Starting phenix.real_space_refine on Wed Aug 5 12:39:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hud_35035/08_2026/8hud_35035_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hud_35035/08_2026/8hud_35035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hud_35035/08_2026/8hud_35035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hud_35035/08_2026/8hud_35035.map" model { file = "/net/cci-nas-00/data/ceres_data/8hud_35035/08_2026/8hud_35035_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hud_35035/08_2026/8hud_35035_neut.cif" } resolution = 3.43 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= -0.000 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1238 atoms to isotropic. 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 106 5.49 5 S 26 5.16 5 C 5114 2.51 5 N 1515 2.21 5 O 1909 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8670 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 6406 Classifications: {'peptide': 767} Link IDs: {'PTRANS': 14, 'TRANS': 752} Chain breaks: 6 Chain: "B" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1526 Classifications: {'RNA': 72} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 33, 'rna3p_pyr': 34} Link IDs: {'rna2p': 5, 'rna3p': 66} Chain: "C" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 574 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "D" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 164 Classifications: {'DNA': 8} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 7} Time building chain proxies: 1.85, per 1000 atoms: 0.21 Number of scatterers: 8670 At special positions: 0 Unit cell: (82, 105.78, 134.48, 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 26 16.00 P 106 15.00 O 1909 8.00 N 1515 7.00 C 5114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 816 " - pdb=" SG CYS A 976 " distance=2.08 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: 0.80 Conformation dependent library (CDL) restraints added in 161.9 milliseconds 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1462 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 7 sheets defined 46.5% alpha, 10.3% beta 40 base pairs and 65 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 38 through 71 Processing helix chain 'A' and resid 82 through 93 removed outlier: 3.928A pdb=" N THR A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 108 Processing helix chain 'A' and resid 127 through 140 removed outlier: 3.500A pdb=" N LYS A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 155 Processing helix chain 'A' and resid 178 through 196 Processing helix chain 'A' and resid 201 through 213 Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.606A pdb=" N LYS A 253 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 286 removed outlier: 3.748A pdb=" N GLN A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 308 Processing helix chain 'A' and resid 312 through 322 Processing helix chain 'A' and resid 345 through 358 removed outlier: 4.281A pdb=" N THR A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 379 Processing helix chain 'A' and resid 381 through 392 Processing helix chain 'A' and resid 397 through 411 Processing helix chain 'A' and resid 412 through 415 Processing helix chain 'A' and resid 422 through 436 Proline residue: A 431 - end of helix Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 454 through 460 Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 476 through 495 Processing helix chain 'A' and resid 685 through 700 Processing helix chain 'A' and resid 845 through 858 Processing helix chain 'A' and resid 871 through 884 removed outlier: 4.037A pdb=" N ARG A 875 " --> pdb=" O PRO A 871 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP A 876 " --> pdb=" O LYS A 872 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N MET A 877 " --> pdb=" O THR A 873 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 878 " --> pdb=" O TYR A 874 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR A 883 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR A 884 " --> pdb=" O ILE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 931 through 935 removed outlier: 3.735A pdb=" N GLY A 935 " --> pdb=" O HIS A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 995 Processing helix chain 'A' and resid 1007 through 1011 Processing helix chain 'A' and resid 1027 through 1031 removed outlier: 3.651A pdb=" N GLU A1031 " --> pdb=" O LYS A1028 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 267 through 268 removed outlier: 3.543A pdb=" N ALA A 267 " --> pdb=" O HIS A 419 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 291 through 292 removed outlier: 3.517A pdb=" N LYS A 287 " --> pdb=" O SER A 329 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 329 " --> pdb=" O LYS A 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 333 removed outlier: 4.376A pdb=" N ARG A 332 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 916 through 923 removed outlier: 6.575A pdb=" N LYS A 837 " --> pdb=" O SER A 921 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLN A 923 " --> pdb=" O ILE A 835 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE A 835 " --> pdb=" O GLN A 923 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLY A 827 " --> pdb=" O ILE A 838 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 945 " --> pdb=" O ILE A 928 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 964 through 970 removed outlier: 3.948A pdb=" N TYR A 957 " --> pdb=" O THR A1013 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR A1013 " --> pdb=" O TYR A 957 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 964 through 970 Processing sheet with id=AA7, first strand: chain 'A' and resid 1074 through 1075 removed outlier: 3.804A pdb=" N ILE A1074 " --> pdb=" O ILE A1048 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A1048 " --> pdb=" O ILE A1074 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER A1039 " --> pdb=" O GLU A1049 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LYS A1051 " --> pdb=" O PHE A1037 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N PHE A1037 " --> pdb=" O LYS A1051 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY A1083 " --> pdb=" O GLN A1025 " (cutoff:3.500A) 267 hydrogen bonds defined for protein. 759 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 65 stacking parallelities Total time for adding SS restraints: 1.74 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 - 1.34: 2247 1.34 - 1.46: 2793 1.46 - 1.59: 3756 1.59 - 1.71: 211 1.71 - 1.84: 41 Bond restraints: 9048 Sorted by residual: bond pdb=" O3' DG C 10 " pdb=" P DC C 11 " ideal model delta sigma weight residual 1.607 1.672 -0.065 1.20e-02 6.94e+03 2.91e+01 bond pdb=" O3' DG D 6 " pdb=" P DC D 7 " ideal model delta sigma weight residual 1.607 1.660 -0.053 1.20e-02 6.94e+03 1.96e+01 bond pdb=" O3' U B 32 " pdb=" P G B 33 " ideal model delta sigma weight residual 1.607 1.652 -0.045 1.20e-02 6.94e+03 1.43e+01 bond pdb=" O3' A B 70 " pdb=" P A B 71 " ideal model delta sigma weight residual 1.607 1.648 -0.041 1.20e-02 6.94e+03 1.18e+01 bond pdb=" O3' U B 39 " pdb=" P C B 40 " ideal model delta sigma weight residual 1.607 1.648 -0.041 1.20e-02 6.94e+03 1.17e+01 ... (remaining 9043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 12131 2.21 - 4.42: 463 4.42 - 6.63: 38 6.63 - 8.85: 7 8.85 - 11.06: 4 Bond angle restraints: 12643 Sorted by residual: angle pdb=" N ILE A 200 " pdb=" CA ILE A 200 " pdb=" C ILE A 200 " ideal model delta sigma weight residual 109.58 116.95 -7.37 1.29e+00 6.01e-01 3.26e+01 angle pdb=" C SER A 839 " pdb=" CA SER A 839 " pdb=" CB SER A 839 " ideal model delta sigma weight residual 109.37 118.96 -9.59 1.91e+00 2.74e-01 2.52e+01 angle pdb=" O4' DC C 11 " pdb=" C4' DC C 11 " pdb=" C3' DC C 11 " ideal model delta sigma weight residual 106.00 102.99 3.01 6.00e-01 2.78e+00 2.51e+01 angle pdb=" O4' DT C 26 " pdb=" C4' DT C 26 " pdb=" C3' DT C 26 " ideal model delta sigma weight residual 106.00 103.01 2.99 6.00e-01 2.78e+00 2.49e+01 angle pdb=" CA PHE A 344 " pdb=" CB PHE A 344 " pdb=" CG PHE A 344 " ideal model delta sigma weight residual 113.80 118.73 -4.93 1.00e+00 1.00e+00 2.43e+01 ... (remaining 12638 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 4362 17.77 - 35.54: 694 35.54 - 53.31: 295 53.31 - 71.08: 122 71.08 - 88.85: 25 Dihedral angle restraints: 5498 sinusoidal: 3218 harmonic: 2280 Sorted by residual: dihedral pdb=" CB CYS A 816 " pdb=" SG CYS A 816 " pdb=" SG CYS A 976 " pdb=" CB CYS A 976 " ideal model delta sinusoidal sigma weight residual -86.00 -29.71 -56.29 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" CA GLY A1030 " pdb=" C GLY A1030 " pdb=" N GLU A1031 " pdb=" CA GLU A1031 " ideal model delta harmonic sigma weight residual 180.00 155.55 24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA TYR A 158 " pdb=" C TYR A 158 " pdb=" N HIS A 159 " pdb=" CA HIS A 159 " ideal model delta harmonic sigma weight residual 180.00 -162.50 -17.50 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 5495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1156 0.070 - 0.141: 224 0.141 - 0.211: 41 0.211 - 0.281: 9 0.281 - 0.352: 2 Chirality restraints: 1432 Sorted by residual: chirality pdb=" C3' DG C 10 " pdb=" C4' DG C 10 " pdb=" O3' DG C 10 " pdb=" C2' DG C 10 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA ILE A1053 " pdb=" N ILE A1053 " pdb=" C ILE A1053 " pdb=" CB ILE A1053 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C3' U B 44 " pdb=" C4' U B 44 " pdb=" O3' U B 44 " pdb=" C2' U B 44 " both_signs ideal model delta sigma weight residual False -2.48 -2.75 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 1429 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC D 7 " 0.006 2.00e-02 2.50e+03 2.05e-02 9.49e+00 pdb=" N1 DC D 7 " 0.024 2.00e-02 2.50e+03 pdb=" C2 DC D 7 " -0.028 2.00e-02 2.50e+03 pdb=" O2 DC D 7 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DC D 7 " 0.023 2.00e-02 2.50e+03 pdb=" C4 DC D 7 " -0.016 2.00e-02 2.50e+03 pdb=" N4 DC D 7 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DC D 7 " 0.023 2.00e-02 2.50e+03 pdb=" C6 DC D 7 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 32 " -0.019 2.00e-02 2.50e+03 1.83e-02 7.56e+00 pdb=" N1 U B 32 " 0.008 2.00e-02 2.50e+03 pdb=" C2 U B 32 " 0.043 2.00e-02 2.50e+03 pdb=" O2 U B 32 " -0.010 2.00e-02 2.50e+03 pdb=" N3 U B 32 " -0.017 2.00e-02 2.50e+03 pdb=" C4 U B 32 " -0.011 2.00e-02 2.50e+03 pdb=" O4 U B 32 " -0.004 2.00e-02 2.50e+03 pdb=" C5 U B 32 " 0.013 2.00e-02 2.50e+03 pdb=" C6 U B 32 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG D 8 " -0.004 2.00e-02 2.50e+03 1.58e-02 7.51e+00 pdb=" N9 DG D 8 " -0.001 2.00e-02 2.50e+03 pdb=" C8 DG D 8 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DG D 8 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DG D 8 " 0.031 2.00e-02 2.50e+03 pdb=" C6 DG D 8 " -0.001 2.00e-02 2.50e+03 pdb=" O6 DG D 8 " 0.000 2.00e-02 2.50e+03 pdb=" N1 DG D 8 " -0.029 2.00e-02 2.50e+03 pdb=" C2 DG D 8 " -0.015 2.00e-02 2.50e+03 pdb=" N2 DG D 8 " 0.030 2.00e-02 2.50e+03 pdb=" N3 DG D 8 " -0.010 2.00e-02 2.50e+03 pdb=" C4 DG D 8 " -0.000 2.00e-02 2.50e+03 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2295 2.81 - 3.33: 7622 3.33 - 3.85: 14998 3.85 - 4.38: 17138 4.38 - 4.90: 26612 Nonbonded interactions: 68665 Sorted by model distance: nonbonded pdb=" O GLY A 131 " pdb=" OD1 ASN A 135 " model vdw 2.284 3.040 nonbonded pdb=" OD2 ASP A 954 " pdb=" OH TYR A 988 " model vdw 2.290 3.040 nonbonded pdb=" OG SER A 268 " pdb=" OD1 ASP A 374 " model vdw 2.294 3.040 nonbonded pdb=" OH TYR A 234 " pdb=" O4 U B 64 " model vdw 2.316 3.040 nonbonded pdb=" O ASP A 360 " pdb=" OG SER A 363 " model vdw 2.337 3.040 ... (remaining 68660 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: 4.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.660 Find NCS groups from input model: 0.030 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9049 Z= 0.378 Angle : 0.878 11.058 12645 Z= 0.621 Chirality : 0.062 0.352 1432 Planarity : 0.004 0.046 1206 Dihedral : 20.890 88.851 4033 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 0.56 % Allowed : 23.22 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.31), residues: 753 helix: 0.44 (0.29), residues: 319 sheet: -1.73 (0.68), residues: 52 loop : -2.05 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 314 TYR 0.036 0.002 TYR A 272 PHE 0.032 0.002 PHE A 344 TRP 0.012 0.002 TRP A1067 HIS 0.009 0.002 HIS A 973 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.38 ( 9048) covalent geometry : angle 0.87372 / 0.62 (12643) SS BOND : bond 0.04955 / 2.61 ( 1) SS BOND : angle 6.97606 / 3.96 ( 2) hydrogen bonds : bond 0.15082 / 9.93 ( 363) hydrogen bonds : angle 6.62569 / 4.75 ( 963) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 90 average time/residue: 0.0886 time to fit residues: 10.9961 Evaluate side-chains 70 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN A 327 GLN A 392 GLN A 705 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.195593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.168584 restraints weight = 13984.961| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 1.84 r_work: 0.3902 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9049 Z= 0.140 Angle : 0.557 5.666 12645 Z= 0.325 Chirality : 0.040 0.223 1432 Planarity : 0.004 0.040 1206 Dihedral : 20.173 78.318 2323 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 3.64 % Allowed : 22.66 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.31), residues: 753 helix: 0.90 (0.29), residues: 319 sheet: -1.44 (0.75), residues: 49 loop : -1.90 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 56 TYR 0.014 0.001 TYR A 341 PHE 0.020 0.002 PHE A 134 TRP 0.009 0.001 TRP A1067 HIS 0.006 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 ( 9048) covalent geometry : angle 0.55670 / 0.32 (12643) SS BOND : bond 0.00485 / 0.26 ( 1) SS BOND : angle 2.21038 / 1.21 ( 2) hydrogen bonds : bond 0.05417 / 3.68 ( 363) hydrogen bonds : angle 4.51780 / 3.30 ( 963) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.6327 (m-80) cc_final: 0.6091 (m-80) REVERT: A 327 GLN cc_start: 0.6045 (OUTLIER) cc_final: 0.5108 (pm20) REVERT: A 347 TYR cc_start: 0.6303 (OUTLIER) cc_final: 0.5281 (m-80) REVERT: A 981 TYR cc_start: 0.5799 (OUTLIER) cc_final: 0.4336 (m-80) REVERT: A 992 LEU cc_start: 0.6147 (mt) cc_final: 0.5867 (mt) outliers start: 26 outliers final: 8 residues processed: 95 average time/residue: 0.0739 time to fit residues: 10.0790 Evaluate side-chains 80 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 981 TYR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1074 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 6 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 ASN A 327 GLN A 410 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.194483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.164003 restraints weight = 14420.071| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 2.12 r_work: 0.3938 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9049 Z= 0.160 Angle : 0.546 5.144 12645 Z= 0.317 Chirality : 0.041 0.199 1432 Planarity : 0.003 0.038 1206 Dihedral : 20.028 79.157 2323 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 3.78 % Allowed : 22.52 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.31), residues: 753 helix: 1.03 (0.29), residues: 320 sheet: -1.47 (0.66), residues: 62 loop : -1.97 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 51 TYR 0.011 0.002 TYR A 874 PHE 0.015 0.002 PHE A 277 TRP 0.008 0.001 TRP A 68 HIS 0.006 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 ( 9048) covalent geometry : angle 0.54556 / 0.32 (12643) SS BOND : bond 0.00109 / 0.06 ( 1) SS BOND : angle 0.90113 / 0.52 ( 2) hydrogen bonds : bond 0.05255 / 3.60 ( 363) hydrogen bonds : angle 4.36998 / 3.17 ( 963) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.6457 (m-80) cc_final: 0.6034 (m-80) REVERT: A 327 GLN cc_start: 0.6133 (OUTLIER) cc_final: 0.5533 (pm20) REVERT: A 347 TYR cc_start: 0.6435 (OUTLIER) cc_final: 0.5502 (m-80) REVERT: A 981 TYR cc_start: 0.5742 (OUTLIER) cc_final: 0.4221 (m-80) REVERT: A 992 LEU cc_start: 0.6284 (mt) cc_final: 0.5997 (mt) outliers start: 27 outliers final: 12 residues processed: 91 average time/residue: 0.0746 time to fit residues: 9.8758 Evaluate side-chains 82 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 981 TYR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1074 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 1 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 chunk 30 optimal weight: 0.0870 chunk 63 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN A 312 ASN ** A 342 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 = 0.4407 r_free = 0.4407 target = 0.194901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.163314 restraints weight = 14756.192| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 2.29 r_work: 0.3923 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9049 Z= 0.139 Angle : 0.524 9.682 12645 Z= 0.304 Chirality : 0.039 0.189 1432 Planarity : 0.003 0.034 1206 Dihedral : 19.915 79.276 2323 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 3.36 % Allowed : 22.66 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.31), residues: 753 helix: 1.17 (0.29), residues: 320 sheet: -1.88 (0.64), residues: 64 loop : -1.85 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 829 TYR 0.011 0.001 TYR A 208 PHE 0.013 0.001 PHE A 277 TRP 0.008 0.001 TRP A 68 HIS 0.011 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 9048) covalent geometry : angle 0.52425 / 0.30 (12643) SS BOND : bond 0.00097 / 0.05 ( 1) SS BOND : angle 0.74317 / 0.42 ( 2) hydrogen bonds : bond 0.04762 / 3.26 ( 363) hydrogen bonds : angle 4.21301 / 3.07 ( 963) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.6543 (m-80) cc_final: 0.6091 (m-80) REVERT: A 347 TYR cc_start: 0.6387 (OUTLIER) cc_final: 0.5826 (m-80) REVERT: A 981 TYR cc_start: 0.5726 (OUTLIER) cc_final: 0.4251 (m-80) REVERT: A 992 LEU cc_start: 0.6341 (mt) cc_final: 0.6056 (mt) outliers start: 24 outliers final: 9 residues processed: 92 average time/residue: 0.0768 time to fit residues: 10.3326 Evaluate side-chains 78 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 981 TYR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1074 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 2 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 ASN ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.193845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.163209 restraints weight = 14562.834| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 2.15 r_work: 0.3926 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9049 Z= 0.142 Angle : 0.523 6.834 12645 Z= 0.302 Chirality : 0.040 0.174 1432 Planarity : 0.003 0.031 1206 Dihedral : 19.806 79.306 2323 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 3.92 % Allowed : 23.08 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.31), residues: 753 helix: 1.20 (0.29), residues: 320 sheet: -1.82 (0.74), residues: 53 loop : -1.91 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 829 TYR 0.016 0.002 TYR A 128 PHE 0.015 0.001 PHE A 277 TRP 0.007 0.001 TRP A 68 HIS 0.005 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 9048) covalent geometry : angle 0.52263 / 0.30 (12643) SS BOND : bond 0.00006 / 0.00 ( 1) SS BOND : angle 0.47191 / 0.27 ( 2) hydrogen bonds : bond 0.04632 / 3.18 ( 363) hydrogen bonds : angle 4.16176 / 3.03 ( 963) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.6552 (m-80) cc_final: 0.6066 (m-80) REVERT: A 347 TYR cc_start: 0.6435 (OUTLIER) cc_final: 0.5924 (m-80) REVERT: A 403 LYS cc_start: 0.7876 (mmtt) cc_final: 0.7381 (ttpt) REVERT: A 981 TYR cc_start: 0.5824 (OUTLIER) cc_final: 0.4252 (m-80) outliers start: 28 outliers final: 16 residues processed: 99 average time/residue: 0.0739 time to fit residues: 10.6166 Evaluate side-chains 88 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 981 TYR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1103 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 84 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 GLN A 148 GLN A 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.190885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.162190 restraints weight = 14625.914| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 1.97 r_work: 0.3875 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9049 Z= 0.183 Angle : 0.581 8.783 12645 Z= 0.329 Chirality : 0.043 0.197 1432 Planarity : 0.004 0.031 1206 Dihedral : 19.781 78.115 2323 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 5.03 % Allowed : 23.22 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.30), residues: 753 helix: 1.05 (0.29), residues: 321 sheet: -1.36 (0.66), residues: 63 loop : -2.09 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 408 TYR 0.015 0.002 TYR A1014 PHE 0.017 0.002 PHE A 277 TRP 0.007 0.002 TRP A 68 HIS 0.003 0.001 HIS A 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 ( 9048) covalent geometry : angle 0.58135 / 0.33 (12643) SS BOND : bond 0.00205 / 0.11 ( 1) SS BOND : angle 0.31327 / 0.18 ( 2) hydrogen bonds : bond 0.05150 / 3.54 ( 363) hydrogen bonds : angle 4.30197 / 3.15 ( 963) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 78 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.4340 (ptt) cc_final: 0.4114 (ppp) REVERT: A 328 TYR cc_start: 0.5971 (OUTLIER) cc_final: 0.3543 (t80) REVERT: A 347 TYR cc_start: 0.6597 (OUTLIER) cc_final: 0.5641 (m-80) REVERT: A 357 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7537 (pt) REVERT: A 403 LYS cc_start: 0.7941 (mmtt) cc_final: 0.7468 (mmtm) REVERT: A 707 LYS cc_start: 0.7921 (mmtm) cc_final: 0.7446 (mmtt) REVERT: A 981 TYR cc_start: 0.5932 (OUTLIER) cc_final: 0.4272 (m-80) REVERT: A 986 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.5980 (mp0) outliers start: 36 outliers final: 22 residues processed: 109 average time/residue: 0.0766 time to fit residues: 12.0424 Evaluate side-chains 100 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 328 TYR Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 981 TYR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 986 GLU Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1103 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 7 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.428 > 50:) chunk 42 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.192252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.163965 restraints weight = 14753.768| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 2.00 r_work: 0.3891 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9049 Z= 0.146 Angle : 0.534 7.261 12645 Z= 0.308 Chirality : 0.040 0.182 1432 Planarity : 0.003 0.028 1206 Dihedral : 19.723 79.201 2323 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 4.06 % Allowed : 23.92 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.30), residues: 753 helix: 1.16 (0.29), residues: 319 sheet: -1.43 (0.69), residues: 58 loop : -1.98 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 829 TYR 0.017 0.001 TYR A 128 PHE 0.013 0.001 PHE A 277 TRP 0.008 0.001 TRP A 68 HIS 0.004 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 ( 9048) covalent geometry : angle 0.53371 / 0.31 (12643) SS BOND : bond 0.00090 / 0.05 ( 1) SS BOND : angle 0.40943 / 0.24 ( 2) hydrogen bonds : bond 0.04598 / 3.16 ( 363) hydrogen bonds : angle 4.23146 / 3.10 ( 963) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8234 (ptp90) REVERT: A 313 MET cc_start: 0.4364 (ptt) cc_final: 0.4136 (ppp) REVERT: A 328 TYR cc_start: 0.5664 (OUTLIER) cc_final: 0.3214 (t80) REVERT: A 347 TYR cc_start: 0.6530 (OUTLIER) cc_final: 0.5660 (m-80) REVERT: A 403 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7531 (ttpt) REVERT: A 707 LYS cc_start: 0.7917 (mmtm) cc_final: 0.7448 (mmtt) REVERT: A 981 TYR cc_start: 0.5967 (OUTLIER) cc_final: 0.4320 (m-80) REVERT: A 986 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.5969 (mp0) outliers start: 29 outliers final: 19 residues processed: 98 average time/residue: 0.0915 time to fit residues: 12.4918 Evaluate side-chains 96 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 328 TYR Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 981 TYR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 986 GLU Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1074 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 84 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 chunk 64 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 41 optimal weight: 0.0670 chunk 15 optimal weight: 0.5980 chunk 83 optimal weight: 10.0000 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.196468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.170790 restraints weight = 14598.191| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 1.87 r_work: 0.3967 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9049 Z= 0.124 Angle : 0.504 6.493 12645 Z= 0.295 Chirality : 0.039 0.175 1432 Planarity : 0.003 0.027 1206 Dihedral : 19.644 80.124 2323 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 3.92 % Allowed : 23.50 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.31), residues: 753 helix: 1.28 (0.29), residues: 319 sheet: -1.91 (0.73), residues: 53 loop : -1.87 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 48 TYR 0.024 0.001 TYR A 128 PHE 0.013 0.001 PHE A 364 TRP 0.008 0.001 TRP A1067 HIS 0.004 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 ( 9048) covalent geometry : angle 0.50403 / 0.30 (12643) SS BOND : bond 0.00033 / 0.02 ( 1) SS BOND : angle 0.54224 / 0.29 ( 2) hydrogen bonds : bond 0.04215 / 2.88 ( 363) hydrogen bonds : angle 4.08572 / 2.99 ( 963) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8215 (ptp90) REVERT: A 328 TYR cc_start: 0.5626 (OUTLIER) cc_final: 0.3098 (t80) REVERT: A 357 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7425 (pt) REVERT: A 403 LYS cc_start: 0.7908 (mmtt) cc_final: 0.7536 (mmtm) REVERT: A 707 LYS cc_start: 0.7959 (mmtm) cc_final: 0.7518 (mmtt) REVERT: A 981 TYR cc_start: 0.5954 (OUTLIER) cc_final: 0.4335 (m-80) REVERT: A 986 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.5974 (mp0) outliers start: 28 outliers final: 17 residues processed: 97 average time/residue: 0.0922 time to fit residues: 12.5293 Evaluate side-chains 93 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 328 TYR Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 981 TYR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 986 GLU Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1074 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 64 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 47 optimal weight: 0.2980 chunk 65 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 ASN ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.196522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.169632 restraints weight = 14523.300| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 1.86 r_work: 0.3972 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9049 Z= 0.124 Angle : 0.500 6.196 12645 Z= 0.292 Chirality : 0.038 0.157 1432 Planarity : 0.003 0.062 1206 Dihedral : 19.598 80.340 2323 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 2.94 % Allowed : 24.62 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.31), residues: 753 helix: 1.29 (0.29), residues: 319 sheet: -1.71 (0.75), residues: 52 loop : -1.84 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 829 TYR 0.023 0.001 TYR A 128 PHE 0.030 0.002 PHE A 134 TRP 0.008 0.001 TRP A1067 HIS 0.006 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 9048) covalent geometry : angle 0.49993 / 0.29 (12643) SS BOND : bond 0.00010 / 0.01 ( 1) SS BOND : angle 0.39951 / 0.22 ( 2) hydrogen bonds : bond 0.04107 / 2.81 ( 363) hydrogen bonds : angle 3.99988 / 2.92 ( 963) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8214 (ptp90) REVERT: A 313 MET cc_start: 0.5907 (ppp) cc_final: 0.5409 (ptp) REVERT: A 328 TYR cc_start: 0.5416 (OUTLIER) cc_final: 0.3468 (t80) REVERT: A 347 TYR cc_start: 0.6362 (OUTLIER) cc_final: 0.5550 (m-80) REVERT: A 403 LYS cc_start: 0.7892 (mmtt) cc_final: 0.7491 (ttpt) REVERT: A 707 LYS cc_start: 0.7931 (mmtm) cc_final: 0.7465 (mmtt) REVERT: A 981 TYR cc_start: 0.5898 (OUTLIER) cc_final: 0.4298 (m-80) outliers start: 21 outliers final: 14 residues processed: 89 average time/residue: 0.0829 time to fit residues: 10.5713 Evaluate side-chains 88 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 328 TYR Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 981 TYR Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1074 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 57 optimal weight: 0.0470 chunk 50 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 43 optimal weight: 0.2980 chunk 39 optimal weight: 3.9990 chunk 65 optimal weight: 0.0030 chunk 35 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.3088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN A 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.198010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.171594 restraints weight = 14791.503| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 1.90 r_work: 0.4015 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9049 Z= 0.113 Angle : 0.488 6.623 12645 Z= 0.288 Chirality : 0.037 0.154 1432 Planarity : 0.003 0.064 1206 Dihedral : 19.565 80.805 2323 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 2.94 % Allowed : 24.48 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.31), residues: 753 helix: 1.34 (0.29), residues: 320 sheet: -1.68 (0.75), residues: 52 loop : -1.83 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 829 TYR 0.031 0.001 TYR A 128 PHE 0.014 0.002 PHE A 364 TRP 0.009 0.001 TRP A1067 HIS 0.003 0.000 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 ( 9048) covalent geometry : angle 0.48796 / 0.29 (12643) SS BOND : bond 0.00092 / 0.05 ( 1) SS BOND : angle 0.64294 / 0.34 ( 2) hydrogen bonds : bond 0.03858 / 2.62 ( 363) hydrogen bonds : angle 3.88995 / 2.83 ( 963) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1506 Ramachandran restraints generated. 753 Oldfield, 0 Emsley, 753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8160 (ptp90) REVERT: A 328 TYR cc_start: 0.5267 (OUTLIER) cc_final: 0.3444 (t80) REVERT: A 357 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7348 (pt) REVERT: A 403 LYS cc_start: 0.7874 (mmtt) cc_final: 0.7484 (mmtm) REVERT: A 707 LYS cc_start: 0.7958 (mmtm) cc_final: 0.7526 (mmtt) REVERT: A 981 TYR cc_start: 0.5833 (OUTLIER) cc_final: 0.4329 (m-80) outliers start: 21 outliers final: 16 residues processed: 88 average time/residue: 0.0882 time to fit residues: 11.0263 Evaluate side-chains 89 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 145 CYS Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 328 TYR Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 981 TYR Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1074 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 58 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 59 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 83 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.196780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.170137 restraints weight = 14512.247| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 1.89 r_work: 0.3964 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9049 Z= 0.128 Angle : 0.504 6.239 12645 Z= 0.295 Chirality : 0.038 0.158 1432 Planarity : 0.003 0.060 1206 Dihedral : 19.530 80.584 2323 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 3.22 % Allowed : 25.17 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.31), residues: 753 helix: 1.24 (0.29), residues: 319 sheet: -1.58 (0.76), residues: 52 loop : -1.77 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 829 TYR 0.028 0.001 TYR A 128 PHE 0.028 0.002 PHE A 134 TRP 0.007 0.001 TRP A1067 HIS 0.004 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 9048) covalent geometry : angle 0.50368 / 0.29 (12643) SS BOND : bond 0.00047 / 0.02 ( 1) SS BOND : angle 0.30917 / 0.17 ( 2) hydrogen bonds : bond 0.04073 / 2.78 ( 363) hydrogen bonds : angle 3.93900 / 2.87 ( 963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1804.71 seconds wall clock time: 31 minutes 40.48 seconds (1900.48 seconds total)