Starting phenix.real_space_refine on Fri Jul 3 04:37:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mn7_48415/07_2026/9mn7_48415.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mn7_48415/07_2026/9mn7_48415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mn7_48415/07_2026/9mn7_48415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mn7_48415/07_2026/9mn7_48415.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mn7_48415/07_2026/9mn7_48415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mn7_48415/07_2026/9mn7_48415.map" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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: 6 Type Number sf(0) Gaussians P 69 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 7300 2.51 5 N 2112 2.21 5 O 2243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11788 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2440 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 19, 'TRANS': 281} Chain breaks: 1 Chain: "E" Number of atoms: 7953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 997, 7953 Classifications: {'peptide': 997} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 64, 'TRANS': 932} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 618 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "R" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 133 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 5} Link IDs: {'rna3p': 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 612 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.34, per 1000 atoms: 0.20 Number of scatterers: 11788 At special positions: 0 Unit cell: (94.17, 129.94, 110.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 69 15.00 Mg 1 11.99 O 2243 8.00 N 2112 7.00 C 7300 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: 0.71 Conformation dependent library (CDL) restraints added in 346.6 milliseconds 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2462 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 11 sheets defined 56.2% alpha, 6.2% beta 23 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'B' and resid 80 through 90 Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 129 through 135 removed outlier: 3.778A pdb=" N LEU B 133 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 134 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER B 135 " --> pdb=" O PRO B 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 129 through 135' Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 199 through 213 removed outlier: 3.902A pdb=" N SER B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 219 Processing helix chain 'B' and resid 231 through 237 Processing helix chain 'B' and resid 248 through 258 Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.535A pdb=" N HIS B 322 " --> pdb=" O ASN B 318 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B 323 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS B 326 " --> pdb=" O HIS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 343 removed outlier: 3.538A pdb=" N HIS B 338 " --> pdb=" O THR B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 355 Processing helix chain 'B' and resid 366 through 379 removed outlier: 3.632A pdb=" N PHE B 370 " --> pdb=" O HIS B 366 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU B 378 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 236 Processing helix chain 'E' and resid 238 through 249 removed outlier: 3.582A pdb=" N ALA E 242 " --> pdb=" O GLN E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 274 Processing helix chain 'E' and resid 277 through 290 removed outlier: 3.522A pdb=" N ALA E 290 " --> pdb=" O MET E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 309 Processing helix chain 'E' and resid 312 through 327 removed outlier: 3.783A pdb=" N GLY E 327 " --> pdb=" O MET E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 336 removed outlier: 3.910A pdb=" N PHE E 334 " --> pdb=" O LEU E 330 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR E 335 " --> pdb=" O GLN E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 353 Processing helix chain 'E' and resid 392 through 410 Processing helix chain 'E' and resid 424 through 462 Processing helix chain 'E' and resid 467 through 472 Processing helix chain 'E' and resid 475 through 489 Processing helix chain 'E' and resid 497 through 520 removed outlier: 3.758A pdb=" N VAL E 514 " --> pdb=" O SER E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 538 removed outlier: 3.550A pdb=" N ALA E 525 " --> pdb=" O GLY E 521 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS E 532 " --> pdb=" O ASN E 528 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N CYS E 535 " --> pdb=" O ARG E 531 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU E 536 " --> pdb=" O LYS E 532 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU E 537 " --> pdb=" O TYR E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 556 Processing helix chain 'E' and resid 568 through 587 Processing helix chain 'E' and resid 624 through 634 Processing helix chain 'E' and resid 644 through 646 No H-bonds generated for 'chain 'E' and resid 644 through 646' Processing helix chain 'E' and resid 679 through 687 removed outlier: 3.721A pdb=" N CYS E 687 " --> pdb=" O LEU E 683 " (cutoff:3.500A) Processing helix chain 'E' and resid 692 through 704 Processing helix chain 'E' and resid 710 through 723 removed outlier: 3.718A pdb=" N ALA E 723 " --> pdb=" O GLN E 719 " (cutoff:3.500A) Processing helix chain 'E' and resid 758 through 789 Processing helix chain 'E' and resid 818 through 824 Processing helix chain 'E' and resid 836 through 850 removed outlier: 3.884A pdb=" N TRP E 840 " --> pdb=" O HIS E 836 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY E 850 " --> pdb=" O VAL E 846 " (cutoff:3.500A) Processing helix chain 'E' and resid 856 through 867 Processing helix chain 'E' and resid 867 through 877 Processing helix chain 'E' and resid 883 through 888 removed outlier: 3.561A pdb=" N MET E 886 " --> pdb=" O LYS E 883 " (cutoff:3.500A) Processing helix chain 'E' and resid 890 through 906 Processing helix chain 'E' and resid 925 through 936 Processing helix chain 'E' and resid 937 through 944 Processing helix chain 'E' and resid 954 through 971 removed outlier: 3.926A pdb=" N GLY E 958 " --> pdb=" O ASP E 954 " (cutoff:3.500A) Processing helix chain 'E' and resid 975 through 982 removed outlier: 4.364A pdb=" N GLN E 979 " --> pdb=" O MET E 975 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU E 982 " --> pdb=" O ALA E 978 " (cutoff:3.500A) Processing helix chain 'E' and resid 986 through 997 removed outlier: 3.848A pdb=" N VAL E 990 " --> pdb=" O THR E 986 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN E 992 " --> pdb=" O LYS E 988 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N THR E 993 " --> pdb=" O VAL E 989 " (cutoff:3.500A) Processing helix chain 'E' and resid 1004 through 1010 removed outlier: 3.863A pdb=" N LEU E1008 " --> pdb=" O TYR E1004 " (cutoff:3.500A) Processing helix chain 'E' and resid 1011 through 1016 Processing helix chain 'E' and resid 1024 through 1034 Processing helix chain 'E' and resid 1036 through 1041 Processing helix chain 'E' and resid 1044 through 1064 Processing helix chain 'E' and resid 1111 through 1141 Proline residue: E1120 - end of helix removed outlier: 3.841A pdb=" N ILE E1124 " --> pdb=" O PRO E1120 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG E1141 " --> pdb=" O LEU E1137 " (cutoff:3.500A) Processing helix chain 'E' and resid 1159 through 1177 removed outlier: 3.954A pdb=" N GLU E1177 " --> pdb=" O ARG E1173 " (cutoff:3.500A) Processing helix chain 'E' and resid 1178 through 1192 Processing helix chain 'E' and resid 1196 through 1200 removed outlier: 3.761A pdb=" N LEU E1199 " --> pdb=" O GLN E1196 " (cutoff:3.500A) Processing helix chain 'E' and resid 1201 through 1209 Processing helix chain 'E' and resid 1218 through 1225 removed outlier: 3.524A pdb=" N GLN E1221 " --> pdb=" O ASP E1218 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 120 through 122 removed outlier: 5.799A pdb=" N LEU B 99 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 192 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY B 193 " --> pdb=" O ASN B 226 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS B 264 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 411 through 415 Processing sheet with id=AA3, first strand: chain 'E' and resid 495 through 496 removed outlier: 3.741A pdb=" N GLU E 495 " --> pdb=" O LEU E 621 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 588 through 590 Processing sheet with id=AA5, first strand: chain 'E' and resid 794 through 795 Processing sheet with id=AA6, first strand: chain 'E' and resid 798 through 800 Processing sheet with id=AA7, first strand: chain 'E' and resid 831 through 832 Processing sheet with id=AA8, first strand: chain 'E' and resid 1146 through 1149 Processing sheet with id=AA9, first strand: chain 'E' and resid 1069 through 1071 Processing sheet with id=AB1, first strand: chain 'E' and resid 1083 through 1084 removed outlier: 4.580A pdb=" N LYS E1109 " --> pdb=" O LEU E1084 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 1087 through 1090 removed outlier: 3.811A pdb=" N LYS E1087 " --> pdb=" O HIS E1102 " (cutoff:3.500A) 514 hydrogen bonds defined for protein. 1500 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2913 1.33 - 1.45: 2588 1.45 - 1.57: 6475 1.57 - 1.69: 134 1.69 - 1.81: 96 Bond restraints: 12206 Sorted by residual: bond pdb=" C3' DA N 36 " pdb=" C2' DA N 36 " ideal model delta sigma weight residual 1.516 1.551 -0.035 8.00e-03 1.56e+04 1.94e+01 bond pdb=" C1' DC T 12 " pdb=" N1 DC T 12 " ideal model delta sigma weight residual 1.468 1.527 -0.059 1.40e-02 5.10e+03 1.80e+01 bond pdb=" C3' DA N 41 " pdb=" C2' DA N 41 " ideal model delta sigma weight residual 1.516 1.549 -0.033 8.00e-03 1.56e+04 1.74e+01 bond pdb=" C3' DG T 18 " pdb=" C2' DG T 18 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.38e+01 bond pdb=" C3' DT T 16 " pdb=" C2' DT T 16 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.35e+01 ... (remaining 12201 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 16493 2.85 - 5.69: 286 5.69 - 8.54: 45 8.54 - 11.39: 10 11.39 - 14.24: 1 Bond angle restraints: 16835 Sorted by residual: angle pdb=" O4' DA N 35 " pdb=" C4' DA N 35 " pdb=" C3' DA N 35 " ideal model delta sigma weight residual 106.00 101.96 4.04 6.00e-01 2.78e+00 4.54e+01 angle pdb=" C HIS E1150 " pdb=" N ASP E1151 " pdb=" CA ASP E1151 " ideal model delta sigma weight residual 126.32 136.40 -10.08 1.74e+00 3.30e-01 3.36e+01 angle pdb=" O4' G R 8 " pdb=" C1' G R 8 " pdb=" N9 G R 8 " ideal model delta sigma weight residual 108.50 112.55 -4.05 7.00e-01 2.04e+00 3.35e+01 angle pdb=" N VAL E1149 " pdb=" CA VAL E1149 " pdb=" C VAL E1149 " ideal model delta sigma weight residual 110.05 104.06 5.99 1.09e+00 8.42e-01 3.02e+01 angle pdb=" N PRO B 95 " pdb=" CA PRO B 95 " pdb=" C PRO B 95 " ideal model delta sigma weight residual 110.70 116.74 -6.04 1.22e+00 6.72e-01 2.45e+01 ... (remaining 16830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.68: 6663 25.68 - 51.36: 482 51.36 - 77.03: 109 77.03 - 102.71: 7 102.71 - 128.39: 1 Dihedral angle restraints: 7262 sinusoidal: 3469 harmonic: 3793 Sorted by residual: dihedral pdb=" CA GLN B 357 " pdb=" C GLN B 357 " pdb=" N GLU B 358 " pdb=" CA GLU B 358 " ideal model delta harmonic sigma weight residual 180.00 148.50 31.50 0 5.00e+00 4.00e-02 3.97e+01 dihedral pdb=" CA VAL E 944 " pdb=" C VAL E 944 " pdb=" N ASN E 945 " pdb=" CA ASN E 945 " ideal model delta harmonic sigma weight residual 180.00 -153.52 -26.48 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA SER E1148 " pdb=" C SER E1148 " pdb=" N VAL E1149 " pdb=" CA VAL E1149 " ideal model delta harmonic sigma weight residual 180.00 153.85 26.15 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 7259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1590 0.070 - 0.141: 254 0.141 - 0.211: 24 0.211 - 0.282: 2 0.282 - 0.352: 1 Chirality restraints: 1871 Sorted by residual: chirality pdb=" C3' DA N 35 " pdb=" C4' DA N 35 " pdb=" O3' DA N 35 " pdb=" C2' DA N 35 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" P DG N 37 " pdb=" OP1 DG N 37 " pdb=" OP2 DG N 37 " pdb=" O5' DG N 37 " both_signs ideal model delta sigma weight residual True 2.34 -2.58 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB ILE E1010 " pdb=" CA ILE E1010 " pdb=" CG1 ILE E1010 " pdb=" CG2 ILE E1010 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1868 not shown) Planarity restraints: 1924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN E1165 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.51e+00 pdb=" C GLN E1165 " 0.050 2.00e-02 2.50e+03 pdb=" O GLN E1165 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL E1166 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS E1167 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.93e+00 pdb=" C CYS E1167 " -0.049 2.00e-02 2.50e+03 pdb=" O CYS E1167 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG E1168 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 225 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.08e+00 pdb=" C VAL B 225 " 0.046 2.00e-02 2.50e+03 pdb=" O VAL B 225 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN B 226 " -0.015 2.00e-02 2.50e+03 ... (remaining 1921 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1906 2.77 - 3.30: 10692 3.30 - 3.83: 20086 3.83 - 4.37: 23787 4.37 - 4.90: 38893 Nonbonded interactions: 95364 Sorted by model distance: nonbonded pdb=" O LYS B 236 " pdb=" OG SER B 251 " model vdw 2.236 3.040 nonbonded pdb=" OH TYR E 956 " pdb=" O1B ATP E1301 " model vdw 2.262 3.040 nonbonded pdb=" O PRO E1121 " pdb=" ND1 HIS E1125 " model vdw 2.274 3.120 nonbonded pdb=" OH TYR E 530 " pdb=" O PRO E 651 " model vdw 2.280 3.040 nonbonded pdb=" NE2 GLN E1165 " pdb=" OE2 GLU E1169 " model vdw 2.300 3.120 ... (remaining 95359 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: 5.250 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.500 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5162 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 12206 Z= 0.341 Angle : 0.963 14.236 16835 Z= 0.586 Chirality : 0.053 0.352 1871 Planarity : 0.008 0.084 1924 Dihedral : 17.445 128.389 4800 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.21), residues: 1290 helix: -0.56 (0.18), residues: 668 sheet: -0.17 (0.58), residues: 75 loop : -1.20 (0.24), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 516 TYR 0.034 0.003 TYR B 212 PHE 0.038 0.003 PHE E 229 TRP 0.025 0.002 TRP E1026 HIS 0.011 0.002 HIS E1131 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.34 (12206) covalent geometry : angle 0.96327 / 0.59 (16835) hydrogen bonds : bond 0.13951 / 9.25 ( 571) hydrogen bonds : angle 5.84372 / 4.26 ( 1614) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 229 PHE cc_start: 0.7003 (t80) cc_final: 0.6739 (t80) REVERT: E 401 GLU cc_start: 0.6739 (mm-30) cc_final: 0.6518 (mm-30) REVERT: E 411 ARG cc_start: 0.6325 (ptp-170) cc_final: 0.6076 (ptp-170) REVERT: E 632 GLU cc_start: 0.6321 (mp0) cc_final: 0.6114 (mp0) REVERT: E 776 ARG cc_start: 0.6821 (ttt90) cc_final: 0.6417 (ttt180) REVERT: E 975 MET cc_start: 0.5430 (mtm) cc_final: 0.4913 (ptm) REVERT: E 1084 LEU cc_start: 0.6716 (pt) cc_final: 0.6465 (pt) REVERT: E 1165 GLN cc_start: 0.6256 (tm-30) cc_final: 0.6047 (tm-30) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.5495 time to fit residues: 97.5906 Evaluate side-chains 145 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 226 ASN B 255 GLN B 300 GLN E 252 GLN E 304 GLN E 309 GLN E 369 ASN E 512 HIS E 528 ASN E 877 GLN E 921 GLN E 945 ASN E 992 GLN E1009 GLN E1030 HIS E1051 GLN E1111 ASN E1115 GLN E1138 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.200089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.164051 restraints weight = 16410.159| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 1.86 r_work: 0.3935 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3793 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 12206 Z= 0.192 Angle : 0.682 8.690 16835 Z= 0.361 Chirality : 0.045 0.334 1871 Planarity : 0.006 0.051 1924 Dihedral : 19.342 123.281 2191 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.67 % Allowed : 6.51 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.22), residues: 1290 helix: 0.20 (0.19), residues: 690 sheet: -0.33 (0.56), residues: 82 loop : -0.90 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 78 TYR 0.024 0.002 TYR B 212 PHE 0.025 0.002 PHE E1229 TRP 0.018 0.002 TRP E1026 HIS 0.007 0.001 HIS E1150 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (12206) covalent geometry : angle 0.68202 / 0.36 (16835) hydrogen bonds : bond 0.05330 / 3.49 ( 571) hydrogen bonds : angle 4.64077 / 3.38 ( 1614) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 352 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.7340 (mpp) REVERT: E 238 GLN cc_start: 0.7848 (mt0) cc_final: 0.7624 (mt0) REVERT: E 975 MET cc_start: 0.6105 (mtm) cc_final: 0.5485 (mtp) REVERT: E 1084 LEU cc_start: 0.7387 (pt) cc_final: 0.7179 (pt) outliers start: 19 outliers final: 7 residues processed: 160 average time/residue: 0.4900 time to fit residues: 84.8684 Evaluate side-chains 160 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 352 MET Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 659 HIS Chi-restraints excluded: chain E residue 1211 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 25 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 92 optimal weight: 0.4980 chunk 120 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 304 GLN E 528 ASN E 877 GLN ** E 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 953 GLN E1111 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.198711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.162133 restraints weight = 16537.332| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 1.89 r_work: 0.3912 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12206 Z= 0.204 Angle : 0.666 8.258 16835 Z= 0.352 Chirality : 0.044 0.287 1871 Planarity : 0.006 0.062 1924 Dihedral : 19.266 123.045 2191 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.85 % Allowed : 9.42 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.23), residues: 1290 helix: 0.38 (0.19), residues: 690 sheet: -0.39 (0.55), residues: 82 loop : -0.86 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 447 TYR 0.026 0.002 TYR B 212 PHE 0.026 0.002 PHE E1229 TRP 0.013 0.002 TRP B 254 HIS 0.009 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (12206) covalent geometry : angle 0.66552 / 0.35 (16835) hydrogen bonds : bond 0.05186 / 3.40 ( 571) hydrogen bonds : angle 4.56702 / 3.31 ( 1614) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: B 227 MET cc_start: 0.5931 (pp-130) cc_final: 0.5709 (pp-130) REVERT: E 318 ARG cc_start: 0.7246 (tmt-80) cc_final: 0.6661 (tpt90) REVERT: E 975 MET cc_start: 0.5581 (mtm) cc_final: 0.5288 (mtm) REVERT: E 1007 ARG cc_start: 0.7047 (ttp80) cc_final: 0.6654 (ttp-110) outliers start: 21 outliers final: 6 residues processed: 160 average time/residue: 0.5209 time to fit residues: 90.4370 Evaluate side-chains 159 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 153 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 659 HIS Chi-restraints excluded: chain E residue 1211 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 91 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 HIS E 369 ASN E 528 ASN E 877 GLN ** E 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1103 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.198861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.162414 restraints weight = 16631.418| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 1.88 r_work: 0.3913 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3768 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12206 Z= 0.180 Angle : 0.639 9.491 16835 Z= 0.336 Chirality : 0.043 0.277 1871 Planarity : 0.006 0.055 1924 Dihedral : 19.189 122.788 2191 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.02 % Allowed : 10.65 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.23), residues: 1290 helix: 0.60 (0.20), residues: 685 sheet: -0.47 (0.55), residues: 82 loop : -0.85 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1173 TYR 0.024 0.002 TYR B 212 PHE 0.016 0.002 PHE E 509 TRP 0.012 0.002 TRP E 707 HIS 0.007 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (12206) covalent geometry : angle 0.63931 / 0.34 (16835) hydrogen bonds : bond 0.04842 / 3.19 ( 571) hydrogen bonds : angle 4.49909 / 3.26 ( 1614) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: B 227 MET cc_start: 0.5966 (pp-130) cc_final: 0.5673 (pp-130) REVERT: E 318 ARG cc_start: 0.7273 (tmt-80) cc_final: 0.6687 (tpt90) outliers start: 23 outliers final: 10 residues processed: 158 average time/residue: 0.5733 time to fit residues: 98.4631 Evaluate side-chains 161 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 659 HIS Chi-restraints excluded: chain E residue 1083 ARG Chi-restraints excluded: chain E residue 1211 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 25 optimal weight: 0.0050 chunk 45 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 304 GLN E 528 ASN E 877 GLN E1111 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.199158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.162847 restraints weight = 16580.192| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 1.87 r_work: 0.3917 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3773 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12206 Z= 0.158 Angle : 0.616 7.778 16835 Z= 0.325 Chirality : 0.042 0.268 1871 Planarity : 0.005 0.062 1924 Dihedral : 19.203 122.433 2191 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.02 % Allowed : 11.80 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.23), residues: 1290 helix: 0.77 (0.20), residues: 687 sheet: -0.55 (0.54), residues: 82 loop : -0.85 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 458 TYR 0.020 0.001 TYR B 212 PHE 0.012 0.001 PHE E 802 TRP 0.011 0.001 TRP E 707 HIS 0.005 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (12206) covalent geometry : angle 0.61631 / 0.32 (16835) hydrogen bonds : bond 0.04654 / 3.07 ( 571) hydrogen bonds : angle 4.40971 / 3.20 ( 1614) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 227 MET cc_start: 0.6040 (pp-130) cc_final: 0.5693 (pp-130) REVERT: E 318 ARG cc_start: 0.7272 (tmt-80) cc_final: 0.6712 (tpt90) outliers start: 23 outliers final: 13 residues processed: 161 average time/residue: 0.5168 time to fit residues: 90.4688 Evaluate side-chains 163 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 659 HIS Chi-restraints excluded: chain E residue 673 THR Chi-restraints excluded: chain E residue 1083 ARG Chi-restraints excluded: chain E residue 1211 VAL Chi-restraints excluded: chain E residue 1219 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 85 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 40 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 75 optimal weight: 0.0970 chunk 34 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 304 GLN E 528 ASN E 877 GLN E1111 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.198549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.162109 restraints weight = 16572.129| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 1.87 r_work: 0.3914 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12206 Z= 0.162 Angle : 0.613 7.933 16835 Z= 0.322 Chirality : 0.042 0.246 1871 Planarity : 0.006 0.067 1924 Dihedral : 19.187 121.948 2191 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.20 % Allowed : 12.76 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.23), residues: 1290 helix: 0.83 (0.20), residues: 694 sheet: -0.55 (0.54), residues: 82 loop : -0.73 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 447 TYR 0.023 0.002 TYR B 212 PHE 0.028 0.002 PHE E 229 TRP 0.015 0.002 TRP B 254 HIS 0.005 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (12206) covalent geometry : angle 0.61324 / 0.32 (16835) hydrogen bonds : bond 0.04546 / 3.00 ( 571) hydrogen bonds : angle 4.33321 / 3.14 ( 1614) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 227 MET cc_start: 0.6088 (pp-130) cc_final: 0.5719 (pp-130) REVERT: B 301 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7757 (mmt) REVERT: E 318 ARG cc_start: 0.7265 (tmt-80) cc_final: 0.6695 (tpt90) REVERT: E 445 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8059 (mm) outliers start: 25 outliers final: 12 residues processed: 160 average time/residue: 0.5080 time to fit residues: 88.2612 Evaluate side-chains 168 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 659 HIS Chi-restraints excluded: chain E residue 673 THR Chi-restraints excluded: chain E residue 1083 ARG Chi-restraints excluded: chain E residue 1211 VAL Chi-restraints excluded: chain E residue 1219 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 32 optimal weight: 0.9990 chunk 14 optimal weight: 0.0970 chunk 130 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 chunk 62 optimal weight: 0.2980 chunk 52 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 528 ASN E 877 GLN E1111 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.199829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.163522 restraints weight = 16567.768| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 1.87 r_work: 0.3918 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3774 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12206 Z= 0.149 Angle : 0.615 10.356 16835 Z= 0.319 Chirality : 0.042 0.234 1871 Planarity : 0.005 0.063 1924 Dihedral : 19.158 121.475 2191 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.94 % Allowed : 13.56 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.23), residues: 1290 helix: 0.91 (0.20), residues: 693 sheet: -0.52 (0.54), residues: 82 loop : -0.73 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 458 TYR 0.019 0.001 TYR B 212 PHE 0.030 0.002 PHE E 229 TRP 0.012 0.001 TRP E 707 HIS 0.005 0.001 HIS E1125 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (12206) covalent geometry : angle 0.61500 / 0.32 (16835) hydrogen bonds : bond 0.04415 / 2.91 ( 571) hydrogen bonds : angle 4.28565 / 3.11 ( 1614) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: B 227 MET cc_start: 0.6120 (pp-130) cc_final: 0.5758 (pp-130) REVERT: E 318 ARG cc_start: 0.7305 (tmt-80) cc_final: 0.6676 (tpt90) REVERT: E 443 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7795 (mmpt) REVERT: E 445 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8060 (mm) outliers start: 22 outliers final: 14 residues processed: 165 average time/residue: 0.4731 time to fit residues: 85.1831 Evaluate side-chains 165 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 443 LYS Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 659 HIS Chi-restraints excluded: chain E residue 673 THR Chi-restraints excluded: chain E residue 1064 MET Chi-restraints excluded: chain E residue 1083 ARG Chi-restraints excluded: chain E residue 1211 VAL Chi-restraints excluded: chain E residue 1219 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 131 optimal weight: 30.0000 chunk 50 optimal weight: 0.9980 chunk 114 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 528 ASN E 877 GLN E1111 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.196459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.159790 restraints weight = 16500.759| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 1.87 r_work: 0.3879 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 12206 Z= 0.254 Angle : 0.703 9.155 16835 Z= 0.367 Chirality : 0.047 0.243 1871 Planarity : 0.006 0.070 1924 Dihedral : 19.268 121.106 2191 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.94 % Allowed : 14.26 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.23), residues: 1290 helix: 0.58 (0.20), residues: 693 sheet: -0.68 (0.54), residues: 82 loop : -0.83 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 447 TYR 0.033 0.002 TYR B 212 PHE 0.028 0.002 PHE E 229 TRP 0.021 0.002 TRP B 254 HIS 0.009 0.002 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.25 (12206) covalent geometry : angle 0.70334 / 0.37 (16835) hydrogen bonds : bond 0.05223 / 3.41 ( 571) hydrogen bonds : angle 4.58044 / 3.29 ( 1614) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: B 167 MET cc_start: 0.6436 (OUTLIER) cc_final: 0.6006 (mtp) REVERT: B 227 MET cc_start: 0.6120 (pp-130) cc_final: 0.5739 (pp-130) REVERT: E 445 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8119 (mm) REVERT: E 458 ARG cc_start: 0.6960 (ttp80) cc_final: 0.6685 (ttp80) REVERT: E 955 VAL cc_start: 0.8065 (m) cc_final: 0.7846 (t) REVERT: E 1151 ASP cc_start: 0.6314 (p0) cc_final: 0.6046 (p0) outliers start: 22 outliers final: 13 residues processed: 165 average time/residue: 0.5708 time to fit residues: 102.6493 Evaluate side-chains 173 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 659 HIS Chi-restraints excluded: chain E residue 673 THR Chi-restraints excluded: chain E residue 1083 ARG Chi-restraints excluded: chain E residue 1084 LEU Chi-restraints excluded: chain E residue 1211 VAL Chi-restraints excluded: chain E residue 1219 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 11 optimal weight: 0.0040 chunk 67 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 129 optimal weight: 30.0000 chunk 16 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 108 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 528 ASN E 877 GLN E1111 ASN E1165 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.197833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.161508 restraints weight = 16382.361| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 1.85 r_work: 0.3898 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12206 Z= 0.155 Angle : 0.631 8.696 16835 Z= 0.330 Chirality : 0.043 0.306 1871 Planarity : 0.006 0.074 1924 Dihedral : 19.210 120.580 2191 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.67 % Allowed : 15.05 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.23), residues: 1290 helix: 0.81 (0.20), residues: 691 sheet: -0.61 (0.54), residues: 82 loop : -0.74 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 458 TYR 0.018 0.001 TYR B 212 PHE 0.031 0.002 PHE E 229 TRP 0.012 0.002 TRP E 707 HIS 0.005 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (12206) covalent geometry : angle 0.63088 / 0.33 (16835) hydrogen bonds : bond 0.04590 / 3.02 ( 571) hydrogen bonds : angle 4.41394 / 3.19 ( 1614) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: B 167 MET cc_start: 0.6338 (OUTLIER) cc_final: 0.5897 (mtp) REVERT: E 318 ARG cc_start: 0.7328 (tmt-80) cc_final: 0.6771 (tpt90) REVERT: E 445 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8065 (mm) REVERT: E 458 ARG cc_start: 0.6908 (ttp80) cc_final: 0.6665 (ttp80) REVERT: E 955 VAL cc_start: 0.8051 (m) cc_final: 0.7785 (t) outliers start: 19 outliers final: 12 residues processed: 164 average time/residue: 0.5637 time to fit residues: 100.8837 Evaluate side-chains 164 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 415 VAL Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 659 HIS Chi-restraints excluded: chain E residue 673 THR Chi-restraints excluded: chain E residue 1083 ARG Chi-restraints excluded: chain E residue 1211 VAL Chi-restraints excluded: chain E residue 1219 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 9 optimal weight: 8.9990 chunk 44 optimal weight: 0.0270 chunk 125 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 41 optimal weight: 0.0870 chunk 129 optimal weight: 40.0000 chunk 72 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 528 ASN E 877 GLN E1111 ASN E1165 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.198361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.162061 restraints weight = 16596.841| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 1.86 r_work: 0.3915 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3773 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12206 Z= 0.151 Angle : 0.628 9.624 16835 Z= 0.328 Chirality : 0.042 0.271 1871 Planarity : 0.006 0.064 1924 Dihedral : 19.200 119.902 2191 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.41 % Allowed : 15.67 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.23), residues: 1290 helix: 0.89 (0.20), residues: 695 sheet: -0.54 (0.54), residues: 82 loop : -0.68 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 447 TYR 0.017 0.001 TYR B 212 PHE 0.034 0.002 PHE E 229 TRP 0.011 0.001 TRP E 707 HIS 0.005 0.001 HIS E1125 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (12206) covalent geometry : angle 0.62794 / 0.33 (16835) hydrogen bonds : bond 0.04472 / 2.95 ( 571) hydrogen bonds : angle 4.35830 / 3.16 ( 1614) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: B 167 MET cc_start: 0.6359 (OUTLIER) cc_final: 0.5934 (mtp) REVERT: E 318 ARG cc_start: 0.7302 (tmt-80) cc_final: 0.6728 (tpt90) REVERT: E 445 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8038 (mm) REVERT: E 458 ARG cc_start: 0.6898 (ttp80) cc_final: 0.6662 (ttp80) outliers start: 16 outliers final: 11 residues processed: 159 average time/residue: 0.5725 time to fit residues: 99.4370 Evaluate side-chains 166 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 673 THR Chi-restraints excluded: chain E residue 1083 ARG Chi-restraints excluded: chain E residue 1211 VAL Chi-restraints excluded: chain E residue 1219 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 59 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 21 optimal weight: 0.3980 chunk 134 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 80 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 528 ASN E 877 GLN E1111 ASN E1165 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.197990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.161709 restraints weight = 16468.447| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 1.86 r_work: 0.3907 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3763 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12206 Z= 0.168 Angle : 0.634 11.219 16835 Z= 0.329 Chirality : 0.043 0.269 1871 Planarity : 0.006 0.060 1924 Dihedral : 19.214 119.323 2191 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.58 % Allowed : 15.67 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.23), residues: 1290 helix: 0.91 (0.20), residues: 690 sheet: -0.55 (0.53), residues: 82 loop : -0.66 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 447 TYR 0.020 0.001 TYR B 212 PHE 0.031 0.002 PHE E 229 TRP 0.012 0.002 TRP E 707 HIS 0.005 0.001 HIS E1125 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (12206) covalent geometry : angle 0.63376 / 0.33 (16835) hydrogen bonds : bond 0.04512 / 2.97 ( 571) hydrogen bonds : angle 4.36991 / 3.16 ( 1614) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4830.97 seconds wall clock time: 82 minutes 55.18 seconds (4975.18 seconds total)