8109 (tp) REVERT: A 690 SER cc_start: 0.8207 (t) cc_final: 0.7725 (m) REVERT: A 711 GLN cc_start: 0.8271 (tp40) cc_final: 0.7846 (tp40) REVERT: A 721 CYS cc_start: 0.8316 (m) cc_final: 0.7856 (m) REVERT: A 739 VAL cc_start: 0.8978 (t) cc_final: 0.8748 (p) REVERT: A 742 TYR cc_start: 0.8947 (t80) cc_final: 0.8732 (t80) REVERT: A 747 ASN cc_start: 0.8009 (p0) cc_final: 0.7749 (p0) REVERT: A 770 LYS cc_start: 0.8021 (mttp) cc_final: 0.7699 (mttp) REVERT: A 778 ASN cc_start: 0.8766 (m-40) cc_final: 0.8322 (m-40) REVERT: A 793 ASP cc_start: 0.7725 (t0) cc_final: 0.7492 (t0) REVERT: A 804 LYS cc_start: 0.8113 (mmtt) cc_final: 0.7837 (mmtt) REVERT: A 811 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7809 (mtt) REVERT: A 813 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7931 (mm-30) REVERT: A 816 LYS cc_start: 0.8594 (ptpp) cc_final: 0.8057 (ptpp) REVERT: A 818 ARG cc_start: 0.7957 (mtt90) cc_final: 0.7515 (mtt90) REVERT: A 819 ARG cc_start: 0.6997 (ttm-80) cc_final: 0.6547 (ttm110) REVERT: A 831 VAL cc_start: 0.8750 (m) cc_final: 0.8478 (p) REVERT: A 834 VAL cc_start: 0.8782 (t) cc_final: 0.8519 (p) REVERT: A 842 MET cc_start: 0.7824 (ttt) cc_final: 0.7420 (tpp) REVERT: A 847 PHE cc_start: 0.8502 (t80) cc_final: 0.8268 (t80) REVERT: A 851 ILE cc_start: 0.8682 (mt) cc_final: 0.8436 (mp) REVERT: A 872 MET cc_start: 0.8078 (mmm) cc_final: 0.7791 (mmm) REVERT: A 900 TYR cc_start: 0.7990 (p90) cc_final: 0.7415 (p90) REVERT: A 932 LYS cc_start: 0.8883 (mmtt) cc_final: 0.8557 (mmtt) REVERT: A 946 ASN cc_start: 0.8418 (m110) cc_final: 0.7917 (m110) REVERT: A 952 CYS cc_start: 0.8303 (t) cc_final: 0.8004 (t) REVERT: A 976 GLN cc_start: 0.7541 (tt0) cc_final: 0.7192 (tt0) outliers start: 24 outliers final: 13 residues processed: 326 average time/residue: 0.1154 time to fit residues: 48.8679 Evaluate side-chains 330 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 313 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 189 THR Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 811 MET Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 958 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 23 optimal weight: 0.6980 chunk 54 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.143856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.116596 restraints weight = 12865.826| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.50 r_work: 0.3403 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8970 Z= 0.149 Angle : 0.575 8.535 12274 Z= 0.300 Chirality : 0.042 0.236 1332 Planarity : 0.004 0.043 1448 Dihedral : 17.955 137.671 1460 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.28 % Favored : 96.62 % Rotamer: Outliers : 3.07 % Allowed : 23.66 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.28), residues: 975 helix: 2.02 (0.25), residues: 444 sheet: 0.24 (0.40), residues: 158 loop : -0.39 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 790 TYR 0.026 0.001 TYR A 772 PHE 0.031 0.002 PHE A 126 TRP 0.007 0.001 TRP A 241 HIS 0.004 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8970) covalent geometry : angle 0.57493 (12274) hydrogen bonds : bond 0.03930 ( 452) hydrogen bonds : angle 4.09789 ( 1274) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 316 time to evaluate : 0.337 Fit side-chains REVERT: A 22 VAL cc_start: 0.8677 (t) cc_final: 0.8441 (t) REVERT: A 23 THR cc_start: 0.8711 (t) cc_final: 0.8425 (p) REVERT: A 27 GLN cc_start: 0.8600 (tp40) cc_final: 0.8160 (tp-100) REVERT: A 38 ASP cc_start: 0.7636 (t0) cc_final: 0.7372 (t0) REVERT: A 39 ILE cc_start: 0.8553 (mm) cc_final: 0.8179 (mm) REVERT: A 41 GLU cc_start: 0.7970 (pt0) cc_final: 0.7615 (pt0) REVERT: A 54 SER cc_start: 0.8511 (m) cc_final: 0.8256 (t) REVERT: A 56 GLU cc_start: 0.7756 (pt0) cc_final: 0.7236 (pt0) REVERT: A 62 GLU cc_start: 0.7634 (tt0) cc_final: 0.7421 (tt0) REVERT: A 74 VAL cc_start: 0.8604 (t) cc_final: 0.8238 (m) REVERT: A 75 GLN cc_start: 0.8410 (tm-30) cc_final: 0.7739 (tm-30) REVERT: A 85 PHE cc_start: 0.8971 (t80) cc_final: 0.8559 (t80) REVERT: A 91 THR cc_start: 0.8576 (m) cc_final: 0.8372 (p) REVERT: A 109 MET cc_start: 0.7948 (mmm) cc_final: 0.7713 (mmt) REVERT: A 127 LYS cc_start: 0.8593 (ttmm) cc_final: 0.8166 (ttmm) REVERT: A 134 LYS cc_start: 0.8035 (mmmm) cc_final: 0.7770 (mmmm) REVERT: A 142 MET cc_start: 0.8061 (mmm) cc_final: 0.7720 (tmm) REVERT: A 149 ASP cc_start: 0.7505 (p0) cc_final: 0.7056 (p0) REVERT: A 157 MET cc_start: 0.8342 (mmm) cc_final: 0.8105 (tpp) REVERT: A 175 TYR cc_start: 0.8419 (p90) cc_final: 0.8138 (p90) REVERT: A 180 ARG cc_start: 0.7759 (mtm110) cc_final: 0.7310 (mtm110) REVERT: A 183 VAL cc_start: 0.8452 (p) cc_final: 0.8239 (m) REVERT: A 191 GLU cc_start: 0.7805 (mp0) cc_final: 0.7441 (mp0) REVERT: A 194 VAL cc_start: 0.8606 (p) cc_final: 0.8308 (m) REVERT: A 208 MET cc_start: 0.8257 (ttm) cc_final: 0.8053 (ttp) REVERT: A 255 MET cc_start: 0.8321 (mmt) cc_final: 0.7952 (mmt) REVERT: A 277 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8108 (mm) REVERT: A 285 ARG cc_start: 0.8479 (ttm-80) cc_final: 0.7986 (mmm-85) REVERT: A 289 ASP cc_start: 0.8028 (m-30) cc_final: 0.7596 (m-30) REVERT: A 307 LYS cc_start: 0.8536 (mmtt) cc_final: 0.8007 (mmmt) REVERT: A 321 MET cc_start: 0.8270 (ttp) cc_final: 0.8029 (ttm) REVERT: A 349 LYS cc_start: 0.8365 (tttt) cc_final: 0.8112 (tttm) REVERT: A 369 MET cc_start: 0.8077 (mmp) cc_final: 0.7874 (mmt) REVERT: A 375 PRO cc_start: 0.8487 (Cg_endo) cc_final: 0.8170 (Cg_exo) REVERT: A 376 LYS cc_start: 0.8261 (mmtt) cc_final: 0.7951 (mmtm) REVERT: A 399 TYR cc_start: 0.7884 (m-80) cc_final: 0.6986 (m-80) REVERT: A 404 LYS cc_start: 0.8306 (tttm) cc_final: 0.8006 (tttm) REVERT: A 434 ARG cc_start: 0.8316 (mmm160) cc_final: 0.8050 (tpt90) REVERT: A 475 ASP cc_start: 0.7826 (t0) cc_final: 0.7620 (t0) REVERT: A 476 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7417 (tm-30) REVERT: A 511 LYS cc_start: 0.8600 (ptpp) cc_final: 0.8274 (ptpp) REVERT: A 579 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7623 (ttm) REVERT: A 588 ASP cc_start: 0.8050 (t70) cc_final: 0.7596 (t0) REVERT: A 599 GLU cc_start: 0.8011 (tt0) cc_final: 0.7772 (tt0) REVERT: A 632 LYS cc_start: 0.8368 (tptt) cc_final: 0.7812 (ttmm) REVERT: A 635 LYS cc_start: 0.8373 (ttpp) cc_final: 0.7938 (ttpp) REVERT: A 636 ILE cc_start: 0.8528 (tt) cc_final: 0.8150 (tp) REVERT: A 690 SER cc_start: 0.8244 (t) cc_final: 0.7893 (m) REVERT: A 704 THR cc_start: 0.8138 (p) cc_final: 0.7628 (t) REVERT: A 711 GLN cc_start: 0.8316 (tp40) cc_final: 0.7896 (tp40) REVERT: A 718 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: A 747 ASN cc_start: 0.8012 (p0) cc_final: 0.7773 (p0) REVERT: A 770 LYS cc_start: 0.8059 (mttp) cc_final: 0.7745 (mttp) REVERT: A 778 ASN cc_start: 0.8767 (m-40) cc_final: 0.8337 (m-40) REVERT: A 782 PHE cc_start: 0.8788 (m-80) cc_final: 0.8410 (m-10) REVERT: A 793 ASP cc_start: 0.7793 (t0) cc_final: 0.7578 (t0) REVERT: A 804 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7954 (mmtt) REVERT: A 813 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7859 (mm-30) REVERT: A 816 LYS cc_start: 0.8514 (ptpp) cc_final: 0.7628 (ptpp) REVERT: A 819 ARG cc_start: 0.7263 (ttm-80) cc_final: 0.6756 (ttm110) REVERT: A 834 VAL cc_start: 0.8781 (t) cc_final: 0.8530 (p) REVERT: A 842 MET cc_start: 0.7902 (ttt) cc_final: 0.7492 (tpp) REVERT: A 847 PHE cc_start: 0.8518 (t80) cc_final: 0.8253 (t80) REVERT: A 851 ILE cc_start: 0.8693 (mt) cc_final: 0.8451 (mp) REVERT: A 923 ASP cc_start: 0.7827 (m-30) cc_final: 0.7335 (m-30) REVERT: A 932 LYS cc_start: 0.8839 (mmtt) cc_final: 0.8447 (mmtt) REVERT: A 946 ASN cc_start: 0.8465 (m110) cc_final: 0.8109 (m110) REVERT: A 952 CYS cc_start: 0.8264 (t) cc_final: 0.7835 (t) outliers start: 27 outliers final: 16 residues processed: 325 average time/residue: 0.1186 time to fit residues: 49.9458 Evaluate side-chains 341 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 322 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 579 MET 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 774 ILE Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 958 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 52 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 81 optimal weight: 0.0270 chunk 86 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 823 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.144523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.117682 restraints weight = 12669.996| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.39 r_work: 0.3419 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.5345 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= 0.132 Angle : 0.578 8.685 12274 Z= 0.303 Chirality : 0.042 0.239 1332 Planarity : 0.004 0.045 1448 Dihedral : 17.942 138.029 1460 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.67 % Favored : 97.23 % Rotamer: Outliers : 2.39 % Allowed : 24.80 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.28), residues: 975 helix: 2.00 (0.25), residues: 443 sheet: 0.18 (0.39), residues: 163 loop : -0.36 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 13 TYR 0.025 0.001 TYR A 772 PHE 0.034 0.002 PHE A 126 TRP 0.006 0.001 TRP A 325 HIS 0.016 0.001 HIS A 823 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8970) covalent geometry : angle 0.57819 (12274) hydrogen bonds : bond 0.03722 ( 452) hydrogen bonds : angle 4.09607 ( 1274) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 330 time to evaluate : 0.243 Fit side-chains REVERT: A 5 MET cc_start: 0.7368 (ttp) cc_final: 0.6627 (ttm) REVERT: A 9 GLU cc_start: 0.7760 (tt0) cc_final: 0.7255 (tt0) REVERT: A 21 ARG cc_start: 0.8301 (ttp80) cc_final: 0.8086 (ttp80) REVERT: A 22 VAL cc_start: 0.8686 (t) cc_final: 0.8454 (t) REVERT: A 23 THR cc_start: 0.8694 (t) cc_final: 0.8415 (p) REVERT: A 38 ASP cc_start: 0.7611 (t0) cc_final: 0.7312 (t0) REVERT: A 39 ILE cc_start: 0.8541 (mm) cc_final: 0.8148 (mm) REVERT: A 41 GLU cc_start: 0.7912 (pt0) cc_final: 0.7568 (pt0) REVERT: A 54 SER cc_start: 0.8510 (m) cc_final: 0.8238 (t) REVERT: A 56 GLU cc_start: 0.7754 (pt0) cc_final: 0.7372 (pt0) REVERT: A 74 VAL cc_start: 0.8606 (t) cc_final: 0.8235 (m) REVERT: A 75 GLN cc_start: 0.8387 (tm-30) cc_final: 0.7714 (tm-30) REVERT: A 85 PHE cc_start: 0.8959 (t80) cc_final: 0.8541 (t80) REVERT: A 91 THR cc_start: 0.8584 (m) cc_final: 0.8364 (p) REVERT: A 127 LYS cc_start: 0.8601 (ttmm) cc_final: 0.8184 (ttmm) REVERT: A 134 LYS cc_start: 0.7989 (mmmm) cc_final: 0.7728 (mmmm) REVERT: A 142 MET cc_start: 0.8078 (mmm) cc_final: 0.7698 (tmm) REVERT: A 149 ASP cc_start: 0.7500 (p0) cc_final: 0.7047 (p0) REVERT: A 157 MET cc_start: 0.8298 (mmm) cc_final: 0.8086 (tpp) REVERT: A 175 TYR cc_start: 0.8389 (p90) cc_final: 0.8113 (p90) REVERT: A 180 ARG cc_start: 0.7711 (mtm110) cc_final: 0.7240 (mtm110) REVERT: A 183 VAL cc_start: 0.8427 (p) cc_final: 0.8211 (m) REVERT: A 191 GLU cc_start: 0.7799 (mp0) cc_final: 0.7446 (mp0) REVERT: A 194 VAL cc_start: 0.8592 (p) cc_final: 0.8301 (m) REVERT: A 255 MET cc_start: 0.8321 (mmt) cc_final: 0.7988 (mmt) REVERT: A 277 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8069 (mm) REVERT: A 282 GLN cc_start: 0.8286 (tp40) cc_final: 0.7995 (tp40) REVERT: A 285 ARG cc_start: 0.8435 (ttm-80) cc_final: 0.7953 (mmm-85) REVERT: A 289 ASP cc_start: 0.7960 (m-30) cc_final: 0.7562 (m-30) REVERT: A 307 LYS cc_start: 0.8514 (mmtt) cc_final: 0.8005 (mmmt) REVERT: A 321 MET cc_start: 0.8251 (ttp) cc_final: 0.8009 (ttm) REVERT: A 339 LYS cc_start: 0.8450 (mtmm) cc_final: 0.8140 (mtpp) REVERT: A 349 LYS cc_start: 0.8346 (tttt) cc_final: 0.8092 (tttm) REVERT: A 369 MET cc_start: 0.7978 (mmp) cc_final: 0.7771 (mmt) REVERT: A 375 PRO cc_start: 0.8445 (Cg_endo) cc_final: 0.8118 (Cg_exo) REVERT: A 376 LYS cc_start: 0.8256 (mmtt) cc_final: 0.7928 (mmtm) REVERT: A 399 TYR cc_start: 0.7850 (m-80) cc_final: 0.6921 (m-80) REVERT: A 404 LYS cc_start: 0.8285 (tttm) cc_final: 0.7965 (tttm) REVERT: A 426 GLN cc_start: 0.8574 (tp40) cc_final: 0.7842 (tp-100) REVERT: A 434 ARG cc_start: 0.8279 (mmm160) cc_final: 0.8021 (tpt90) REVERT: A 476 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7348 (tm-30) REVERT: A 511 LYS cc_start: 0.8684 (ptpp) cc_final: 0.8166 (ptpp) REVERT: A 529 TYR cc_start: 0.8134 (m-80) cc_final: 0.7908 (m-80) REVERT: A 579 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7613 (ttm) REVERT: A 588 ASP cc_start: 0.8027 (t70) cc_final: 0.7564 (t0) REVERT: A 599 GLU cc_start: 0.8007 (tt0) cc_final: 0.7771 (tt0) REVERT: A 630 LYS cc_start: 0.8462 (mttt) cc_final: 0.8155 (mttp) REVERT: A 632 LYS cc_start: 0.8357 (tptt) cc_final: 0.7810 (ttmm) REVERT: A 635 LYS cc_start: 0.8355 (ttpp) cc_final: 0.7947 (ttpp) REVERT: A 636 ILE cc_start: 0.8543 (tt) cc_final: 0.8153 (tp) REVERT: A 666 GLN cc_start: 0.8354 (mm-40) cc_final: 0.7988 (mm110) REVERT: A 670 LYS cc_start: 0.8476 (ttmm) cc_final: 0.8214 (ttmm) REVERT: A 690 SER cc_start: 0.8275 (t) cc_final: 0.7868 (m) REVERT: A 711 GLN cc_start: 0.8345 (tp40) cc_final: 0.7873 (tp40) REVERT: A 718 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: A 742 TYR cc_start: 0.8981 (t80) cc_final: 0.8772 (t80) REVERT: A 770 LYS cc_start: 0.8061 (mttp) cc_final: 0.7752 (mttp) REVERT: A 778 ASN cc_start: 0.8750 (m-40) cc_final: 0.8267 (m-40) REVERT: A 782 PHE cc_start: 0.8697 (m-80) cc_final: 0.8427 (m-80) REVERT: A 793 ASP cc_start: 0.7795 (t0) cc_final: 0.7585 (t0) REVERT: A 804 LYS cc_start: 0.8332 (mmtt) cc_final: 0.8062 (mmtt) REVERT: A 813 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7970 (mm-30) REVERT: A 816 LYS cc_start: 0.8711 (ptpp) cc_final: 0.8261 (ptpp) REVERT: A 819 ARG cc_start: 0.7267 (ttm-80) cc_final: 0.6819 (ttm110) REVERT: A 834 VAL cc_start: 0.8747 (t) cc_final: 0.8499 (p) REVERT: A 842 MET cc_start: 0.7855 (ttt) cc_final: 0.7507 (tpp) REVERT: A 847 PHE cc_start: 0.8555 (t80) cc_final: 0.8312 (t80) REVERT: A 850 PHE cc_start: 0.8184 (m-10) cc_final: 0.7931 (m-80) REVERT: A 851 ILE cc_start: 0.8690 (mt) cc_final: 0.8418 (mp) REVERT: A 942 PHE cc_start: 0.8010 (t80) cc_final: 0.7540 (t80) REVERT: A 946 ASN cc_start: 0.8460 (m110) cc_final: 0.7955 (m110) REVERT: A 952 CYS cc_start: 0.8262 (t) cc_final: 0.7777 (t) REVERT: A 958 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6865 (mp0) REVERT: A 963 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8275 (mm110) REVERT: A 978 ARG cc_start: 0.8320 (mtt180) cc_final: 0.8056 (mtt180) outliers start: 21 outliers final: 13 residues processed: 338 average time/residue: 0.1183 time to fit residues: 51.9800 Evaluate side-chains 332 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 315 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 712 LYS Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 943 TYR Chi-restraints excluded: chain A residue 958 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 79 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 174 HIS A 227 GLN A 844 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.144395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.117819 restraints weight = 12630.404| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.36 r_work: 0.3429 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8970 Z= 0.132 Angle : 0.596 8.381 12274 Z= 0.310 Chirality : 0.042 0.244 1332 Planarity : 0.004 0.042 1448 Dihedral : 17.860 138.348 1458 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.97 % Favored : 96.92 % Rotamer: Outliers : 2.05 % Allowed : 26.51 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.28), residues: 975 helix: 1.98 (0.25), residues: 444 sheet: 0.08 (0.40), residues: 167 loop : -0.29 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 13 TYR 0.024 0.001 TYR A 772 PHE 0.035 0.002 PHE A 126 TRP 0.006 0.001 TRP A 241 HIS 0.007 0.001 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8970) covalent geometry : angle 0.59596 (12274) hydrogen bonds : bond 0.03627 ( 452) hydrogen bonds : angle 4.08300 ( 1274) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 330 time to evaluate : 0.301 Fit side-chains REVERT: A 5 MET cc_start: 0.7301 (ttp) cc_final: 0.6509 (ttm) REVERT: A 9 GLU cc_start: 0.7765 (tt0) cc_final: 0.7273 (tt0) REVERT: A 11 VAL cc_start: 0.8631 (t) cc_final: 0.8331 (p) REVERT: A 21 ARG cc_start: 0.8284 (ttp80) cc_final: 0.8064 (ttp80) REVERT: A 22 VAL cc_start: 0.8686 (t) cc_final: 0.8460 (t) REVERT: A 23 THR cc_start: 0.8667 (t) cc_final: 0.8396 (p) REVERT: A 38 ASP cc_start: 0.7602 (t0) cc_final: 0.7327 (t0) REVERT: A 39 ILE cc_start: 0.8550 (mm) cc_final: 0.8254 (mm) REVERT: A 41 GLU cc_start: 0.7915 (pt0) cc_final: 0.7567 (pt0) REVERT: A 54 SER cc_start: 0.8521 (m) cc_final: 0.8219 (t) REVERT: A 56 GLU cc_start: 0.7709 (pt0) cc_final: 0.7349 (pt0) REVERT: A 74 VAL cc_start: 0.8603 (t) cc_final: 0.8250 (m) REVERT: A 75 GLN cc_start: 0.8387 (tm-30) cc_final: 0.7714 (tm-30) REVERT: A 85 PHE cc_start: 0.8917 (t80) cc_final: 0.8503 (t80) REVERT: A 91 THR cc_start: 0.8569 (m) cc_final: 0.8350 (p) REVERT: A 109 MET cc_start: 0.7923 (mmm) cc_final: 0.7710 (mmt) REVERT: A 127 LYS cc_start: 0.8522 (ttmm) cc_final: 0.8115 (ttmm) REVERT: A 134 LYS cc_start: 0.7977 (mmmm) cc_final: 0.7729 (mmmm) REVERT: A 142 MET cc_start: 0.8091 (mmm) cc_final: 0.7713 (tmm) REVERT: A 149 ASP cc_start: 0.7509 (p0) cc_final: 0.7064 (p0) REVERT: A 175 TYR cc_start: 0.8365 (p90) cc_final: 0.8062 (p90) REVERT: A 180 ARG cc_start: 0.7689 (mtm110) cc_final: 0.7481 (mtm110) REVERT: A 183 VAL cc_start: 0.8400 (p) cc_final: 0.8189 (m) REVERT: A 191 GLU cc_start: 0.7757 (mp0) cc_final: 0.7420 (mp0) REVERT: A 194 VAL cc_start: 0.8560 (p) cc_final: 0.8298 (m) REVERT: A 255 MET cc_start: 0.8320 (mmt) cc_final: 0.7989 (mmt) REVERT: A 277 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8050 (mm) REVERT: A 282 GLN cc_start: 0.8318 (tp40) cc_final: 0.8096 (tp40) REVERT: A 285 ARG cc_start: 0.8452 (ttm-80) cc_final: 0.7965 (mmm-85) REVERT: A 289 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7602 (m-30) REVERT: A 307 LYS cc_start: 0.8520 (mmtt) cc_final: 0.8010 (mmmt) REVERT: A 321 MET cc_start: 0.8143 (ttp) cc_final: 0.7897 (ttm) REVERT: A 349 LYS cc_start: 0.8335 (tttt) cc_final: 0.8089 (tttm) REVERT: A 375 PRO cc_start: 0.8446 (Cg_endo) cc_final: 0.8108 (Cg_exo) REVERT: A 376 LYS cc_start: 0.8239 (mmtt) cc_final: 0.7917 (mmtm) REVERT: A 399 TYR cc_start: 0.7817 (m-80) cc_final: 0.6877 (m-80) REVERT: A 404 LYS cc_start: 0.8292 (tttm) cc_final: 0.7953 (tttm) REVERT: A 426 GLN cc_start: 0.8568 (tp40) cc_final: 0.8115 (tp40) REVERT: A 434 ARG cc_start: 0.8260 (mmm160) cc_final: 0.7988 (tpt90) REVERT: A 469 ILE cc_start: 0.8494 (mt) cc_final: 0.8184 (tt) REVERT: A 476 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7331 (tm-30) REVERT: A 529 TYR cc_start: 0.8188 (m-80) cc_final: 0.7914 (m-80) REVERT: A 547 MET cc_start: 0.7676 (tpp) cc_final: 0.7150 (mmm) REVERT: A 551 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6442 (mm-30) REVERT: A 579 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7645 (ttm) REVERT: A 588 ASP cc_start: 0.8001 (t70) cc_final: 0.7539 (t0) REVERT: A 599 GLU cc_start: 0.7957 (tt0) cc_final: 0.7718 (tt0) REVERT: A 630 LYS cc_start: 0.8450 (mttt) cc_final: 0.8145 (mttp) REVERT: A 632 LYS cc_start: 0.8359 (tptt) cc_final: 0.7821 (ttmm) REVERT: A 635 LYS cc_start: 0.8367 (ttpp) cc_final: 0.7935 (ttpp) REVERT: A 636 ILE cc_start: 0.8521 (tt) cc_final: 0.8135 (tp) REVERT: A 666 GLN cc_start: 0.8328 (mm-40) cc_final: 0.7977 (mm110) REVERT: A 690 SER cc_start: 0.8251 (t) cc_final: 0.7890 (m) REVERT: A 711 GLN cc_start: 0.8246 (tp40) cc_final: 0.7865 (tp40) REVERT: A 712 LYS cc_start: 0.8491 (tptm) cc_final: 0.8228 (tptm) REVERT: A 718 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: A 742 TYR cc_start: 0.8970 (t80) cc_final: 0.8691 (t80) REVERT: A 756 TYR cc_start: 0.7103 (t80) cc_final: 0.6859 (t80) REVERT: A 770 LYS cc_start: 0.8039 (mttp) cc_final: 0.7728 (mttp) REVERT: A 778 ASN cc_start: 0.8702 (m-40) cc_final: 0.8245 (m-40) REVERT: A 804 LYS cc_start: 0.8269 (mmtt) cc_final: 0.7957 (mmtt) REVERT: A 813 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7762 (mm-30) REVERT: A 816 LYS cc_start: 0.8636 (ptpp) cc_final: 0.7779 (ptpp) REVERT: A 819 ARG cc_start: 0.7294 (ttm-80) cc_final: 0.6816 (ttm110) REVERT: A 834 VAL cc_start: 0.8749 (t) cc_final: 0.8503 (p) REVERT: A 842 MET cc_start: 0.7826 (ttt) cc_final: 0.7488 (tpp) REVERT: A 847 PHE cc_start: 0.8641 (t80) cc_final: 0.8206 (t80) REVERT: A 851 ILE cc_start: 0.8757 (mt) cc_final: 0.8460 (mm) REVERT: A 942 PHE cc_start: 0.8071 (t80) cc_final: 0.7628 (t80) REVERT: A 946 ASN cc_start: 0.8507 (m110) cc_final: 0.7955 (m110) REVERT: A 952 CYS cc_start: 0.8230 (t) cc_final: 0.7781 (t) REVERT: A 958 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6892 (mp0) outliers start: 18 outliers final: 9 residues processed: 336 average time/residue: 0.1214 time to fit residues: 52.7442 Evaluate side-chains 332 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 318 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 836 LYS Chi-restraints excluded: chain A residue 888 GLN Chi-restraints excluded: chain A residue 958 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 58 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 49 optimal weight: 0.2980 chunk 11 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 227 GLN A 722 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.147849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.120843 restraints weight = 12843.388| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.51 r_work: 0.3402 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8970 Z= 0.144 Angle : 0.628 9.636 12274 Z= 0.324 Chirality : 0.043 0.261 1332 Planarity : 0.004 0.040 1448 Dihedral : 17.802 138.638 1458 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.87 % Favored : 97.03 % Rotamer: Outliers : 1.48 % Allowed : 27.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.28), residues: 975 helix: 1.92 (0.25), residues: 444 sheet: 0.14 (0.39), residues: 171 loop : -0.31 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 13 TYR 0.025 0.001 TYR A 772 PHE 0.044 0.002 PHE A 126 TRP 0.006 0.001 TRP A 241 HIS 0.005 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8970) covalent geometry : angle 0.62825 (12274) hydrogen bonds : bond 0.03725 ( 452) hydrogen bonds : angle 4.09964 ( 1274) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1950 Ramachandran restraints generated. 975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 323 time to evaluate : 0.315 Fit side-chains REVERT: A 5 MET cc_start: 0.7500 (ttp) cc_final: 0.6617 (ttm) REVERT: A 9 GLU cc_start: 0.7845 (tt0) cc_final: 0.7308 (tt0) REVERT: A 11 VAL cc_start: 0.8634 (t) cc_final: 0.8321 (p) REVERT: A 19 THR cc_start: 0.8383 (p) cc_final: 0.8076 (t) REVERT: A 21 ARG cc_start: 0.8340 (ttp80) cc_final: 0.8136 (ttp80) REVERT: A 22 VAL cc_start: 0.8689 (t) cc_final: 0.8460 (t) REVERT: A 23 THR cc_start: 0.8666 (t) cc_final: 0.8392 (p) REVERT: A 38 ASP cc_start: 0.7646 (t0) cc_final: 0.7363 (t0) REVERT: A 39 ILE cc_start: 0.8552 (mm) cc_final: 0.8257 (mm) REVERT: A 41 GLU cc_start: 0.8027 (pt0) cc_final: 0.7646 (pt0) REVERT: A 54 SER cc_start: 0.8482 (m) cc_final: 0.8220 (t) REVERT: A 56 GLU cc_start: 0.7763 (pt0) cc_final: 0.7377 (pt0) REVERT: A 74 VAL cc_start: 0.8550 (t) cc_final: 0.8191 (m) REVERT: A 75 GLN cc_start: 0.8385 (tm-30) cc_final: 0.7693 (tm-30) REVERT: A 85 PHE cc_start: 0.8934 (t80) cc_final: 0.8514 (t80) REVERT: A 91 THR cc_start: 0.8640 (m) cc_final: 0.8370 (p) REVERT: A 127 LYS cc_start: 0.8519 (ttmm) cc_final: 0.8086 (ttmm) REVERT: A 134 LYS cc_start: 0.8029 (mmmm) cc_final: 0.7765 (mmmm) REVERT: A 142 MET cc_start: 0.8058 (mmm) cc_final: 0.7650 (tmm) REVERT: A 149 ASP cc_start: 0.7550 (p0) cc_final: 0.7095 (p0) REVERT: A 180 ARG cc_start: 0.7715 (mtm110) cc_final: 0.7471 (mtm110) REVERT: A 183 VAL cc_start: 0.8437 (p) cc_final: 0.8226 (m) REVERT: A 191 GLU cc_start: 0.7812 (mp0) cc_final: 0.7467 (mp0) REVERT: A 194 VAL cc_start: 0.8536 (p) cc_final: 0.8264 (m) REVERT: A 255 MET cc_start: 0.8371 (mmt) cc_final: 0.8031 (mmt) REVERT: A 277 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8027 (mm) REVERT: A 285 ARG cc_start: 0.8501 (ttm-80) cc_final: 0.7986 (mmm-85) REVERT: A 289 ASP cc_start: 0.7966 (m-30) cc_final: 0.7605 (m-30) REVERT: A 307 LYS cc_start: 0.8570 (mmtt) cc_final: 0.8038 (mmmt) REVERT: A 321 MET cc_start: 0.8179 (ttp) cc_final: 0.7949 (ttm) REVERT: A 349 LYS cc_start: 0.8369 (tttt) cc_final: 0.8127 (tttm) REVERT: A 375 PRO cc_start: 0.8452 (Cg_endo) cc_final: 0.8121 (Cg_exo) REVERT: A 376 LYS cc_start: 0.8273 (mmtt) cc_final: 0.7867 (mmtm) REVERT: A 399 TYR cc_start: 0.7894 (m-80) cc_final: 0.6829 (m-80) REVERT: A 404 LYS cc_start: 0.8290 (tttm) cc_final: 0.7952 (tttm) REVERT: A 424 ASP cc_start: 0.8157 (t0) cc_final: 0.7732 (t0) REVERT: A 434 ARG cc_start: 0.8250 (mmm160) cc_final: 0.7991 (tpt90) REVERT: A 467 MET cc_start: 0.8133 (ttp) cc_final: 0.7754 (ttm) REVERT: A 476 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7186 (tm-30) REVERT: A 529 TYR cc_start: 0.8226 (m-80) cc_final: 0.7972 (m-80) REVERT: A 546 LEU cc_start: 0.8642 (mt) cc_final: 0.8409 (mm) REVERT: A 547 MET cc_start: 0.7864 (tpp) cc_final: 0.7326 (mmm) REVERT: A 579 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7645 (ttm) REVERT: A 599 GLU cc_start: 0.7954 (tt0) cc_final: 0.7716 (tt0) REVERT: A 630 LYS cc_start: 0.8436 (mttt) cc_final: 0.8135 (mttp) REVERT: A 632 LYS cc_start: 0.8355 (tptt) cc_final: 0.7792 (ttmm) REVERT: A 635 LYS cc_start: 0.8350 (ttpp) cc_final: 0.7890 (ttpp) REVERT: A 636 ILE cc_start: 0.8467 (tt) cc_final: 0.8099 (tp) REVERT: A 666 GLN cc_start: 0.8314 (mm-40) cc_final: 0.7970 (mm-40) REVERT: A 690 SER cc_start: 0.8195 (t) cc_final: 0.7837 (m) REVERT: A 711 GLN cc_start: 0.8378 (tp40) cc_final: 0.7959 (tp40) REVERT: A 712 LYS cc_start: 0.8500 (tptm) cc_final: 0.8192 (tptm) REVERT: A 718 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: A 732 MET cc_start: 0.7991 (ptp) cc_final: 0.7532 (ptm) REVERT: A 735 LEU cc_start: 0.8834 (tt) cc_final: 0.8534 (tp) REVERT: A 741 GLU cc_start: 0.8247 (tp30) cc_final: 0.7908 (tp30) REVERT: A 742 TYR cc_start: 0.8973 (t80) cc_final: 0.8750 (t80) REVERT: A 756 TYR cc_start: 0.7246 (t80) cc_final: 0.7020 (t80) REVERT: A 770 LYS cc_start: 0.8097 (mttp) cc_final: 0.7757 (mttp) REVERT: A 778 ASN cc_start: 0.8773 (m-40) cc_final: 0.8303 (m-40) REVERT: A 804 LYS cc_start: 0.8380 (mmtt) cc_final: 0.8080 (mmtt) REVERT: A 813 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7880 (mm-30) REVERT: A 816 LYS cc_start: 0.8717 (ptpp) cc_final: 0.8229 (ptpp) REVERT: A 819 ARG cc_start: 0.7409 (ttm-80) cc_final: 0.6911 (ttm110) REVERT: A 834 VAL cc_start: 0.8758 (t) cc_final: 0.8513 (p) REVERT: A 842 MET cc_start: 0.7969 (ttt) cc_final: 0.7507 (tpp) REVERT: A 844 GLN cc_start: 0.8418 (pt0) cc_final: 0.8167 (pt0) REVERT: A 847 PHE cc_start: 0.8665 (t80) cc_final: 0.8233 (t80) REVERT: A 851 ILE cc_start: 0.8758 (mt) cc_final: 0.8449 (mm) REVERT: A 923 ASP cc_start: 0.7942 (m-30) cc_final: 0.7445 (m-30) REVERT: A 946 ASN cc_start: 0.8530 (m110) cc_final: 0.8269 (m110) REVERT: A 952 CYS cc_start: 0.8315 (t) cc_final: 0.7807 (t) REVERT: A 958 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.7006 (mp0) outliers start: 13 outliers final: 8 residues processed: 328 average time/residue: 0.1194 time to fit residues: 50.4013 Evaluate side-chains 339 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 327 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 718 GLU 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 40 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 88 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.141795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.114985 restraints weight = 12825.887| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.49 r_work: 0.3375 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.5748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8970 Z= 0.165 Angle : 0.649 9.736 12274 Z= 0.338 Chirality : 0.043 0.257 1332 Planarity : 0.005 0.074 1448 Dihedral : 17.737 138.909 1458 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.28 % Favored : 96.62 % Rotamer: Outliers : 1.59 % Allowed : 27.99 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.28), residues: 975 helix: 1.89 (0.25), residues: 443 sheet: 0.29 (0.40), residues: 163 loop : -0.39 (0.35), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 99 TYR 0.030 0.001 TYR A 772 PHE 0.046 0.002 PHE A 126 TRP 0.007 0.001 TRP A 169 HIS 0.002 0.001 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8970) covalent geometry : angle 0.64909 (12274) hydrogen bonds : bond 0.03923 ( 452) hydrogen bonds : angle 4.15609 ( 1274) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2152.40 seconds wall clock time: 37 minutes 41.92 seconds (2261.92 seconds total)