Starting phenix.real_space_refine on Fri Mar 14 04:02:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rjd_4902/03_2025/6rjd_4902.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rjd_4902/03_2025/6rjd_4902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rjd_4902/03_2025/6rjd_4902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rjd_4902/03_2025/6rjd_4902.map" model { file = "/net/cci-nas-00/data/ceres_data/6rjd_4902/03_2025/6rjd_4902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rjd_4902/03_2025/6rjd_4902.cif" } resolution = 3.3 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 123 5.49 5 S 14 5.16 5 C 5476 2.51 5 N 1626 2.21 5 O 2093 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9332 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 6757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 831, 6757 Classifications: {'peptide': 831} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 811} Chain breaks: 6 Chain: "D" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1656 Classifications: {'RNA': 78} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 37, 'rna3p_pyr': 32} Link IDs: {'rna2p': 9, 'rna3p': 68} Chain breaks: 2 Chain: "E" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 646 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "G" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 273 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Time building chain proxies: 7.41, per 1000 atoms: 0.79 Number of scatterers: 9332 At special positions: 0 Unit cell: (100.457, 133.35, 113.792, 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 14 16.00 P 123 15.00 O 2093 8.00 N 1626 7.00 C 5476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 863.4 milliseconds 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1560 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 6 sheets defined 43.1% alpha, 11.7% beta 38 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 4.71 Creating SS restraints... Processing helix chain 'C' and resid 40 through 73 removed outlier: 3.725A pdb=" N LEU C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 98 removed outlier: 3.867A pdb=" N THR C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 115 removed outlier: 3.501A pdb=" N HIS C 115 " --> pdb=" O ASN C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 146 removed outlier: 4.257A pdb=" N ILE C 138 " --> pdb=" O ASP C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 163 Processing helix chain 'C' and resid 185 through 204 removed outlier: 3.732A pdb=" N TYR C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 220 Processing helix chain 'C' and resid 250 through 254 removed outlier: 3.541A pdb=" N GLY C 253 " --> pdb=" O ASN C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 3.685A pdb=" N LEU C 287 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 311 Processing helix chain 'C' and resid 315 through 328 removed outlier: 3.734A pdb=" N LEU C 319 " --> pdb=" O GLY C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 358 Processing helix chain 'C' and resid 369 through 382 Processing helix chain 'C' and resid 384 through 396 removed outlier: 3.784A pdb=" N ILE C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 416 Processing helix chain 'C' and resid 418 through 422 removed outlier: 3.621A pdb=" N GLY C 421 " --> pdb=" O SER C 418 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS C 422 " --> pdb=" O ILE C 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 418 through 422' Processing helix chain 'C' and resid 428 through 436 Processing helix chain 'C' and resid 437 through 439 No H-bonds generated for 'chain 'C' and resid 437 through 439' Processing helix chain 'C' and resid 445 through 453 Processing helix chain 'C' and resid 470 through 475 Processing helix chain 'C' and resid 479 through 501 Processing helix chain 'C' and resid 691 through 705 Processing helix chain 'C' and resid 737 through 748 Processing helix chain 'C' and resid 854 through 868 Processing helix chain 'C' and resid 869 through 872 removed outlier: 3.804A pdb=" N PHE C 872 " --> pdb=" O LYS C 869 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 869 through 872' Processing helix chain 'C' and resid 879 through 892 removed outlier: 3.880A pdb=" N GLU C 883 " --> pdb=" O PRO C 879 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS C 884 " --> pdb=" O GLN C 880 " (cutoff:3.500A) Proline residue: C 888 - end of helix Processing helix chain 'C' and resid 910 through 918 Processing helix chain 'C' and resid 1000 through 1012 removed outlier: 3.518A pdb=" N TYR C1004 " --> pdb=" O SER C1000 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 34 removed outlier: 6.651A pdb=" N ILE C 19 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LYS C 30 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL C 17 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER C 32 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N VAL C 15 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN C 505 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 508 " --> pdb=" O SER C 712 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 169 through 172 removed outlier: 3.558A pdb=" N HIS C 178 " --> pdb=" O VAL C 171 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 935 through 941 removed outlier: 5.768A pdb=" N LYS C 936 " --> pdb=" O ILE C 849 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE C 849 " --> pdb=" O LYS C 936 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N TYR C 938 " --> pdb=" O GLY C 847 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLY C 847 " --> pdb=" O TYR C 938 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER C 940 " --> pdb=" O VAL C 845 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ALA C 829 " --> pdb=" O LEU C 846 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 977 through 984 removed outlier: 3.553A pdb=" N LYS C 977 " --> pdb=" O ASN C 972 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 966 " --> pdb=" O LEU C 983 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE C1021 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE C 971 " --> pdb=" O PHE C1019 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N PHE C1019 " --> pdb=" O PHE C 971 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 989 through 990 removed outlier: 3.878A pdb=" N GLN C 989 " --> pdb=" O LYS C 998 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 998 " --> pdb=" O GLN C 989 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 1057 through 1059 removed outlier: 5.516A pdb=" N LYS C1059 " --> pdb=" O PHE C1044 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N PHE C1044 " --> pdb=" O LYS C1059 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU C1028 " --> pdb=" O VAL C1099 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL C1099 " --> pdb=" O LEU C1028 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 819 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 91 hydrogen bonds 178 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 4.67 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2012 1.33 - 1.45: 2680 1.45 - 1.57: 4789 1.57 - 1.69: 241 1.69 - 1.81: 25 Bond restraints: 9747 Sorted by residual: bond pdb=" N LYS C 706 " pdb=" CA LYS C 706 " ideal model delta sigma weight residual 1.460 1.485 -0.026 1.54e-02 4.22e+03 2.80e+00 bond pdb=" C3' DT E 11 " pdb=" O3' DT E 11 " ideal model delta sigma weight residual 1.422 1.472 -0.050 3.00e-02 1.11e+03 2.76e+00 bond pdb=" N GLU C 887 " pdb=" CA GLU C 887 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.41e-02 5.03e+03 2.42e+00 bond pdb=" CB ILE C 827 " pdb=" CG2 ILE C 827 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.36e+00 bond pdb=" C1' DC E 28 " pdb=" N1 DC E 28 " ideal model delta sigma weight residual 1.490 1.536 -0.046 3.00e-02 1.11e+03 2.32e+00 ... (remaining 9742 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 13242 2.22 - 4.44: 377 4.44 - 6.67: 34 6.67 - 8.89: 12 8.89 - 11.11: 4 Bond angle restraints: 13669 Sorted by residual: angle pdb=" C LEU C 248 " pdb=" N ASP C 249 " pdb=" CA ASP C 249 " ideal model delta sigma weight residual 121.54 130.47 -8.93 1.91e+00 2.74e-01 2.19e+01 angle pdb=" C HIS C 705 " pdb=" N LYS C 706 " pdb=" CA LYS C 706 " ideal model delta sigma weight residual 122.46 128.07 -5.61 1.41e+00 5.03e-01 1.58e+01 angle pdb=" C LYS C 457 " pdb=" N THR C 458 " pdb=" CA THR C 458 " ideal model delta sigma weight residual 121.54 129.12 -7.58 1.91e+00 2.74e-01 1.58e+01 angle pdb=" C3' DG G 4 " pdb=" O3' DG G 4 " pdb=" P DA G 5 " ideal model delta sigma weight residual 120.20 125.98 -5.78 1.50e+00 4.44e-01 1.49e+01 angle pdb=" CA LYS C 466 " pdb=" CB LYS C 466 " pdb=" CG LYS C 466 " ideal model delta sigma weight residual 114.10 121.35 -7.25 2.00e+00 2.50e-01 1.31e+01 ... (remaining 13664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.69: 5465 34.69 - 69.37: 405 69.37 - 104.06: 25 104.06 - 138.74: 0 138.74 - 173.43: 2 Dihedral angle restraints: 5897 sinusoidal: 3470 harmonic: 2427 Sorted by residual: dihedral pdb=" CA ASP C 368 " pdb=" C ASP C 368 " pdb=" N ARG C 369 " pdb=" CA ARG C 369 " ideal model delta harmonic sigma weight residual 180.00 157.77 22.23 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA HIS C 115 " pdb=" C HIS C 115 " pdb=" N ARG C 116 " pdb=" CA ARG C 116 " ideal model delta harmonic sigma weight residual 180.00 160.11 19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" C4' DG G 4 " pdb=" C3' DG G 4 " pdb=" O3' DG G 4 " pdb=" P DA G 5 " ideal model delta sinusoidal sigma weight residual -140.00 33.43 -173.43 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 5894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1088 0.046 - 0.093: 361 0.093 - 0.139: 106 0.139 - 0.186: 18 0.186 - 0.232: 6 Chirality restraints: 1579 Sorted by residual: chirality pdb=" CB ILE C 339 " pdb=" CA ILE C 339 " pdb=" CG1 ILE C 339 " pdb=" CG2 ILE C 339 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE C 886 " pdb=" CA ILE C 886 " pdb=" CG1 ILE C 886 " pdb=" CG2 ILE C 886 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C1' A D 68 " pdb=" O4' A D 68 " pdb=" C2' A D 68 " pdb=" N9 A D 68 " both_signs ideal model delta sigma weight residual False 2.46 2.24 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1576 not shown) Planarity restraints: 1301 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A D 63 " -0.030 2.00e-02 2.50e+03 1.81e-02 8.98e+00 pdb=" N9 A D 63 " 0.049 2.00e-02 2.50e+03 pdb=" C8 A D 63 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A D 63 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A D 63 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A D 63 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A D 63 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A D 63 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A D 63 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A D 63 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A D 63 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 466 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.88e+00 pdb=" C LYS C 466 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS C 466 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR C 467 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 249 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C ASP C 249 " 0.044 2.00e-02 2.50e+03 pdb=" O ASP C 249 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN C 250 " -0.015 2.00e-02 2.50e+03 ... (remaining 1298 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2004 2.79 - 3.32: 7363 3.32 - 3.84: 15404 3.84 - 4.37: 18273 4.37 - 4.90: 28971 Nonbonded interactions: 72015 Sorted by model distance: nonbonded pdb=" OH TYR C 89 " pdb=" OP1 A D 63 " model vdw 2.259 3.040 nonbonded pdb=" O ALA C 376 " pdb=" OG1 THR C 380 " model vdw 2.304 3.040 nonbonded pdb=" O SER C 119 " pdb=" OG SER C 119 " model vdw 2.317 3.040 nonbonded pdb=" OG1 THR C 830 " pdb=" O LYS C 956 " model vdw 2.324 3.040 nonbonded pdb=" OD2 ASP C 968 " pdb=" OH TYR C1004 " model vdw 2.346 3.040 ... (remaining 72010 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.980 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 34.180 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:4.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 0.006 0.051 9747 Z= 0.341 Angle : 0.900 11.110 13669 Z= 0.489 Chirality : 0.052 0.232 1579 Planarity : 0.006 0.041 1301 Dihedral : 20.281 173.426 4337 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.27 % Allowed : 10.28 % Favored : 89.45 % 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: -3.53 (0.23), residues: 817 helix: -2.01 (0.22), residues: 328 sheet: -2.03 (0.50), residues: 100 loop : -2.69 (0.25), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 965 HIS 0.006 0.001 HIS C 348 PHE 0.029 0.002 PHE C 169 TYR 0.038 0.002 TYR C1055 ARG 0.015 0.001 ARG C 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: C 367 MET cc_start: 0.4696 (mmm) cc_final: 0.4342 (mtp) REVERT: C 437 PRO cc_start: 0.8637 (Cg_exo) cc_final: 0.8267 (Cg_endo) REVERT: C 438 GLU cc_start: 0.8051 (mp0) cc_final: 0.7160 (mp0) REVERT: C 465 THR cc_start: 0.7825 (m) cc_final: 0.7375 (p) REVERT: C 487 ARG cc_start: 0.7048 (mtp180) cc_final: 0.6255 (mtm180) REVERT: C 699 GLN cc_start: 0.6582 (mt0) cc_final: 0.6113 (tt0) REVERT: C 869 LYS cc_start: 0.8139 (mttt) cc_final: 0.7669 (ttpt) REVERT: C 921 ARG cc_start: 0.8441 (mtt-85) cc_final: 0.8082 (mtp85) REVERT: C 931 GLU cc_start: 0.7496 (mp0) cc_final: 0.7289 (mp0) REVERT: C 1047 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7516 (tpt-90) outliers start: 2 outliers final: 0 residues processed: 114 average time/residue: 0.3078 time to fit residues: 45.6720 Evaluate side-chains 69 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1047 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 GLN C 300 GLN C 494 ASN C 928 ASN C1054 HIS C1108 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.157222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.124895 restraints weight = 14081.704| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.98 r_work: 0.3273 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9747 Z= 0.261 Angle : 0.619 7.749 13669 Z= 0.331 Chirality : 0.038 0.133 1579 Planarity : 0.004 0.037 1301 Dihedral : 20.466 174.226 2601 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.71 % Allowed : 14.07 % Favored : 83.22 % 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: -1.99 (0.26), residues: 817 helix: -0.07 (0.26), residues: 337 sheet: -1.13 (0.54), residues: 86 loop : -2.57 (0.25), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 965 HIS 0.005 0.001 HIS C1108 PHE 0.014 0.002 PHE C1021 TYR 0.023 0.002 TYR C1055 ARG 0.003 0.001 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: C 157 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7294 (mp0) REVERT: C 339 ILE cc_start: 0.8769 (tt) cc_final: 0.8472 (tp) REVERT: C 346 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7372 (tm-30) REVERT: C 367 MET cc_start: 0.4943 (mmm) cc_final: 0.4592 (mtp) REVERT: C 438 GLU cc_start: 0.8274 (mp0) cc_final: 0.7595 (mp0) REVERT: C 465 THR cc_start: 0.7666 (m) cc_final: 0.7238 (p) REVERT: C 487 ARG cc_start: 0.7649 (mtp180) cc_final: 0.6855 (mtm180) REVERT: C 695 LEU cc_start: 0.8258 (tt) cc_final: 0.8022 (tt) REVERT: C 699 GLN cc_start: 0.6763 (mt0) cc_final: 0.6166 (tt0) REVERT: C 869 LYS cc_start: 0.8273 (mttt) cc_final: 0.7814 (ttpt) REVERT: C 931 GLU cc_start: 0.7991 (mp0) cc_final: 0.7749 (mp0) outliers start: 20 outliers final: 14 residues processed: 97 average time/residue: 0.2567 time to fit residues: 33.7316 Evaluate side-chains 80 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 886 ILE Chi-restraints excluded: chain C residue 928 ASN Chi-restraints excluded: chain C residue 1047 ARG Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1104 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 32 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 70 optimal weight: 0.0570 chunk 66 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 overall best weight: 1.3900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 GLN C 928 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.159189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.123373 restraints weight = 14262.898| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.93 r_work: 0.3330 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9747 Z= 0.179 Angle : 0.556 7.245 13669 Z= 0.296 Chirality : 0.036 0.131 1579 Planarity : 0.003 0.033 1301 Dihedral : 20.389 174.873 2601 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.98 % Allowed : 15.29 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.27), residues: 817 helix: 0.81 (0.28), residues: 338 sheet: -1.46 (0.48), residues: 100 loop : -2.28 (0.27), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 965 HIS 0.003 0.001 HIS C 178 PHE 0.008 0.001 PHE C1021 TYR 0.014 0.001 TYR C1055 ARG 0.002 0.000 ARG C 413 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 157 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: C 337 TYR cc_start: 0.7551 (p90) cc_final: 0.7195 (p90) REVERT: C 339 ILE cc_start: 0.8741 (tt) cc_final: 0.8407 (tp) REVERT: C 346 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7328 (tm-30) REVERT: C 367 MET cc_start: 0.4858 (mmm) cc_final: 0.4615 (mtp) REVERT: C 438 GLU cc_start: 0.8209 (mp0) cc_final: 0.7454 (mp0) REVERT: C 465 THR cc_start: 0.7357 (m) cc_final: 0.6918 (p) REVERT: C 487 ARG cc_start: 0.7452 (mtp180) cc_final: 0.6491 (mtm110) REVERT: C 699 GLN cc_start: 0.6676 (mt0) cc_final: 0.6135 (tt0) REVERT: C 851 ASP cc_start: 0.8071 (t0) cc_final: 0.7776 (t0) REVERT: C 869 LYS cc_start: 0.8226 (mttt) cc_final: 0.7955 (mtmt) outliers start: 22 outliers final: 12 residues processed: 93 average time/residue: 0.3029 time to fit residues: 40.1284 Evaluate side-chains 76 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 887 GLU Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1104 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 16 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.155132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.119225 restraints weight = 14169.529| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.92 r_work: 0.3271 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9747 Z= 0.320 Angle : 0.643 11.419 13669 Z= 0.336 Chirality : 0.040 0.135 1579 Planarity : 0.004 0.035 1301 Dihedral : 20.397 173.569 2597 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.38 % Allowed : 17.19 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.12 (0.28), residues: 817 helix: 0.93 (0.28), residues: 341 sheet: -0.95 (0.54), residues: 87 loop : -2.33 (0.27), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 965 HIS 0.003 0.001 HIS C 61 PHE 0.015 0.002 PHE C1021 TYR 0.021 0.002 TYR C1055 ARG 0.004 0.000 ARG C 413 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 1.694 Fit side-chains revert: symmetry clash REVERT: C 157 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: C 337 TYR cc_start: 0.7781 (p90) cc_final: 0.7417 (p90) REVERT: C 346 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7333 (tm-30) REVERT: C 438 GLU cc_start: 0.8303 (mp0) cc_final: 0.7322 (mp0) REVERT: C 487 ARG cc_start: 0.7539 (mtp180) cc_final: 0.6601 (mtm110) REVERT: C 699 GLN cc_start: 0.6741 (mt0) cc_final: 0.6228 (tt0) REVERT: C 869 LYS cc_start: 0.8248 (mttt) cc_final: 0.7979 (mtmt) outliers start: 25 outliers final: 16 residues processed: 83 average time/residue: 0.4110 time to fit residues: 46.8208 Evaluate side-chains 73 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 886 ILE Chi-restraints excluded: chain C residue 1047 ARG Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1104 LEU Chi-restraints excluded: chain C residue 1109 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 35 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.155250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.119398 restraints weight = 14157.991| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.92 r_work: 0.3275 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9747 Z= 0.299 Angle : 0.625 11.547 13669 Z= 0.327 Chirality : 0.040 0.136 1579 Planarity : 0.004 0.037 1301 Dihedral : 20.453 173.050 2597 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.25 % Allowed : 18.00 % Favored : 78.76 % 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: -1.01 (0.28), residues: 817 helix: 1.05 (0.28), residues: 341 sheet: -0.98 (0.54), residues: 87 loop : -2.26 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 965 HIS 0.003 0.001 HIS C 61 PHE 0.014 0.002 PHE C 184 TYR 0.018 0.002 TYR C1055 ARG 0.003 0.000 ARG C 413 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: C 157 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: C 314 MET cc_start: 0.7716 (ptp) cc_final: 0.7491 (ptt) REVERT: C 337 TYR cc_start: 0.7770 (p90) cc_final: 0.7363 (p90) REVERT: C 438 GLU cc_start: 0.8263 (mp0) cc_final: 0.7307 (mp0) REVERT: C 487 ARG cc_start: 0.7530 (mtp180) cc_final: 0.6581 (mtm110) REVERT: C 699 GLN cc_start: 0.6704 (mt0) cc_final: 0.6225 (tt0) outliers start: 24 outliers final: 19 residues processed: 81 average time/residue: 0.2356 time to fit residues: 26.4843 Evaluate side-chains 70 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 886 ILE Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1047 ARG Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1104 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 74 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.154760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.118971 restraints weight = 14177.805| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.91 r_work: 0.3273 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9747 Z= 0.305 Angle : 0.628 10.573 13669 Z= 0.329 Chirality : 0.040 0.137 1579 Planarity : 0.004 0.039 1301 Dihedral : 20.349 173.029 2597 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.19 % Allowed : 18.81 % Favored : 77.00 % 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: -0.94 (0.28), residues: 817 helix: 1.14 (0.28), residues: 341 sheet: -0.95 (0.55), residues: 87 loop : -2.26 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 965 HIS 0.003 0.001 HIS C 61 PHE 0.014 0.002 PHE C 184 TYR 0.018 0.002 TYR C1055 ARG 0.003 0.000 ARG C 820 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 53 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: C 157 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: C 314 MET cc_start: 0.7742 (ptp) cc_final: 0.7466 (ptt) REVERT: C 337 TYR cc_start: 0.7853 (p90) cc_final: 0.7397 (p90) REVERT: C 438 GLU cc_start: 0.8269 (mp0) cc_final: 0.7324 (mp0) REVERT: C 487 ARG cc_start: 0.7525 (mtp180) cc_final: 0.6611 (mtm110) REVERT: C 699 GLN cc_start: 0.6712 (mt0) cc_final: 0.6234 (tt0) outliers start: 31 outliers final: 23 residues processed: 82 average time/residue: 0.2282 time to fit residues: 26.3325 Evaluate side-chains 76 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 52 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 886 ILE Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1047 ARG Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 31 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1108 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 = 0.3827 r_free = 0.3827 target = 0.152017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120263 restraints weight = 14386.823| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.18 r_work: 0.3195 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 9747 Z= 0.448 Angle : 0.730 9.941 13669 Z= 0.382 Chirality : 0.044 0.154 1579 Planarity : 0.005 0.049 1301 Dihedral : 20.364 170.123 2597 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.60 % Allowed : 18.94 % Favored : 76.45 % 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: -1.25 (0.28), residues: 817 helix: 0.78 (0.28), residues: 346 sheet: -1.08 (0.56), residues: 85 loop : -2.37 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 965 HIS 0.004 0.001 HIS C 425 PHE 0.019 0.002 PHE C1021 TYR 0.020 0.002 TYR C1055 ARG 0.004 0.000 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 58 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 157 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6578 (mp0) REVERT: C 438 GLU cc_start: 0.8364 (mp0) cc_final: 0.7502 (mp0) REVERT: C 487 ARG cc_start: 0.7660 (mtp180) cc_final: 0.6849 (mtm110) REVERT: C 699 GLN cc_start: 0.6813 (mt0) cc_final: 0.6331 (tt0) REVERT: C 983 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8312 (mp) outliers start: 34 outliers final: 26 residues processed: 91 average time/residue: 0.2341 time to fit residues: 30.1541 Evaluate side-chains 82 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 54 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 886 ILE Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1047 ARG Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 34 optimal weight: 0.0870 chunk 75 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1108 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 = 0.3883 r_free = 0.3883 target = 0.156670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.121006 restraints weight = 14304.848| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.92 r_work: 0.3303 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9747 Z= 0.196 Angle : 0.585 9.445 13669 Z= 0.306 Chirality : 0.037 0.148 1579 Planarity : 0.003 0.036 1301 Dihedral : 20.184 173.020 2597 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.65 % Allowed : 20.43 % Favored : 75.91 % 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: -0.87 (0.29), residues: 817 helix: 1.17 (0.28), residues: 347 sheet: -0.91 (0.57), residues: 85 loop : -2.25 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 965 HIS 0.002 0.001 HIS C 61 PHE 0.009 0.001 PHE C1066 TYR 0.013 0.001 TYR C 215 ARG 0.003 0.000 ARG C 413 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.829 Fit side-chains REVERT: C 157 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: C 314 MET cc_start: 0.7691 (ptp) cc_final: 0.7429 (ptt) REVERT: C 438 GLU cc_start: 0.8257 (mp0) cc_final: 0.7335 (mp0) REVERT: C 487 ARG cc_start: 0.7497 (mtp180) cc_final: 0.6568 (mtm110) REVERT: C 503 PHE cc_start: 0.6160 (m-80) cc_final: 0.5877 (m-80) REVERT: C 699 GLN cc_start: 0.6679 (mt0) cc_final: 0.6172 (tt0) REVERT: C 983 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8163 (mp) REVERT: C 1047 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.5575 (tpt-90) outliers start: 27 outliers final: 23 residues processed: 87 average time/residue: 0.2301 time to fit residues: 27.8413 Evaluate side-chains 84 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 886 ILE Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1047 ARG Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1104 LEU Chi-restraints excluded: chain C residue 1109 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 71 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 2 optimal weight: 0.0970 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 63 optimal weight: 0.0040 chunk 34 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1108 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 = 0.3916 r_free = 0.3916 target = 0.159472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.127693 restraints weight = 14149.546| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.08 r_work: 0.3295 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9747 Z= 0.161 Angle : 0.550 9.010 13669 Z= 0.286 Chirality : 0.035 0.167 1579 Planarity : 0.003 0.034 1301 Dihedral : 20.056 176.121 2597 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.25 % Allowed : 21.52 % Favored : 75.24 % 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: -0.41 (0.29), residues: 817 helix: 1.75 (0.28), residues: 337 sheet: -0.70 (0.58), residues: 85 loop : -2.10 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 965 HIS 0.002 0.001 HIS C1108 PHE 0.009 0.001 PHE C1066 TYR 0.010 0.001 TYR C 215 ARG 0.002 0.000 ARG C 413 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.906 Fit side-chains REVERT: C 157 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: C 314 MET cc_start: 0.7633 (ptp) cc_final: 0.7428 (ptt) REVERT: C 337 TYR cc_start: 0.7881 (p90) cc_final: 0.7461 (p90) REVERT: C 339 ILE cc_start: 0.8849 (tt) cc_final: 0.8477 (tp) REVERT: C 414 LYS cc_start: 0.7854 (mttm) cc_final: 0.7442 (tttm) REVERT: C 438 GLU cc_start: 0.8215 (mp0) cc_final: 0.7262 (mp0) REVERT: C 487 ARG cc_start: 0.7572 (mtp180) cc_final: 0.6654 (mtm110) REVERT: C 699 GLN cc_start: 0.6670 (mt0) cc_final: 0.6167 (tt0) outliers start: 24 outliers final: 21 residues processed: 88 average time/residue: 0.2171 time to fit residues: 27.0696 Evaluate side-chains 80 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 886 ILE Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 87 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 178 HIS ** C1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.156072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.123708 restraints weight = 14288.208| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.97 r_work: 0.3259 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9747 Z= 0.288 Angle : 0.626 8.905 13669 Z= 0.326 Chirality : 0.039 0.135 1579 Planarity : 0.004 0.038 1301 Dihedral : 20.068 174.792 2597 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.11 % Allowed : 21.92 % Favored : 74.97 % 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 (0.29), residues: 817 helix: 1.39 (0.28), residues: 347 sheet: -0.71 (0.58), residues: 85 loop : -2.18 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 965 HIS 0.004 0.001 HIS C 425 PHE 0.012 0.002 PHE C 818 TYR 0.015 0.002 TYR C 215 ARG 0.002 0.000 ARG C 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1634 Ramachandran restraints generated. 817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.875 Fit side-chains REVERT: C 157 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: C 314 MET cc_start: 0.7665 (ptp) cc_final: 0.7427 (ptt) REVERT: C 438 GLU cc_start: 0.8312 (mp0) cc_final: 0.7430 (mp0) REVERT: C 487 ARG cc_start: 0.7651 (mtp180) cc_final: 0.6905 (mtm110) REVERT: C 699 GLN cc_start: 0.6680 (mt0) cc_final: 0.6215 (tt0) outliers start: 23 outliers final: 21 residues processed: 79 average time/residue: 0.2272 time to fit residues: 25.4452 Evaluate side-chains 78 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 877 HIS Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 886 ILE Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1066 PHE Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.6980 chunk 78 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1108 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 = 0.3875 r_free = 0.3875 target = 0.156065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.124415 restraints weight = 14213.385| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.98 r_work: 0.3254 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9747 Z= 0.254 Angle : 0.606 8.713 13669 Z= 0.317 Chirality : 0.038 0.135 1579 Planarity : 0.003 0.036 1301 Dihedral : 20.072 174.286 2597 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.79 % Allowed : 21.24 % Favored : 74.97 % 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 (0.29), residues: 817 helix: 1.40 (0.28), residues: 347 sheet: -0.71 (0.59), residues: 85 loop : -2.19 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 965 HIS 0.003 0.001 HIS C 61 PHE 0.011 0.001 PHE C1021 TYR 0.014 0.001 TYR C 215 ARG 0.002 0.000 ARG C 413 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4117.58 seconds wall clock time: 74 minutes 19.97 seconds (4459.97 seconds total)