Starting phenix.real_space_refine on Sun Jun 8 20:04:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hud_35035/06_2025/8hud_35035_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hud_35035/06_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_35035/06_2025/8hud_35035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hud_35035/06_2025/8hud_35035.map" model { file = "/net/cci-nas-00/data/ceres_data/8hud_35035/06_2025/8hud_35035_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hud_35035/06_2025/8hud_35035_neut.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.68, per 1000 atoms: 0.89 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: 2.46 Conformation dependent library (CDL) restraints added in 900.7 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: 3.51 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: 3.90 Time building geometry restraints manager: 2.75 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: 8.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 28.970 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.160 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (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 TRP 0.012 0.002 TRP A1067 HIS 0.009 0.002 HIS A 973 PHE 0.032 0.002 PHE A 344 TYR 0.036 0.002 TYR A 272 ARG 0.005 0.001 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.15082 ( 363) hydrogen bonds : angle 6.62569 ( 963) SS BOND : bond 0.04955 ( 1) SS BOND : angle 6.97606 ( 2) covalent geometry : bond 0.00513 ( 9048) covalent geometry : angle 0.83508 (12643) *********************** 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 : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 90 average time/residue: 0.2316 time to fit residues: 28.3402 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 : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.192383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.165358 restraints weight = 13946.443| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 1.78 r_work: 0.3864 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9049 Z= 0.170 Angle : 0.578 5.386 12645 Z= 0.318 Chirality : 0.039 0.160 1432 Planarity : 0.004 0.041 1206 Dihedral : 20.132 78.803 2323 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 3.64 % Allowed : 23.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.31), residues: 753 helix: 0.96 (0.29), residues: 320 sheet: -1.77 (0.70), residues: 56 loop : -1.98 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1067 HIS 0.009 0.001 HIS A 342 PHE 0.015 0.002 PHE A 134 TYR 0.013 0.002 TYR A 208 ARG 0.004 0.001 ARG A 56 Details of bonding type rmsd hydrogen bonds : bond 0.04926 ( 363) hydrogen bonds : angle 4.42429 ( 963) SS BOND : bond 0.00263 ( 1) SS BOND : angle 1.25785 ( 2) covalent geometry : bond 0.00375 ( 9048) covalent geometry : angle 0.57829 (12643) *********************** 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 : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.6363 (m-80) cc_final: 0.6050 (m-80) REVERT: A 981 TYR cc_start: 0.5909 (OUTLIER) cc_final: 0.4383 (m-80) outliers start: 26 outliers final: 11 residues processed: 96 average time/residue: 0.2062 time to fit residues: 27.9919 Evaluate side-chains 81 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU 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 849 CYS Chi-restraints excluded: chain A residue 906 SER 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 45 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 41 optimal weight: 0.0980 chunk 18 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN A1059 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.192113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.161298 restraints weight = 14597.907| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 2.15 r_work: 0.3900 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9049 Z= 0.166 Angle : 0.569 7.549 12645 Z= 0.310 Chirality : 0.039 0.171 1432 Planarity : 0.003 0.038 1206 Dihedral : 19.893 82.305 2323 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 4.20 % Allowed : 22.66 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.31), residues: 753 helix: 1.11 (0.29), residues: 321 sheet: -1.97 (0.63), residues: 64 loop : -1.90 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1067 HIS 0.010 0.001 HIS A 342 PHE 0.015 0.002 PHE A 277 TYR 0.013 0.002 TYR A 208 ARG 0.003 0.000 ARG A 408 Details of bonding type rmsd hydrogen bonds : bond 0.04558 ( 363) hydrogen bonds : angle 4.25086 ( 963) SS BOND : bond 0.00069 ( 1) SS BOND : angle 0.96880 ( 2) covalent geometry : bond 0.00370 ( 9048) covalent geometry : angle 0.56870 (12643) *********************** 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 110 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 PHE cc_start: 0.6592 (m-80) cc_final: 0.6184 (m-80) REVERT: A 347 TYR cc_start: 0.6519 (OUTLIER) cc_final: 0.6056 (m-80) REVERT: A 403 LYS cc_start: 0.7911 (mmtt) cc_final: 0.7335 (ttmt) REVERT: A 981 TYR cc_start: 0.5862 (OUTLIER) cc_final: 0.4282 (m-80) REVERT: A 1098 MET cc_start: 0.7294 (ttm) cc_final: 0.7048 (ttm) outliers start: 30 outliers final: 18 residues processed: 104 average time/residue: 0.2291 time to fit residues: 34.1644 Evaluate side-chains 91 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 385 ILE 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 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 45 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 0.0040 chunk 52 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 44 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN ** A 327 GLN ** 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 = 0.196506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.170131 restraints weight = 14527.170| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 1.94 r_work: 0.3959 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9049 Z= 0.127 Angle : 0.525 6.577 12645 Z= 0.287 Chirality : 0.037 0.152 1432 Planarity : 0.003 0.033 1206 Dihedral : 19.735 82.598 2323 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.50 % Allowed : 22.38 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.31), residues: 753 helix: 1.29 (0.29), residues: 321 sheet: -1.70 (0.75), residues: 52 loop : -1.84 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 68 HIS 0.008 0.001 HIS A 342 PHE 0.011 0.001 PHE A 277 TYR 0.010 0.001 TYR A 208 ARG 0.003 0.000 ARG A 56 Details of bonding type rmsd hydrogen bonds : bond 0.03857 ( 363) hydrogen bonds : angle 4.00348 ( 963) SS BOND : bond 0.00060 ( 1) SS BOND : angle 0.68444 ( 2) covalent geometry : bond 0.00279 ( 9048) covalent geometry : angle 0.52468 (12643) *********************** 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: 25 poor density : 73 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8159 (ptp90) REVERT: A 347 TYR cc_start: 0.6327 (OUTLIER) cc_final: 0.5838 (m-80) REVERT: A 403 LYS cc_start: 0.7832 (mmtt) cc_final: 0.7395 (tttt) REVERT: A 410 ASN cc_start: 0.7663 (t0) cc_final: 0.7420 (t0) REVERT: A 981 TYR cc_start: 0.5863 (OUTLIER) cc_final: 0.4355 (m-80) REVERT: A 986 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.5926 (mp0) outliers start: 25 outliers final: 13 residues processed: 93 average time/residue: 0.2343 time to fit residues: 30.2719 Evaluate side-chains 83 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ARG 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 449 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 148 GLN A 312 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.186026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.155150 restraints weight = 14633.799| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.40 r_work: 0.3807 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 9049 Z= 0.307 Angle : 0.725 8.959 12645 Z= 0.384 Chirality : 0.045 0.244 1432 Planarity : 0.004 0.038 1206 Dihedral : 19.940 79.139 2323 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer: Outliers : 6.29 % Allowed : 22.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.30), residues: 753 helix: 0.82 (0.28), residues: 319 sheet: -1.56 (0.85), residues: 38 loop : -2.19 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 68 HIS 0.011 0.002 HIS A 342 PHE 0.025 0.003 PHE A 277 TYR 0.019 0.003 TYR A 685 ARG 0.006 0.001 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.06106 ( 363) hydrogen bonds : angle 4.59841 ( 963) SS BOND : bond 0.00453 ( 1) SS BOND : angle 0.50702 ( 2) covalent geometry : bond 0.00692 ( 9048) covalent geometry : angle 0.72530 (12643) *********************** 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 123 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 78 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8267 (ptp90) REVERT: A 105 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7668 (tt) REVERT: A 328 TYR cc_start: 0.5927 (OUTLIER) cc_final: 0.4154 (t80) REVERT: A 357 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7613 (pt) REVERT: A 369 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6687 (tt) REVERT: A 403 LYS cc_start: 0.7959 (mmtt) cc_final: 0.7503 (mmtm) REVERT: A 410 ASN cc_start: 0.7723 (t0) cc_final: 0.7515 (t0) REVERT: A 453 LYS cc_start: 0.6267 (OUTLIER) cc_final: 0.3845 (ttmt) REVERT: A 981 TYR cc_start: 0.6119 (OUTLIER) cc_final: 0.4410 (m-80) REVERT: A 986 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6151 (mp0) outliers start: 45 outliers final: 22 residues processed: 114 average time/residue: 0.2380 time to fit residues: 38.4774 Evaluate side-chains 105 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 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 449 VAL Chi-restraints excluded: chain A residue 453 LYS 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 984 ASP 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 62 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.0470 chunk 57 optimal weight: 0.0570 chunk 41 optimal weight: 0.9980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 312 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4428 r_free = 0.4428 target = 0.195439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.168411 restraints weight = 14577.947| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 1.95 r_work: 0.3953 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9049 Z= 0.121 Angle : 0.542 6.815 12645 Z= 0.297 Chirality : 0.038 0.166 1432 Planarity : 0.003 0.026 1206 Dihedral : 19.632 83.246 2323 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 4.20 % Allowed : 24.34 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.30), residues: 753 helix: 1.13 (0.29), residues: 321 sheet: -1.73 (0.75), residues: 52 loop : -1.91 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1067 HIS 0.007 0.001 HIS A 342 PHE 0.011 0.001 PHE A 364 TYR 0.009 0.001 TYR A 208 ARG 0.004 0.000 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 363) hydrogen bonds : angle 4.03953 ( 963) SS BOND : bond 0.00048 ( 1) SS BOND : angle 0.73686 ( 2) covalent geometry : bond 0.00264 ( 9048) covalent geometry : angle 0.54174 (12643) *********************** 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 110 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.802 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: 0.8142 (ptp90) REVERT: A 328 TYR cc_start: 0.5849 (OUTLIER) cc_final: 0.3986 (t80) REVERT: A 357 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7422 (pt) REVERT: A 403 LYS cc_start: 0.7879 (mmtt) cc_final: 0.7433 (mmtm) REVERT: A 707 LYS cc_start: 0.7966 (mmtm) cc_final: 0.7536 (mmtt) REVERT: A 981 TYR cc_start: 0.5897 (OUTLIER) cc_final: 0.4376 (m-80) REVERT: A 986 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6093 (mp0) outliers start: 30 outliers final: 17 residues processed: 102 average time/residue: 0.2255 time to fit residues: 31.5553 Evaluate side-chains 92 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 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 373 MET Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 449 VAL 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 1053 ILE Chi-restraints excluded: chain A residue 1074 ILE 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 25 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4409 r_free = 0.4409 target = 0.193633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.166248 restraints weight = 14771.035| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 1.95 r_work: 0.3921 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9049 Z= 0.155 Angle : 0.563 9.733 12645 Z= 0.306 Chirality : 0.039 0.208 1432 Planarity : 0.003 0.059 1206 Dihedral : 19.600 82.009 2323 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 4.34 % Allowed : 23.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.31), residues: 753 helix: 1.15 (0.29), residues: 320 sheet: -1.75 (0.75), residues: 52 loop : -1.89 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1067 HIS 0.009 0.001 HIS A 342 PHE 0.012 0.001 PHE A 277 TYR 0.015 0.001 TYR A 272 ARG 0.003 0.000 ARG A 56 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 363) hydrogen bonds : angle 4.07824 ( 963) SS BOND : bond 0.00116 ( 1) SS BOND : angle 0.35001 ( 2) covalent geometry : bond 0.00348 ( 9048) covalent geometry : angle 0.56311 (12643) *********************** 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: 31 poor density : 76 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8173 (ptp90) REVERT: A 313 MET cc_start: 0.4317 (ptt) cc_final: 0.4102 (ppp) REVERT: A 328 TYR cc_start: 0.6046 (OUTLIER) cc_final: 0.3952 (t80) REVERT: A 357 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7460 (pt) REVERT: A 403 LYS cc_start: 0.7901 (mmtt) cc_final: 0.7434 (mmtm) REVERT: A 707 LYS cc_start: 0.7986 (mmtm) cc_final: 0.7525 (mmtt) REVERT: A 981 TYR cc_start: 0.5935 (OUTLIER) cc_final: 0.4429 (m-80) REVERT: A 986 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6109 (mp0) outliers start: 31 outliers final: 21 residues processed: 102 average time/residue: 0.2049 time to fit residues: 29.1751 Evaluate side-chains 95 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 372 THR Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 386 VAL 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 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 954 ASP 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 59 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 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 173 GLN A 312 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN A1008 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.194499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.167285 restraints weight = 14873.547| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 1.94 r_work: 0.3938 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9049 Z= 0.140 Angle : 0.549 7.342 12645 Z= 0.299 Chirality : 0.038 0.182 1432 Planarity : 0.003 0.056 1206 Dihedral : 19.567 82.265 2323 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 4.48 % Allowed : 22.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.31), residues: 753 helix: 1.28 (0.29), residues: 314 sheet: -1.72 (0.76), residues: 52 loop : -1.76 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1067 HIS 0.009 0.001 HIS A 342 PHE 0.011 0.001 PHE A 364 TYR 0.015 0.001 TYR A 272 ARG 0.003 0.000 ARG A 56 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 363) hydrogen bonds : angle 4.03809 ( 963) SS BOND : bond 0.00046 ( 1) SS BOND : angle 0.47183 ( 2) covalent geometry : bond 0.00312 ( 9048) covalent geometry : angle 0.54948 (12643) *********************** 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 107 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 75 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8179 (ptp90) REVERT: A 313 MET cc_start: 0.4269 (ptt) cc_final: 0.4014 (ppp) REVERT: A 328 TYR cc_start: 0.5884 (OUTLIER) cc_final: 0.3932 (t80) REVERT: A 357 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7402 (pt) REVERT: A 403 LYS cc_start: 0.7868 (mmtt) cc_final: 0.7413 (mmtm) REVERT: A 707 LYS cc_start: 0.7951 (mmtm) cc_final: 0.7503 (mmtt) REVERT: A 981 TYR cc_start: 0.5941 (OUTLIER) cc_final: 0.4440 (m-80) REVERT: A 986 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6147 (mp0) outliers start: 32 outliers final: 23 residues processed: 101 average time/residue: 0.2086 time to fit residues: 30.4541 Evaluate side-chains 101 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 372 THR Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 386 VAL 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 696 SER Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 954 ASP 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 1034 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 Chi-restraints excluded: chain A residue 1103 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 34 optimal weight: 0.2980 chunk 82 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 0.0170 chunk 45 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 71 optimal weight: 0.2980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4430 r_free = 0.4430 target = 0.196322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.169979 restraints weight = 14669.625| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 1.99 r_work: 0.3957 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9049 Z= 0.124 Angle : 0.523 6.748 12645 Z= 0.288 Chirality : 0.037 0.172 1432 Planarity : 0.003 0.054 1206 Dihedral : 19.522 82.882 2323 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.64 % Allowed : 23.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.31), residues: 753 helix: 1.30 (0.29), residues: 314 sheet: -1.68 (0.75), residues: 52 loop : -1.65 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1067 HIS 0.007 0.001 HIS A 342 PHE 0.010 0.001 PHE A 296 TYR 0.011 0.001 TYR A 272 ARG 0.003 0.000 ARG A 56 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 363) hydrogen bonds : angle 3.97651 ( 963) SS BOND : bond 0.00039 ( 1) SS BOND : angle 0.59501 ( 2) covalent geometry : bond 0.00273 ( 9048) covalent geometry : angle 0.52265 (12643) *********************** 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 103 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8169 (ptp90) REVERT: A 313 MET cc_start: 0.4213 (ptt) cc_final: 0.3976 (ppp) REVERT: A 328 TYR cc_start: 0.5936 (OUTLIER) cc_final: 0.3933 (t80) REVERT: A 357 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7384 (pt) REVERT: A 403 LYS cc_start: 0.7867 (mmtt) cc_final: 0.7396 (mmtm) REVERT: A 707 LYS cc_start: 0.7952 (mmtm) cc_final: 0.7484 (mmtt) REVERT: A 959 ASN cc_start: 0.6977 (m-40) cc_final: 0.6716 (m110) REVERT: A 981 TYR cc_start: 0.5851 (OUTLIER) cc_final: 0.4378 (m-80) REVERT: A 986 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6050 (mp0) outliers start: 26 outliers final: 19 residues processed: 98 average time/residue: 0.2088 time to fit residues: 28.9294 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 : 0.815 ------------------------------------------------------------------------------- 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 373 MET 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 491 LEU Chi-restraints excluded: chain A residue 954 ASP 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 1034 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 Chi-restraints excluded: chain A residue 1103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 54 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 65 optimal weight: 0.0060 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4440 r_free = 0.4440 target = 0.198168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.169791 restraints weight = 14836.954| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.11 r_work: 0.3936 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 9049 Z= 0.137 Angle : 0.534 6.770 12645 Z= 0.294 Chirality : 0.038 0.172 1432 Planarity : 0.003 0.053 1206 Dihedral : 19.507 82.108 2323 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 3.22 % Allowed : 24.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.31), residues: 753 helix: 1.24 (0.29), residues: 314 sheet: -1.59 (0.76), residues: 52 loop : -1.63 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1067 HIS 0.008 0.001 HIS A 342 PHE 0.012 0.001 PHE A 364 TYR 0.013 0.001 TYR A 272 ARG 0.002 0.000 ARG A 56 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 363) hydrogen bonds : angle 4.00543 ( 963) SS BOND : bond 0.00029 ( 1) SS BOND : angle 0.44478 ( 2) covalent geometry : bond 0.00309 ( 9048) covalent geometry : angle 0.53445 (12643) ********************** 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 98 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8178 (ptp90) REVERT: A 313 MET cc_start: 0.4393 (ptt) cc_final: 0.4056 (ppp) REVERT: A 328 TYR cc_start: 0.6025 (OUTLIER) cc_final: 0.3963 (t80) REVERT: A 357 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7374 (pt) REVERT: A 403 LYS cc_start: 0.7938 (mmtt) cc_final: 0.7427 (mmtm) REVERT: A 707 LYS cc_start: 0.7941 (mmtm) cc_final: 0.7498 (mmtt) REVERT: A 981 TYR cc_start: 0.5868 (OUTLIER) cc_final: 0.4383 (m-80) REVERT: A 986 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6052 (mp0) outliers start: 23 outliers final: 17 residues processed: 93 average time/residue: 0.2216 time to fit residues: 29.0986 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 : 0.844 ------------------------------------------------------------------------------- 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 373 MET 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 954 ASP 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 1034 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 19 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 312 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4394 r_free = 0.4394 target = 0.192478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.162427 restraints weight = 14777.166| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 2.16 r_work: 0.3924 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 9049 Z= 0.188 Angle : 0.590 7.159 12645 Z= 0.322 Chirality : 0.040 0.174 1432 Planarity : 0.004 0.059 1206 Dihedral : 19.453 80.039 2323 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 4.06 % Allowed : 24.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.31), residues: 753 helix: 1.11 (0.29), residues: 314 sheet: -1.69 (0.76), residues: 52 loop : -1.68 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 68 HIS 0.009 0.001 HIS A 342 PHE 0.033 0.002 PHE A 407 TYR 0.015 0.002 TYR A 867 ARG 0.007 0.000 ARG A 413 Details of bonding type rmsd hydrogen bonds : bond 0.04554 ( 363) hydrogen bonds : angle 4.19632 ( 963) SS BOND : bond 0.00197 ( 1) SS BOND : angle 0.19626 ( 2) covalent geometry : bond 0.00426 ( 9048) covalent geometry : angle 0.58966 (12643) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4397.56 seconds wall clock time: 77 minutes 58.80 seconds (4678.80 seconds total)