Starting phenix.real_space_refine on Sat Aug 23 05:10:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hud_35035/08_2025/8hud_35035_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hud_35035/08_2025/8hud_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_2025/8hud_35035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hud_35035/08_2025/8hud_35035.map" model { file = "/net/cci-nas-00/data/ceres_data/8hud_35035/08_2025/8hud_35035_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hud_35035/08_2025/8hud_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-2.0-5787/lib/python3.9/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: 1.84, 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: 0.57 Conformation dependent library (CDL) restraints added in 225.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 1.09 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: 1.59 Time building geometry restraints manager: 0.73 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 1.50e-02 4.44e+03 1.86e+01 bond pdb=" O3' DG D 6 " pdb=" P DC D 7 " ideal model delta sigma weight residual 1.607 1.660 -0.053 1.50e-02 4.44e+03 1.25e+01 bond pdb=" CA ARG A1071 " pdb=" C ARG A1071 " ideal model delta sigma weight residual 1.524 1.482 0.042 1.31e-02 5.83e+03 1.05e+01 bond pdb=" O3' U B 32 " pdb=" P G B 33 " ideal model delta sigma weight residual 1.607 1.652 -0.045 1.50e-02 4.44e+03 9.13e+00 bond pdb=" N ILE A1053 " pdb=" CA ILE A1053 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.26e+00 ... (remaining 9043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 12379 2.63 - 5.26: 238 5.26 - 7.89: 22 7.89 - 10.53: 2 10.53 - 13.16: 2 Bond angle restraints: 12643 Sorted by residual: angle pdb=" O3' DG C 2 " pdb=" C3' DG C 2 " pdb=" C2' DG C 2 " ideal model delta sigma weight residual 111.50 98.34 13.16 1.50e+00 4.44e-01 7.69e+01 angle pdb=" O3' DC C 1 " pdb=" C3' DC C 1 " pdb=" C2' DC C 1 " ideal model delta sigma weight residual 111.50 100.01 11.49 1.50e+00 4.44e-01 5.86e+01 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=" O3' DG C 10 " pdb=" C3' DG C 10 " pdb=" C2' DG C 10 " ideal model delta sigma weight residual 111.50 119.89 -8.39 1.50e+00 4.44e-01 3.13e+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 ... (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 - 0.066: 1186 0.066 - 0.132: 179 0.132 - 0.198: 55 0.198 - 0.264: 5 0.264 - 0.330: 7 Chirality restraints: 1432 Sorted by residual: chirality pdb=" C3' DG C 2 " pdb=" C4' DG C 2 " pdb=" O3' DG C 2 " pdb=" C2' DG C 2 " both_signs ideal model delta sigma weight residual False -2.66 -2.99 0.33 2.00e-01 2.50e+01 2.71e+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' DC C 1 " pdb=" C4' DC C 1 " pdb=" O3' DC C 1 " pdb=" C2' DC C 1 " both_signs ideal model delta sigma weight residual False -2.66 -2.97 0.31 2.00e-01 2.50e+01 2.33e+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: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.830 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 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= 0.302 Angle : 0.840 13.158 12645 Z= 0.528 Chirality : 0.058 0.330 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 aren 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 covalent geometry : bond 0.00513 ( 9048) covalent geometry : angle 0.83508 (12643) SS BOND : bond 0.04955 ( 1) SS BOND : angle 6.97606 ( 2) hydrogen bonds : bond 0.15082 ( 363) hydrogen bonds : angle 6.62569 ( 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 : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 90 average time/residue: 0.0949 time to fit residues: 11.6223 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 : 0.222 ------------------------------------------------------------------------------- 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: 0.5980 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 327 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.194232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.166550 restraints weight = 14043.261| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 1.90 r_work: 0.3884 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.1290 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= 0.143 Angle : 0.546 5.196 12645 Z= 0.302 Chirality : 0.038 0.154 1432 Planarity : 0.003 0.040 1206 Dihedral : 20.095 79.420 2323 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % 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 aren not related in a simple way. whole: -0.88 (0.31), residues: 753 helix: 1.01 (0.29), residues: 320 sheet: -1.66 (0.71), residues: 55 loop : -1.90 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 56 TYR 0.012 0.001 TYR A 182 PHE 0.014 0.002 PHE A 134 TRP 0.010 0.001 TRP A1067 HIS 0.007 0.001 HIS A 342 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9048) covalent geometry : angle 0.54594 (12643) SS BOND : bond 0.00072 ( 1) SS BOND : angle 1.06323 ( 2) hydrogen bonds : bond 0.04448 ( 363) hydrogen bonds : angle 4.29435 ( 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 103 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.6381 (m-80) cc_final: 0.6097 (m-80) REVERT: A 327 GLN cc_start: 0.5979 (OUTLIER) cc_final: 0.5107 (pm20) REVERT: A 347 TYR cc_start: 0.6472 (OUTLIER) cc_final: 0.5889 (m-80) REVERT: A 981 TYR cc_start: 0.5808 (OUTLIER) cc_final: 0.4329 (m-80) REVERT: A 992 LEU cc_start: 0.6334 (mt) cc_final: 0.6043 (mt) outliers start: 26 outliers final: 8 residues processed: 97 average time/residue: 0.0904 time to fit residues: 12.3669 Evaluate side-chains 82 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 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 1017 SER 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: 0.9980 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN A 312 ASN A 327 GLN A 392 GLN A 705 ASN A1059 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.192190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.160462 restraints weight = 14403.351| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 2.26 r_work: 0.3891 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.1761 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= 0.176 Angle : 0.573 7.700 12645 Z= 0.312 Chirality : 0.039 0.173 1432 Planarity : 0.003 0.038 1206 Dihedral : 19.915 80.611 2323 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 4.06 % Allowed : 22.52 % Favored : 73.43 % 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 aren not related in a simple way. whole: -0.86 (0.31), residues: 753 helix: 1.11 (0.29), residues: 321 sheet: -1.98 (0.64), residues: 64 loop : -1.90 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 55 TYR 0.013 0.002 TYR A1014 PHE 0.016 0.002 PHE A 277 TRP 0.008 0.002 TRP A 68 HIS 0.009 0.001 HIS A 342 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9048) covalent geometry : angle 0.57291 (12643) SS BOND : bond 0.00004 ( 1) SS BOND : angle 0.79485 ( 2) hydrogen bonds : bond 0.04637 ( 363) hydrogen bonds : angle 4.25754 ( 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 107 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.6583 (m-80) cc_final: 0.6033 (m-80) REVERT: A 347 TYR cc_start: 0.6478 (OUTLIER) cc_final: 0.5981 (m-80) REVERT: A 403 LYS cc_start: 0.7886 (mmtt) cc_final: 0.7376 (ttpt) REVERT: A 981 TYR cc_start: 0.5806 (OUTLIER) cc_final: 0.4229 (m-80) outliers start: 29 outliers final: 17 residues processed: 101 average time/residue: 0.0748 time to fit residues: 10.9940 Evaluate side-chains 92 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 342 HIS 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 824 THR Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 870 ASP 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 1017 SER Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1059 GLN Chi-restraints excluded: chain A residue 1074 ILE Chi-restraints excluded: chain A residue 1089 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 1 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 30 optimal weight: 0.0570 chunk 63 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.192300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.163360 restraints weight = 14716.407| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 2.07 r_work: 0.3885 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2040 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= 0.159 Angle : 0.556 8.006 12645 Z= 0.302 Chirality : 0.039 0.169 1432 Planarity : 0.003 0.035 1206 Dihedral : 19.784 81.315 2323 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 4.48 % Allowed : 22.80 % Favored : 72.73 % 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 aren not related in a simple way. whole: -0.82 (0.30), residues: 753 helix: 1.14 (0.29), residues: 321 sheet: -1.57 (0.67), residues: 58 loop : -1.96 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 56 TYR 0.014 0.002 TYR A 826 PHE 0.014 0.002 PHE A 277 TRP 0.008 0.001 TRP A 68 HIS 0.008 0.001 HIS A 342 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9048) covalent geometry : angle 0.55617 (12643) SS BOND : bond 0.00063 ( 1) SS BOND : angle 0.51918 ( 2) hydrogen bonds : bond 0.04284 ( 363) hydrogen bonds : angle 4.14022 ( 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 110 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 78 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8164 (ptp90) REVERT: A 369 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6464 (tt) REVERT: A 403 LYS cc_start: 0.7874 (mmtt) cc_final: 0.7394 (ttpt) REVERT: A 981 TYR cc_start: 0.5823 (OUTLIER) cc_final: 0.4250 (m-80) REVERT: A 986 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.5828 (mp0) outliers start: 32 outliers final: 17 residues processed: 105 average time/residue: 0.0888 time to fit residues: 12.9934 Evaluate side-chains 90 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG 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 342 HIS 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 2 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 312 ASN ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.194447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.166610 restraints weight = 14652.876| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 1.98 r_work: 0.3927 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2345 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= 0.155 Angle : 0.549 5.947 12645 Z= 0.299 Chirality : 0.039 0.168 1432 Planarity : 0.003 0.033 1206 Dihedral : 19.646 81.684 2323 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 5.31 % Allowed : 22.66 % 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 aren not related in a simple way. whole: -0.75 (0.30), residues: 753 helix: 1.24 (0.29), residues: 320 sheet: -1.55 (0.67), residues: 58 loop : -1.97 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 56 TYR 0.014 0.001 TYR A 874 PHE 0.013 0.002 PHE A 277 TRP 0.008 0.001 TRP A 68 HIS 0.008 0.001 HIS A 342 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9048) covalent geometry : angle 0.54951 (12643) SS BOND : bond 0.00114 ( 1) SS BOND : angle 0.40927 ( 2) hydrogen bonds : bond 0.04170 ( 363) hydrogen bonds : angle 4.05863 ( 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 116 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 78 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8182 (ptp90) REVERT: A 357 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7455 (pt) REVERT: A 403 LYS cc_start: 0.7946 (mmtt) cc_final: 0.7517 (mmtm) REVERT: A 707 LYS cc_start: 0.7926 (mmtm) cc_final: 0.7502 (mmtt) REVERT: A 981 TYR cc_start: 0.5980 (OUTLIER) cc_final: 0.4387 (m-80) REVERT: A 986 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.5960 (mp0) outliers start: 38 outliers final: 24 residues processed: 110 average time/residue: 0.0926 time to fit residues: 14.1463 Evaluate side-chains 99 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 129 LYS 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 342 HIS 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 1103 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 11 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 46 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4426 r_free = 0.4426 target = 0.195358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.167846 restraints weight = 14756.223| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 1.97 r_work: 0.3945 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9049 Z= 0.137 Angle : 0.530 7.168 12645 Z= 0.292 Chirality : 0.038 0.156 1432 Planarity : 0.003 0.030 1206 Dihedral : 19.544 81.986 2323 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 4.48 % Allowed : 22.80 % Favored : 72.73 % 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 aren not related in a simple way. whole: -0.68 (0.31), residues: 753 helix: 1.26 (0.29), residues: 320 sheet: -1.54 (0.67), residues: 58 loop : -1.89 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 56 TYR 0.014 0.001 TYR A 826 PHE 0.011 0.001 PHE A 277 TRP 0.009 0.001 TRP A1067 HIS 0.008 0.001 HIS A 342 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9048) covalent geometry : angle 0.53045 (12643) SS BOND : bond 0.00030 ( 1) SS BOND : angle 0.46715 ( 2) hydrogen bonds : bond 0.03937 ( 363) hydrogen bonds : angle 4.00559 ( 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 108 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 76 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8149 (ptp90) REVERT: A 328 TYR cc_start: 0.5542 (OUTLIER) cc_final: 0.4553 (t80) REVERT: A 357 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7444 (pt) REVERT: A 403 LYS cc_start: 0.7930 (mmtt) cc_final: 0.7497 (mmtm) REVERT: A 707 LYS cc_start: 0.7982 (mmtm) cc_final: 0.7546 (mmtt) REVERT: A 981 TYR cc_start: 0.6005 (OUTLIER) cc_final: 0.4437 (m-80) REVERT: A 986 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.5998 (mp0) outliers start: 32 outliers final: 19 residues processed: 103 average time/residue: 0.0888 time to fit residues: 12.8168 Evaluate side-chains 95 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 328 TYR Chi-restraints excluded: chain A residue 342 HIS 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 410 ASN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 41 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 312 ASN ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.194289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.167499 restraints weight = 14883.342| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 1.96 r_work: 0.3926 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2674 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= 0.156 Angle : 0.550 7.542 12645 Z= 0.301 Chirality : 0.038 0.166 1432 Planarity : 0.004 0.061 1206 Dihedral : 19.525 81.599 2323 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 4.20 % Allowed : 23.50 % Favored : 72.31 % 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 aren not related in a simple way. whole: -0.68 (0.31), residues: 753 helix: 1.30 (0.29), residues: 320 sheet: -1.51 (0.68), residues: 58 loop : -1.92 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 408 TYR 0.025 0.002 TYR A 826 PHE 0.013 0.002 PHE A 277 TRP 0.008 0.001 TRP A1067 HIS 0.007 0.001 HIS A 342 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9048) covalent geometry : angle 0.55028 (12643) SS BOND : bond 0.00107 ( 1) SS BOND : angle 0.32432 ( 2) hydrogen bonds : bond 0.04124 ( 363) hydrogen bonds : angle 4.02209 ( 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 107 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8164 (ptp90) REVERT: A 328 TYR cc_start: 0.5666 (OUTLIER) cc_final: 0.3873 (t80) REVERT: A 357 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7442 (pt) REVERT: A 403 LYS cc_start: 0.7902 (mmtt) cc_final: 0.7433 (mmtm) REVERT: A 707 LYS cc_start: 0.7961 (mmtm) cc_final: 0.7503 (mmtt) REVERT: A 981 TYR cc_start: 0.6026 (OUTLIER) cc_final: 0.4421 (m-80) REVERT: A 986 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6118 (mp0) outliers start: 30 outliers final: 20 residues processed: 104 average time/residue: 0.0888 time to fit residues: 13.2379 Evaluate side-chains 95 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 229 THR 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 410 ASN 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 84 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 41 optimal weight: 0.0770 chunk 15 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 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 = 0.4426 r_free = 0.4426 target = 0.195936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.169351 restraints weight = 14609.140| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 1.99 r_work: 0.3949 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2778 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= 0.126 Angle : 0.528 7.316 12645 Z= 0.289 Chirality : 0.038 0.199 1432 Planarity : 0.003 0.057 1206 Dihedral : 19.477 82.394 2323 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 3.78 % Allowed : 23.92 % Favored : 72.31 % 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 aren not related in a simple way. whole: -0.63 (0.31), residues: 753 helix: 1.35 (0.29), residues: 320 sheet: -1.88 (0.73), residues: 52 loop : -1.84 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 56 TYR 0.023 0.001 TYR A 826 PHE 0.010 0.001 PHE A 134 TRP 0.009 0.001 TRP A1067 HIS 0.009 0.001 HIS A 342 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9048) covalent geometry : angle 0.52793 (12643) SS BOND : bond 0.00012 ( 1) SS BOND : angle 0.47363 ( 2) hydrogen bonds : bond 0.03766 ( 363) hydrogen bonds : angle 3.91938 ( 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 104 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8137 (ptp90) REVERT: A 313 MET cc_start: 0.4309 (ptt) cc_final: 0.4020 (ppp) REVERT: A 328 TYR cc_start: 0.5681 (OUTLIER) cc_final: 0.3346 (t80) REVERT: A 357 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7402 (pt) REVERT: A 403 LYS cc_start: 0.7879 (mmtt) cc_final: 0.7427 (mmtm) REVERT: A 707 LYS cc_start: 0.7946 (mmtm) cc_final: 0.7483 (mmtt) REVERT: A 981 TYR cc_start: 0.5881 (OUTLIER) cc_final: 0.4380 (m-80) REVERT: A 986 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6141 (mp0) outliers start: 27 outliers final: 19 residues processed: 101 average time/residue: 0.0999 time to fit residues: 14.3695 Evaluate side-chains 93 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 229 THR 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 410 ASN 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 64 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 0.0030 chunk 47 optimal weight: 0.9980 chunk 65 optimal weight: 0.0980 chunk 15 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4436 r_free = 0.4436 target = 0.197073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.170801 restraints weight = 14502.566| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 1.97 r_work: 0.3964 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2969 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= 0.123 Angle : 0.527 7.168 12645 Z= 0.288 Chirality : 0.037 0.177 1432 Planarity : 0.003 0.055 1206 Dihedral : 19.434 82.704 2323 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 3.78 % Allowed : 24.62 % 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 aren not related in a simple way. whole: -0.55 (0.31), residues: 753 helix: 1.41 (0.29), residues: 320 sheet: -1.79 (0.75), residues: 52 loop : -1.80 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 56 TYR 0.022 0.001 TYR A 826 PHE 0.012 0.001 PHE A 364 TRP 0.010 0.001 TRP A1067 HIS 0.006 0.001 HIS A 342 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9048) covalent geometry : angle 0.52672 (12643) SS BOND : bond 0.00000 ( 1) SS BOND : angle 0.46894 ( 2) hydrogen bonds : bond 0.03607 ( 363) hydrogen bonds : angle 3.90685 ( 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 102 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.8140 (ptp90) REVERT: A 313 MET cc_start: 0.4117 (ptt) cc_final: 0.3849 (ppp) REVERT: A 328 TYR cc_start: 0.5854 (OUTLIER) cc_final: 0.3484 (t80) REVERT: A 357 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7309 (pt) REVERT: A 403 LYS cc_start: 0.7924 (mmtt) cc_final: 0.7428 (mmtm) REVERT: A 707 LYS cc_start: 0.7929 (mmtm) cc_final: 0.7488 (mmtt) REVERT: A 959 ASN cc_start: 0.6912 (m-40) cc_final: 0.6633 (m110) REVERT: A 981 TYR cc_start: 0.5886 (OUTLIER) cc_final: 0.4399 (m-80) REVERT: A 986 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.5962 (mp0) outliers start: 27 outliers final: 17 residues processed: 98 average time/residue: 0.0914 time to fit residues: 12.7083 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 : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 229 THR 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 410 ASN 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 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 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: 0.9980 chunk 50 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4417 r_free = 0.4417 target = 0.195181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.165373 restraints weight = 14778.402| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 2.14 r_work: 0.3951 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9049 Z= 0.150 Angle : 0.548 7.077 12645 Z= 0.299 Chirality : 0.038 0.174 1432 Planarity : 0.003 0.052 1206 Dihedral : 19.446 81.841 2323 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 3.36 % Allowed : 24.34 % Favored : 72.31 % 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 aren not related in a simple way. whole: -0.62 (0.31), residues: 753 helix: 1.28 (0.28), residues: 320 sheet: -1.41 (0.70), residues: 58 loop : -1.83 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 413 TYR 0.028 0.002 TYR A 272 PHE 0.012 0.001 PHE A 277 TRP 0.008 0.001 TRP A1067 HIS 0.008 0.001 HIS A 342 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9048) covalent geometry : angle 0.54771 (12643) SS BOND : bond 0.00084 ( 1) SS BOND : angle 0.30692 ( 2) hydrogen bonds : bond 0.03924 ( 363) hydrogen bonds : angle 3.96162 ( 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 96 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8149 (ptp90) REVERT: A 313 MET cc_start: 0.4081 (ptt) cc_final: 0.3842 (ppp) REVERT: A 328 TYR cc_start: 0.6031 (OUTLIER) cc_final: 0.3734 (t80) REVERT: A 357 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7358 (pt) REVERT: A 403 LYS cc_start: 0.7874 (mmtt) cc_final: 0.7408 (mmtm) REVERT: A 707 LYS cc_start: 0.7908 (mmtm) cc_final: 0.7447 (mmtt) REVERT: A 959 ASN cc_start: 0.6919 (m-40) cc_final: 0.6683 (m110) REVERT: A 981 TYR cc_start: 0.5924 (OUTLIER) cc_final: 0.4378 (m-80) REVERT: A 986 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.5989 (mp0) outliers start: 24 outliers final: 18 residues processed: 92 average time/residue: 0.0967 time to fit residues: 12.7281 Evaluate side-chains 91 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 229 THR 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 410 ASN 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 58 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 75 optimal weight: 0.0170 chunk 76 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4424 r_free = 0.4424 target = 0.195807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.169239 restraints weight = 14531.914| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 1.98 r_work: 0.3947 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9049 Z= 0.135 Angle : 0.535 6.867 12645 Z= 0.294 Chirality : 0.038 0.172 1432 Planarity : 0.003 0.051 1206 Dihedral : 19.426 82.013 2323 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 3.64 % Allowed : 24.06 % Favored : 72.31 % 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 aren not related in a simple way. whole: -0.50 (0.31), residues: 753 helix: 1.41 (0.29), residues: 314 sheet: -1.79 (0.75), residues: 52 loop : -1.67 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 56 TYR 0.022 0.001 TYR A 826 PHE 0.031 0.002 PHE A 407 TRP 0.009 0.001 TRP A1067 HIS 0.008 0.001 HIS A 342 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9048) covalent geometry : angle 0.53530 (12643) SS BOND : bond 0.00040 ( 1) SS BOND : angle 0.41063 ( 2) hydrogen bonds : bond 0.03788 ( 363) hydrogen bonds : angle 3.93443 ( 963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1903.38 seconds wall clock time: 33 minutes 35.04 seconds (2015.04 seconds total)