Starting phenix.real_space_refine on Fri Feb 14 00:07:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rjd_4902/02_2025/6rjd_4902.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rjd_4902/02_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_4902/02_2025/6rjd_4902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rjd_4902/02_2025/6rjd_4902.map" model { file = "/net/cci-nas-00/data/ceres_data/6rjd_4902/02_2025/6rjd_4902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rjd_4902/02_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-5592/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: 6.42, per 1000 atoms: 0.69 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: 2.39 Conformation dependent library (CDL) restraints added in 776.1 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: 3.03 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: 3.58 Time building geometry restraints manager: 2.65 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: 1.210 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.270 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.030 ------------------------------------------------------------------------------- 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 : 0.862 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: 0.2766 time to fit residues: 41.0743 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 : 0.919 ------------------------------------------------------------------------------- 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 = 14081.709| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.98 r_work: 0.3273 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 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 : 0.879 Fit side-chains revert: symmetry clash REVERT: C 157 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: C 339 ILE cc_start: 0.8769 (tt) cc_final: 0.8472 (tp) REVERT: C 346 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7374 (tm-30) REVERT: C 367 MET cc_start: 0.4950 (mmm) cc_final: 0.4596 (mtp) REVERT: C 438 GLU cc_start: 0.8272 (mp0) cc_final: 0.7598 (mp0) REVERT: C 465 THR cc_start: 0.7664 (m) cc_final: 0.7233 (p) REVERT: C 487 ARG cc_start: 0.7649 (mtp180) cc_final: 0.6857 (mtm180) REVERT: C 695 LEU cc_start: 0.8253 (tt) cc_final: 0.8018 (tt) REVERT: C 699 GLN cc_start: 0.6763 (mt0) cc_final: 0.6162 (tt0) REVERT: C 869 LYS cc_start: 0.8273 (mttt) cc_final: 0.7815 (ttpt) REVERT: C 931 GLU cc_start: 0.7987 (mp0) cc_final: 0.7747 (mp0) outliers start: 20 outliers final: 14 residues processed: 97 average time/residue: 0.2683 time to fit residues: 35.0089 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 : 0.915 ------------------------------------------------------------------------------- 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: 0.8980 chunk 9 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.3888 r_free = 0.3888 target = 0.156961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124694 restraints weight = 14268.306| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.04 r_work: 0.3261 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9747 Z= 0.256 Angle : 0.601 7.910 13669 Z= 0.320 Chirality : 0.038 0.135 1579 Planarity : 0.004 0.034 1301 Dihedral : 20.407 173.943 2601 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.65 % Allowed : 15.29 % Favored : 81.06 % 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: -1.39 (0.27), residues: 817 helix: 0.68 (0.27), residues: 338 sheet: -1.04 (0.53), residues: 87 loop : -2.44 (0.26), residues: 392 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 0.012 0.001 PHE C1021 TYR 0.019 0.002 TYR C1055 ARG 0.003 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: 27 poor density : 68 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 157 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: C 337 TYR cc_start: 0.7653 (p90) cc_final: 0.7287 (p90) REVERT: C 339 ILE cc_start: 0.8771 (tt) cc_final: 0.8437 (tp) REVERT: C 346 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7433 (tm-30) REVERT: C 367 MET cc_start: 0.4939 (mmm) cc_final: 0.4549 (mtp) REVERT: C 438 GLU cc_start: 0.8306 (mp0) cc_final: 0.7602 (mp0) REVERT: C 465 THR cc_start: 0.7324 (m) cc_final: 0.6894 (p) REVERT: C 487 ARG cc_start: 0.7652 (mtp180) cc_final: 0.6714 (mtm110) REVERT: C 695 LEU cc_start: 0.8307 (tt) cc_final: 0.8094 (tt) REVERT: C 699 GLN cc_start: 0.6739 (mt0) cc_final: 0.6174 (tt0) REVERT: C 851 ASP cc_start: 0.8075 (t0) cc_final: 0.7822 (t0) REVERT: C 869 LYS cc_start: 0.8254 (mttt) cc_final: 0.7983 (mtmt) outliers start: 27 outliers final: 17 residues processed: 93 average time/residue: 0.2521 time to fit residues: 32.8933 Evaluate side-chains 79 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 1.441 ------------------------------------------------------------------------------- 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 183 VAL Chi-restraints excluded: chain C residue 208 THR 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 881 THR Chi-restraints excluded: chain C residue 886 ILE Chi-restraints excluded: chain C residue 1047 ARG Chi-restraints excluded: chain C residue 1058 LEU 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: 3.9990 chunk 90 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 41 optimal weight: 0.3980 chunk 60 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.154803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.118854 restraints weight = 14169.555| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.92 r_work: 0.3271 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9747 Z= 0.315 Angle : 0.640 11.917 13669 Z= 0.336 Chirality : 0.040 0.136 1579 Planarity : 0.004 0.036 1301 Dihedral : 20.462 173.337 2601 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.92 % Allowed : 17.86 % Favored : 78.21 % 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: -1.17 (0.28), residues: 817 helix: 0.91 (0.28), residues: 341 sheet: -1.00 (0.54), residues: 87 loop : -2.36 (0.27), 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 0.016 0.002 PHE C 184 TYR 0.022 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 87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 58 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: C 157 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: C 337 TYR cc_start: 0.7807 (p90) cc_final: 0.7413 (p90) REVERT: C 346 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7323 (tm-30) REVERT: C 438 GLU cc_start: 0.8288 (mp0) cc_final: 0.7312 (mp0) REVERT: C 487 ARG cc_start: 0.7549 (mtp180) cc_final: 0.6584 (mtm110) REVERT: C 695 LEU cc_start: 0.8305 (tt) cc_final: 0.8103 (tt) REVERT: C 699 GLN cc_start: 0.6705 (mt0) cc_final: 0.6231 (tt0) outliers start: 29 outliers final: 20 residues processed: 83 average time/residue: 0.2492 time to fit residues: 28.7635 Evaluate side-chains 74 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 157 GLU Chi-restraints excluded: chain C residue 208 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 35 optimal weight: 3.9990 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: 3.9990 chunk 12 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.155026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.120948 restraints weight = 14141.728| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.86 r_work: 0.3255 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1937 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= 0.306 Angle : 0.626 11.692 13669 Z= 0.329 Chirality : 0.040 0.136 1579 Planarity : 0.004 0.037 1301 Dihedral : 20.455 172.988 2601 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.06 % Allowed : 18.54 % Favored : 77.40 % 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: -1.04 (0.28), residues: 817 helix: 1.03 (0.28), residues: 341 sheet: -0.98 (0.54), residues: 87 loop : -2.31 (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 C1021 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 88 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 58 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: C 157 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: C 337 TYR cc_start: 0.7828 (p90) cc_final: 0.7389 (p90) REVERT: C 438 GLU cc_start: 0.8309 (mp0) cc_final: 0.7370 (mp0) REVERT: C 487 ARG cc_start: 0.7587 (mtp180) cc_final: 0.6650 (mtm110) REVERT: C 695 LEU cc_start: 0.8306 (tt) cc_final: 0.8104 (tt) REVERT: C 699 GLN cc_start: 0.6694 (mt0) cc_final: 0.6242 (tt0) outliers start: 30 outliers final: 24 residues processed: 86 average time/residue: 0.2275 time to fit residues: 27.5063 Evaluate side-chains 76 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 51 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 208 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 442 THR Chi-restraints excluded: chain C residue 477 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 74 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.153957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.118134 restraints weight = 14190.510| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.91 r_work: 0.3262 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 9747 Z= 0.339 Angle : 0.649 10.887 13669 Z= 0.342 Chirality : 0.041 0.137 1579 Planarity : 0.004 0.041 1301 Dihedral : 20.357 172.335 2601 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 4.87 % Allowed : 18.67 % 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: -1.09 (0.28), residues: 817 helix: 0.95 (0.28), residues: 347 sheet: -0.99 (0.56), residues: 85 loop : -2.34 (0.28), residues: 385 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 0.015 0.002 PHE C1021 TYR 0.019 0.002 TYR C1055 ARG 0.003 0.000 ARG C 62 *********************** 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 88 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 52 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: C 157 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6513 (mp0) REVERT: C 438 GLU cc_start: 0.8308 (mp0) cc_final: 0.7415 (mp0) REVERT: C 487 ARG cc_start: 0.7550 (mtp180) cc_final: 0.6748 (mtm110) REVERT: C 699 GLN cc_start: 0.6743 (mt0) cc_final: 0.6298 (tt0) outliers start: 36 outliers final: 26 residues processed: 86 average time/residue: 0.2209 time to fit residues: 26.7315 Evaluate side-chains 79 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 52 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 208 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 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=2.50 ------------------------------------------------------------------------------- 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: 4.9990 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: 3.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.152792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.118767 restraints weight = 14388.919| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.88 r_work: 0.3233 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 9747 Z= 0.396 Angle : 0.695 10.163 13669 Z= 0.363 Chirality : 0.042 0.145 1579 Planarity : 0.004 0.045 1301 Dihedral : 20.336 171.276 2601 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 5.01 % Allowed : 20.16 % Favored : 74.83 % 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 (0.28), residues: 817 helix: 0.85 (0.28), residues: 347 sheet: -1.05 (0.56), residues: 85 loop : -2.38 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 965 HIS 0.004 0.001 HIS C 425 PHE 0.017 0.002 PHE C1021 TYR 0.018 0.002 TYR C 215 ARG 0.003 0.000 ARG C 413 *********************** 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: 37 poor density : 55 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 157 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6514 (mp0) REVERT: C 438 GLU cc_start: 0.8325 (mp0) cc_final: 0.7461 (mp0) REVERT: C 470 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.5945 (mt-10) REVERT: C 487 ARG cc_start: 0.7584 (mtp180) cc_final: 0.6756 (mtm110) REVERT: C 699 GLN cc_start: 0.6780 (mt0) cc_final: 0.6311 (tt0) REVERT: C 983 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8293 (mp) REVERT: C 1108 HIS cc_start: 0.7273 (OUTLIER) cc_final: 0.6525 (m90) outliers start: 37 outliers final: 30 residues processed: 91 average time/residue: 0.2315 time to fit residues: 29.8119 Evaluate side-chains 86 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 52 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 208 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 470 GLU Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 507 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 1101 THR Chi-restraints excluded: chain C residue 1104 LEU Chi-restraints excluded: chain C residue 1108 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 40 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.154773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119069 restraints weight = 14330.639| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.91 r_work: 0.3277 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2195 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= 0.290 Angle : 0.632 9.606 13669 Z= 0.332 Chirality : 0.039 0.137 1579 Planarity : 0.004 0.037 1301 Dihedral : 20.296 172.516 2601 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 4.87 % Allowed : 20.57 % Favored : 74.56 % 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: -1.02 (0.28), residues: 817 helix: 1.06 (0.28), residues: 347 sheet: -1.03 (0.57), residues: 85 loop : -2.34 (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 0.013 0.002 PHE C1021 TYR 0.015 0.002 TYR C 215 ARG 0.003 0.000 ARG C1047 *********************** 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 91 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 55 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: C 157 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6527 (mp0) REVERT: C 429 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8242 (t) REVERT: C 438 GLU cc_start: 0.8255 (mp0) cc_final: 0.7368 (mp0) REVERT: C 487 ARG cc_start: 0.7541 (mtp180) cc_final: 0.6733 (mtm110) REVERT: C 503 PHE cc_start: 0.6237 (m-80) cc_final: 0.5897 (m-80) REVERT: C 699 GLN cc_start: 0.6680 (mt0) cc_final: 0.6246 (tt0) REVERT: C 983 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8249 (mp) outliers start: 36 outliers final: 30 residues processed: 90 average time/residue: 0.2269 time to fit residues: 28.9894 Evaluate side-chains 87 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 54 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 208 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 356 MET Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 507 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 1101 THR Chi-restraints excluded: chain C residue 1104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 71 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 0.0020 chunk 41 optimal weight: 0.0270 chunk 58 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.7048 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.159651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.128518 restraints weight = 14141.240| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.03 r_work: 0.3315 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9747 Z= 0.143 Angle : 0.539 9.146 13669 Z= 0.282 Chirality : 0.035 0.132 1579 Planarity : 0.003 0.035 1301 Dihedral : 20.163 175.400 2601 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.38 % Allowed : 22.46 % Favored : 74.15 % 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: -0.52 (0.29), residues: 817 helix: 1.71 (0.28), residues: 337 sheet: -1.24 (0.51), residues: 99 loop : -2.10 (0.28), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 965 HIS 0.002 0.001 HIS C 61 PHE 0.010 0.001 PHE C1066 TYR 0.010 0.001 TYR C 215 ARG 0.002 0.000 ARG C1047 *********************** 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 94 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.792 Fit side-chains REVERT: C 157 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: C 337 TYR cc_start: 0.7913 (p90) cc_final: 0.7513 (p90) REVERT: C 339 ILE cc_start: 0.8822 (tt) cc_final: 0.8456 (tp) REVERT: C 438 GLU cc_start: 0.8229 (mp0) cc_final: 0.7262 (mp0) REVERT: C 487 ARG cc_start: 0.7499 (mtp180) cc_final: 0.6554 (mtm110) REVERT: C 503 PHE cc_start: 0.6033 (m-80) cc_final: 0.5803 (m-80) REVERT: C 699 GLN cc_start: 0.6659 (mt0) cc_final: 0.6166 (tt0) REVERT: C 1047 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.4766 (tpt-90) outliers start: 25 outliers final: 17 residues processed: 92 average time/residue: 0.2346 time to fit residues: 30.0237 Evaluate side-chains 79 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 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 208 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 507 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 877 HIS 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=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: 8.9990 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 178 HIS C1108 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.153778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.121375 restraints weight = 14359.988| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.12 r_work: 0.3220 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9747 Z= 0.362 Angle : 0.662 9.076 13669 Z= 0.346 Chirality : 0.041 0.137 1579 Planarity : 0.004 0.041 1301 Dihedral : 20.201 173.012 2601 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.57 % Allowed : 22.60 % Favored : 74.83 % 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: -0.84 (0.29), residues: 817 helix: 1.25 (0.28), residues: 347 sheet: -0.89 (0.58), residues: 85 loop : -2.30 (0.27), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 965 HIS 0.004 0.001 HIS C 425 PHE 0.015 0.002 PHE C1021 TYR 0.018 0.002 TYR C1055 ARG 0.003 0.000 ARG C 62 ********************** 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 74 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: C 157 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6662 (mp0) REVERT: C 438 GLU cc_start: 0.8345 (mp0) cc_final: 0.7466 (mp0) REVERT: C 487 ARG cc_start: 0.7650 (mtp180) cc_final: 0.6852 (mtm110) REVERT: C 503 PHE cc_start: 0.6262 (m-80) cc_final: 0.5925 (m-80) REVERT: C 699 GLN cc_start: 0.6738 (mt0) cc_final: 0.6225 (tt0) outliers start: 19 outliers final: 17 residues processed: 73 average time/residue: 0.2463 time to fit residues: 24.9391 Evaluate side-chains 73 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 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 208 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 507 VAL Chi-restraints excluded: chain C residue 691 SER Chi-restraints excluded: chain C residue 877 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 75 optimal weight: 0.0570 chunk 74 optimal weight: 7.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.159443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.127971 restraints weight = 14201.358| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.12 r_work: 0.3296 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9747 Z= 0.155 Angle : 0.544 8.717 13669 Z= 0.283 Chirality : 0.035 0.135 1579 Planarity : 0.003 0.035 1301 Dihedral : 20.072 175.009 2601 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.57 % Allowed : 22.73 % Favored : 74.70 % 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: -0.38 (0.29), residues: 817 helix: 1.82 (0.28), residues: 337 sheet: -0.73 (0.58), residues: 85 loop : -2.12 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 965 HIS 0.002 0.001 HIS C 61 PHE 0.010 0.001 PHE C1066 TYR 0.010 0.001 TYR C 215 ARG 0.003 0.000 ARG C 413 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3965.45 seconds wall clock time: 71 minutes 20.35 seconds (4280.35 seconds total)