Starting phenix.real_space_refine on Sat Mar 16 19:10:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dga_27420/03_2024/8dga_27420_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dga_27420/03_2024/8dga_27420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dga_27420/03_2024/8dga_27420.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dga_27420/03_2024/8dga_27420.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dga_27420/03_2024/8dga_27420_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dga_27420/03_2024/8dga_27420_updated.pdb" } resolution = 3.73 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= 0.028 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 42 5.49 5 S 80 5.16 5 C 9663 2.51 5 N 2710 2.21 5 O 2978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 77": "OE1" <-> "OE2" Residue "A ASP 99": "OD1" <-> "OD2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A ASP 588": "OD1" <-> "OD2" Residue "A TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 989": "OE1" <-> "OE2" Residue "A ASP 1133": "OD1" <-> "OD2" Residue "A PHE 1149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1222": "OE1" <-> "OE2" Residue "A PHE 1552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1630": "OD1" <-> "OD2" Residue "A TYR 1655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1676": "OD1" <-> "OD2" Residue "A GLU 1677": "OE1" <-> "OE2" Residue "A GLU 1742": "OE1" <-> "OE2" Residue "A PHE 1751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1769": "OE1" <-> "OE2" Residue "A GLU 1819": "OE1" <-> "OE2" Residue "A GLU 1917": "OE1" <-> "OE2" Residue "A TYR 2028": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2112": "OE1" <-> "OE2" Residue "A GLU 2119": "OE1" <-> "OE2" Residue "A TYR 2160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2167": "OE1" <-> "OE2" Residue "A GLU 2169": "OE1" <-> "OE2" Residue "K PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15473 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 13162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1629, 13162 Classifications: {'peptide': 1629} Link IDs: {'PCIS': 1, 'PTRANS': 95, 'TRANS': 1532} Chain breaks: 11 Chain: "E" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 414 Classifications: {'RNA': 19} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 6} Link IDs: {'rna3p': 18} Chain: "F" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 452 Classifications: {'RNA': 22} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 16} Link IDs: {'rna3p': 21} Chain: "K" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1424 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 175} Chain breaks: 1 Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 8.27, per 1000 atoms: 0.53 Number of scatterers: 15473 At special positions: 0 Unit cell: (158.53, 129.48, 145.25, 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 80 16.00 P 42 15.00 O 2978 8.00 N 2710 7.00 C 9663 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 - 3.50 Amino acid : False - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.39 Conformation dependent library (CDL) restraints added in 2.4 seconds 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3460 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 10 sheets defined 42.6% alpha, 8.4% beta 18 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 8.24 Creating SS restraints... Processing helix chain 'A' and resid 20 through 30 Processing helix chain 'A' and resid 40 through 60 removed outlier: 4.137A pdb=" N ARG A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARG A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 87 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 118 through 126 Processing helix chain 'A' and resid 146 through 159 Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 185 through 199 Processing helix chain 'A' and resid 208 through 214 Processing helix chain 'A' and resid 233 through 251 removed outlier: 4.141A pdb=" N ASP A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 292 removed outlier: 4.088A pdb=" N VAL A 288 " --> pdb=" O ASN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 312 removed outlier: 4.199A pdb=" N HIS A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 343 removed outlier: 4.128A pdb=" N PHE A 343 " --> pdb=" O CYS A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 360 removed outlier: 3.733A pdb=" N TYR A 360 " --> pdb=" O THR A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 373 Processing helix chain 'A' and resid 502 through 518 Processing helix chain 'A' and resid 542 through 559 Processing helix chain 'A' and resid 593 through 602 removed outlier: 4.909A pdb=" N ARG A 602 " --> pdb=" O GLN A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 784 Processing helix chain 'A' and resid 792 through 803 removed outlier: 3.844A pdb=" N ALA A 803 " --> pdb=" O GLU A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 834 removed outlier: 3.784A pdb=" N ALA A 825 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ILE A 826 " --> pdb=" O GLY A 823 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA A 827 " --> pdb=" O SER A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 903 removed outlier: 3.730A pdb=" N ILE A 903 " --> pdb=" O GLU A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 927 Processing helix chain 'A' and resid 932 through 939 Processing helix chain 'A' and resid 961 through 963 No H-bonds generated for 'chain 'A' and resid 961 through 963' Processing helix chain 'A' and resid 1001 through 1003 No H-bonds generated for 'chain 'A' and resid 1001 through 1003' Processing helix chain 'A' and resid 1046 through 1061 Processing helix chain 'A' and resid 1099 through 1107 Processing helix chain 'A' and resid 1118 through 1123 Processing helix chain 'A' and resid 1128 through 1131 No H-bonds generated for 'chain 'A' and resid 1128 through 1131' Processing helix chain 'A' and resid 1172 through 1179 Processing helix chain 'A' and resid 1221 through 1229 removed outlier: 4.083A pdb=" N LYS A1227 " --> pdb=" O THR A1223 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A1229 " --> pdb=" O ARG A1225 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1241 No H-bonds generated for 'chain 'A' and resid 1239 through 1241' Processing helix chain 'A' and resid 1249 through 1281 Proline residue: A1259 - end of helix Processing helix chain 'A' and resid 1538 through 1549 Processing helix chain 'A' and resid 1566 through 1580 Processing helix chain 'A' and resid 1608 through 1615 Processing helix chain 'A' and resid 1623 through 1628 Processing helix chain 'A' and resid 1636 through 1649 Processing helix chain 'A' and resid 1723 through 1730 Processing helix chain 'A' and resid 1742 through 1763 Processing helix chain 'A' and resid 1769 through 1779 Processing helix chain 'A' and resid 1782 through 1792 Processing helix chain 'A' and resid 1795 through 1797 No H-bonds generated for 'chain 'A' and resid 1795 through 1797' Processing helix chain 'A' and resid 1819 through 1824 removed outlier: 3.574A pdb=" N LEU A1824 " --> pdb=" O GLU A1821 " (cutoff:3.500A) Processing helix chain 'A' and resid 1847 through 1855 Processing helix chain 'A' and resid 1900 through 1930 Proline residue: A1920 - end of helix Processing helix chain 'A' and resid 1982 through 1989 Processing helix chain 'A' and resid 1993 through 2000 Processing helix chain 'A' and resid 2007 through 2013 Processing helix chain 'A' and resid 2029 through 2048 removed outlier: 3.955A pdb=" N ALA A2037 " --> pdb=" O PHE A2033 " (cutoff:3.500A) Processing helix chain 'A' and resid 2056 through 2066 Processing helix chain 'A' and resid 2069 through 2078 Processing helix chain 'A' and resid 2090 through 2104 Processing helix chain 'A' and resid 2132 through 2149 Processing helix chain 'A' and resid 2153 through 2173 removed outlier: 4.618A pdb=" N ASN A2162 " --> pdb=" O HIS A2158 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET A2163 " --> pdb=" O VAL A2159 " (cutoff:3.500A) Proline residue: A2166 - end of helix Processing helix chain 'A' and resid 2179 through 2186 removed outlier: 3.807A pdb=" N LEU A2183 " --> pdb=" O PRO A2179 " (cutoff:3.500A) Processing helix chain 'A' and resid 2224 through 2238 Processing helix chain 'K' and resid 136 through 145 Processing helix chain 'K' and resid 189 through 204 removed outlier: 3.890A pdb=" N LEU K 204 " --> pdb=" O LEU K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 375 removed outlier: 3.740A pdb=" N PHE K 367 " --> pdb=" O LYS K 363 " (cutoff:3.500A) Processing helix chain 'K' and resid 378 through 383 Processing helix chain 'K' and resid 394 through 404 Processing helix chain 'K' and resid 444 through 461 Processing sheet with id= A, first strand: chain 'A' and resid 202 through 204 removed outlier: 7.471A pdb=" N VAL A 64 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE A 138 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL A 66 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU A 140 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A 68 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 219 through 224 removed outlier: 7.489A pdb=" N ALA A 608 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N TYR A 222 " --> pdb=" O ALA A 608 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS A 610 " --> pdb=" O TYR A 222 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N VAL A 224 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE A 612 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU A 496 " --> pdb=" O VAL A 585 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 858 through 866 removed outlier: 4.339A pdb=" N CYS A 850 " --> pdb=" O MET A1658 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 852 " --> pdb=" O ASN A1656 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 952 through 956 Processing sheet with id= E, first strand: chain 'A' and resid 1095 through 1097 removed outlier: 3.529A pdb=" N THR A1087 " --> pdb=" O GLY A1007 " (cutoff:3.500A) removed outlier: 11.414A pdb=" N GLN A1006 " --> pdb=" O LEU A 981 " (cutoff:3.500A) removed outlier: 9.659A pdb=" N LEU A 981 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N PHE A1008 " --> pdb=" O ILE A 979 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU A1030 " --> pdb=" O GLN A 984 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1153 through 1155 Processing sheet with id= G, first strand: chain 'A' and resid 1937 through 1940 removed outlier: 3.836A pdb=" N VAL A1964 " --> pdb=" O THR A1938 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 2209 through 2211 Processing sheet with id= I, first strand: chain 'K' and resid 180 through 186 removed outlier: 6.172A pdb=" N ARG K 170 " --> pdb=" O LEU K 155 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LEU K 155 " --> pdb=" O ARG K 170 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N SER K 172 " --> pdb=" O TYR K 153 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N TYR K 153 " --> pdb=" O SER K 172 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'K' and resid 409 through 412 588 hydrogen bonds defined for protein. 1683 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 6.43 Time building geometry restraints manager: 6.93 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: 3969 1.33 - 1.46: 3438 1.46 - 1.58: 8294 1.58 - 1.70: 83 1.70 - 1.82: 109 Bond restraints: 15893 Sorted by residual: bond pdb=" C GLU A 931 " pdb=" N PRO A 932 " ideal model delta sigma weight residual 1.335 1.371 -0.036 1.38e-02 5.25e+03 6.95e+00 bond pdb=" CG LEU A1915 " pdb=" CD1 LEU A1915 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.70e+00 bond pdb=" CB GLN A2053 " pdb=" CG GLN A2053 " ideal model delta sigma weight residual 1.520 1.591 -0.071 3.00e-02 1.11e+03 5.63e+00 bond pdb=" CG LEU A2147 " pdb=" CD1 LEU A2147 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.52e+00 bond pdb=" C LEU A 867 " pdb=" N PRO A 868 " ideal model delta sigma weight residual 1.330 1.359 -0.029 1.25e-02 6.40e+03 5.20e+00 ... (remaining 15888 not shown) Histogram of bond angle deviations from ideal: 95.22 - 103.83: 380 103.83 - 112.45: 8026 112.45 - 121.06: 8794 121.06 - 129.67: 4396 129.67 - 138.28: 126 Bond angle restraints: 21722 Sorted by residual: angle pdb=" C ARG A 866 " pdb=" N LEU A 867 " pdb=" CA LEU A 867 " ideal model delta sigma weight residual 121.03 129.62 -8.59 1.60e+00 3.91e-01 2.88e+01 angle pdb=" C CYS A 107 " pdb=" N TRP A 108 " pdb=" CA TRP A 108 " ideal model delta sigma weight residual 120.72 129.39 -8.67 1.67e+00 3.59e-01 2.69e+01 angle pdb=" N GLU A 196 " pdb=" CA GLU A 196 " pdb=" CB GLU A 196 " ideal model delta sigma weight residual 110.16 117.75 -7.59 1.48e+00 4.57e-01 2.63e+01 angle pdb=" CB GLN A2053 " pdb=" CG GLN A2053 " pdb=" CD GLN A2053 " ideal model delta sigma weight residual 112.60 121.05 -8.45 1.70e+00 3.46e-01 2.47e+01 angle pdb=" N ASP A2123 " pdb=" CA ASP A2123 " pdb=" C ASP A2123 " ideal model delta sigma weight residual 112.92 106.96 5.96 1.23e+00 6.61e-01 2.35e+01 ... (remaining 21717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8738 17.90 - 35.80: 782 35.80 - 53.70: 147 53.70 - 71.59: 60 71.59 - 89.49: 17 Dihedral angle restraints: 9744 sinusoidal: 4419 harmonic: 5325 Sorted by residual: dihedral pdb=" CA VAL A 14 " pdb=" C VAL A 14 " pdb=" N PHE A 15 " pdb=" CA PHE A 15 " ideal model delta harmonic sigma weight residual -180.00 -119.71 -60.29 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" CA LEU A2117 " pdb=" C LEU A2117 " pdb=" N SER A2118 " pdb=" CA SER A2118 " ideal model delta harmonic sigma weight residual 180.00 132.42 47.58 0 5.00e+00 4.00e-02 9.06e+01 dihedral pdb=" CA ILE A1829 " pdb=" C ILE A1829 " pdb=" N PRO A1830 " pdb=" CA PRO A1830 " ideal model delta harmonic sigma weight residual 180.00 145.26 34.74 0 5.00e+00 4.00e-02 4.83e+01 ... (remaining 9741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2256 0.105 - 0.211: 184 0.211 - 0.316: 14 0.316 - 0.421: 3 0.421 - 0.527: 2 Chirality restraints: 2459 Sorted by residual: chirality pdb=" CG LEU A 496 " pdb=" CB LEU A 496 " pdb=" CD1 LEU A 496 " pdb=" CD2 LEU A 496 " both_signs ideal model delta sigma weight residual False -2.59 -2.06 -0.53 2.00e-01 2.50e+01 6.94e+00 chirality pdb=" CB ILE A1829 " pdb=" CA ILE A1829 " pdb=" CG1 ILE A1829 " pdb=" CG2 ILE A1829 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.52 2.00e-01 2.50e+01 6.72e+00 chirality pdb=" CB ILE A1010 " pdb=" CA ILE A1010 " pdb=" CG1 ILE A1010 " pdb=" CG2 ILE A1010 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.81e+00 ... (remaining 2456 not shown) Planarity restraints: 2656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 108 " 0.058 2.00e-02 2.50e+03 6.16e-02 9.49e+01 pdb=" CG TRP A 108 " -0.154 2.00e-02 2.50e+03 pdb=" CD1 TRP A 108 " 0.099 2.00e-02 2.50e+03 pdb=" CD2 TRP A 108 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP A 108 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TRP A 108 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 108 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 108 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 108 " 0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP A 108 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 848 " -0.032 2.00e-02 2.50e+03 4.46e-02 4.97e+01 pdb=" CG TRP A 848 " 0.098 2.00e-02 2.50e+03 pdb=" CD1 TRP A 848 " -0.083 2.00e-02 2.50e+03 pdb=" CD2 TRP A 848 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 848 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TRP A 848 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 848 " 0.016 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 848 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 848 " -0.038 2.00e-02 2.50e+03 pdb=" CH2 TRP A 848 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A2053 " 0.018 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C GLN A2053 " -0.064 2.00e-02 2.50e+03 pdb=" O GLN A2053 " 0.025 2.00e-02 2.50e+03 pdb=" N HIS A2054 " 0.021 2.00e-02 2.50e+03 ... (remaining 2653 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1746 2.75 - 3.29: 15171 3.29 - 3.82: 27369 3.82 - 4.36: 31893 4.36 - 4.90: 51189 Nonbonded interactions: 127368 Sorted by model distance: nonbonded pdb=" O ARG A1207 " pdb=" O2' A F 50 " model vdw 2.210 2.440 nonbonded pdb=" O LEU K 459 " pdb=" OG1 THR K 463 " model vdw 2.264 2.440 nonbonded pdb=" O PHE A 841 " pdb=" OG SER A2089 " model vdw 2.266 2.440 nonbonded pdb=" O VAL A1767 " pdb=" NH1 ARG A2030 " model vdw 2.283 2.520 nonbonded pdb=" O GLY A 294 " pdb=" OG1 THR A 298 " model vdw 2.283 2.440 ... (remaining 127363 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.860 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: 18.880 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 48.660 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.080 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5914 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 : 0.007 0.093 15893 Z= 0.462 Angle : 1.166 16.872 21722 Z= 0.598 Chirality : 0.062 0.527 2459 Planarity : 0.009 0.121 2656 Dihedral : 14.987 89.493 6284 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.01 % Favored : 92.65 % Rotamer: Outliers : 0.12 % Allowed : 0.81 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.99 % Twisted General : 0.18 % 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: -2.35 (0.18), residues: 1783 helix: -1.42 (0.15), residues: 818 sheet: -0.79 (0.39), residues: 160 loop : -1.77 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.154 0.009 TRP A 108 HIS 0.014 0.002 HIS A1196 PHE 0.047 0.004 PHE A 15 TYR 0.031 0.004 TYR A1175 ARG 0.023 0.001 ARG A2045 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 184 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1112 MET cc_start: 0.6330 (tpt) cc_final: 0.6048 (tpt) REVERT: A 2151 MET cc_start: 0.7153 (mpp) cc_final: 0.6568 (mpp) REVERT: A 2163 MET cc_start: 0.7367 (mpp) cc_final: 0.6996 (mmt) REVERT: K 405 ASN cc_start: 0.5972 (t160) cc_final: 0.5726 (t0) outliers start: 2 outliers final: 0 residues processed: 184 average time/residue: 0.2921 time to fit residues: 79.3417 Evaluate side-chains 119 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 106 optimal weight: 0.0050 chunk 166 optimal weight: 0.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS A 187 GLN A 197 GLN ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2016 HIS K 163 HIS ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 405 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5871 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15893 Z= 0.181 Angle : 0.626 14.770 21722 Z= 0.316 Chirality : 0.041 0.239 2459 Planarity : 0.005 0.057 2656 Dihedral : 12.777 95.246 2633 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.44 % Favored : 94.22 % Rotamer: Outliers : 1.00 % Allowed : 8.02 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 (0.19), residues: 1783 helix: -0.08 (0.17), residues: 821 sheet: -0.80 (0.39), residues: 167 loop : -1.51 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A 108 HIS 0.007 0.001 HIS K 368 PHE 0.021 0.002 PHE A1552 TYR 0.018 0.001 TYR A 322 ARG 0.009 0.000 ARG A 775 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.3921 (mpp) cc_final: 0.3506 (mmt) REVERT: A 196 GLU cc_start: 0.6570 (mp0) cc_final: 0.6290 (mm-30) REVERT: A 2151 MET cc_start: 0.6934 (mpp) cc_final: 0.6541 (mpp) REVERT: A 2163 MET cc_start: 0.7441 (mpp) cc_final: 0.6948 (mmt) REVERT: K 405 ASN cc_start: 0.6282 (t0) cc_final: 0.6018 (t0) outliers start: 16 outliers final: 11 residues processed: 161 average time/residue: 0.2576 time to fit residues: 64.0901 Evaluate side-chains 134 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 848 TRP Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1662 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 92 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 chunk 148 optimal weight: 0.7980 chunk 165 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS A 101 GLN A 341 HIS ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5970 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15893 Z= 0.213 Angle : 0.620 12.500 21722 Z= 0.314 Chirality : 0.041 0.207 2459 Planarity : 0.005 0.056 2656 Dihedral : 12.519 95.627 2633 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.39 % Favored : 93.27 % Rotamer: Outliers : 1.87 % Allowed : 10.57 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.19), residues: 1783 helix: 0.26 (0.17), residues: 825 sheet: -0.66 (0.40), residues: 172 loop : -1.42 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1834 HIS 0.011 0.001 HIS K 194 PHE 0.021 0.001 PHE K 367 TYR 0.016 0.001 TYR A1148 ARG 0.004 0.000 ARG A1540 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 144 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.5866 (mpp) cc_final: 0.5164 (tpp) REVERT: A 108 TRP cc_start: 0.5248 (m-10) cc_final: 0.5017 (m-10) REVERT: A 1112 MET cc_start: 0.6134 (tpt) cc_final: 0.5884 (tpt) REVERT: A 1959 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8258 (pm20) REVERT: A 2151 MET cc_start: 0.6969 (mpp) cc_final: 0.6550 (mpp) REVERT: A 2163 MET cc_start: 0.7473 (mpp) cc_final: 0.6846 (mmt) REVERT: K 368 HIS cc_start: 0.1414 (m-70) cc_final: 0.1162 (m-70) REVERT: K 405 ASN cc_start: 0.6250 (t0) cc_final: 0.6029 (t0) outliers start: 30 outliers final: 20 residues processed: 160 average time/residue: 0.2507 time to fit residues: 62.8227 Evaluate side-chains 145 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 848 TRP Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1662 ASP Chi-restraints excluded: chain A residue 1903 ILE Chi-restraints excluded: chain A residue 1959 GLU Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2025 THR Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain K residue 423 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 164 optimal weight: 10.0000 chunk 125 optimal weight: 0.3980 chunk 86 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 176 optimal weight: 0.4980 chunk 87 optimal weight: 20.0000 chunk 158 optimal weight: 0.2980 chunk 47 optimal weight: 5.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 341 HIS A 770 GLN ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5882 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15893 Z= 0.154 Angle : 0.566 11.486 21722 Z= 0.286 Chirality : 0.040 0.206 2459 Planarity : 0.004 0.055 2656 Dihedral : 12.201 96.062 2633 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.72 % Favored : 93.94 % Rotamer: Outliers : 2.05 % Allowed : 12.19 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % 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: -0.44 (0.20), residues: 1783 helix: 0.71 (0.18), residues: 812 sheet: -0.55 (0.40), residues: 172 loop : -1.26 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1834 HIS 0.005 0.001 HIS K 194 PHE 0.017 0.001 PHE K 367 TYR 0.015 0.001 TYR A 322 ARG 0.007 0.000 ARG A2204 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 149 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.5903 (mpp) cc_final: 0.5540 (mpp) REVERT: A 1112 MET cc_start: 0.6258 (tpt) cc_final: 0.5979 (tpt) REVERT: A 1613 LYS cc_start: 0.8383 (mmtp) cc_final: 0.8181 (mmtp) REVERT: A 1664 PHE cc_start: 0.4696 (OUTLIER) cc_final: 0.3880 (m-10) REVERT: A 2151 MET cc_start: 0.6842 (mpp) cc_final: 0.6482 (mpp) REVERT: A 2163 MET cc_start: 0.7581 (mpp) cc_final: 0.7004 (mmt) REVERT: K 164 GLU cc_start: 0.3464 (OUTLIER) cc_final: 0.3186 (pp20) REVERT: K 368 HIS cc_start: 0.1826 (m-70) cc_final: 0.1522 (m-70) REVERT: K 405 ASN cc_start: 0.6085 (t0) cc_final: 0.5845 (t0) outliers start: 33 outliers final: 22 residues processed: 168 average time/residue: 0.2487 time to fit residues: 65.9942 Evaluate side-chains 151 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 848 TRP Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1662 ASP Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 1959 GLU Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 370 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 147 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 131 optimal weight: 0.5980 chunk 72 optimal weight: 0.2980 chunk 150 optimal weight: 8.9990 chunk 122 optimal weight: 0.1980 chunk 0 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 GLN ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5957 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15893 Z= 0.191 Angle : 0.578 7.882 21722 Z= 0.294 Chirality : 0.040 0.202 2459 Planarity : 0.004 0.052 2656 Dihedral : 12.083 92.773 2633 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.23 % Favored : 93.44 % Rotamer: Outliers : 2.05 % Allowed : 13.87 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % 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: -0.36 (0.20), residues: 1783 helix: 0.86 (0.18), residues: 806 sheet: -0.68 (0.39), residues: 179 loop : -1.26 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1834 HIS 0.005 0.001 HIS A 112 PHE 0.018 0.001 PHE K 367 TYR 0.014 0.001 TYR A 322 ARG 0.003 0.000 ARG A2222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 136 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TRP cc_start: 0.5207 (m-90) cc_final: 0.4961 (m-10) REVERT: A 900 LEU cc_start: 0.6272 (mt) cc_final: 0.6065 (mt) REVERT: A 1112 MET cc_start: 0.6364 (tpt) cc_final: 0.6026 (tpt) REVERT: A 1593 LEU cc_start: 0.1512 (OUTLIER) cc_final: 0.0514 (mt) REVERT: A 1664 PHE cc_start: 0.4917 (OUTLIER) cc_final: 0.4083 (m-10) REVERT: A 1929 TRP cc_start: 0.7572 (t60) cc_final: 0.7126 (t60) REVERT: A 1959 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8135 (pm20) REVERT: A 2151 MET cc_start: 0.6867 (mpp) cc_final: 0.6400 (mpp) REVERT: A 2163 MET cc_start: 0.7578 (mpp) cc_final: 0.7003 (mmt) REVERT: K 164 GLU cc_start: 0.3688 (OUTLIER) cc_final: 0.3364 (pp20) REVERT: K 368 HIS cc_start: 0.2152 (m-70) cc_final: 0.1819 (m-70) outliers start: 33 outliers final: 23 residues processed: 158 average time/residue: 0.2514 time to fit residues: 62.5824 Evaluate side-chains 153 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 848 TRP Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1621 GLU Chi-restraints excluded: chain A residue 1662 ASP Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1959 GLU Chi-restraints excluded: chain A residue 1963 THR Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 370 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 59 optimal weight: 4.9990 chunk 159 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 GLN ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1543 GLN A1833 HIS ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15893 Z= 0.190 Angle : 0.581 10.013 21722 Z= 0.294 Chirality : 0.040 0.210 2459 Planarity : 0.004 0.056 2656 Dihedral : 11.991 92.030 2633 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.11 % Favored : 93.55 % Rotamer: Outliers : 2.43 % Allowed : 14.86 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % 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: -0.23 (0.20), residues: 1783 helix: 0.99 (0.18), residues: 807 sheet: -0.63 (0.40), residues: 177 loop : -1.21 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1834 HIS 0.006 0.001 HIS A 112 PHE 0.021 0.001 PHE K 180 TYR 0.022 0.001 TYR A1148 ARG 0.005 0.000 ARG A2098 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 135 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.5944 (mpp) cc_final: 0.5546 (mpp) REVERT: A 100 MET cc_start: 0.5900 (tpp) cc_final: 0.5670 (tmm) REVERT: A 108 TRP cc_start: 0.5388 (m-90) cc_final: 0.5151 (m-10) REVERT: A 1112 MET cc_start: 0.6445 (tpt) cc_final: 0.6073 (tpt) REVERT: A 1593 LEU cc_start: 0.1132 (OUTLIER) cc_final: 0.0086 (mt) REVERT: A 1664 PHE cc_start: 0.4990 (OUTLIER) cc_final: 0.4238 (m-10) REVERT: A 1929 TRP cc_start: 0.7594 (t60) cc_final: 0.7137 (t60) REVERT: A 2151 MET cc_start: 0.6879 (mpp) cc_final: 0.6474 (mpp) REVERT: A 2163 MET cc_start: 0.7614 (mpp) cc_final: 0.7115 (mmt) REVERT: K 164 GLU cc_start: 0.3634 (OUTLIER) cc_final: 0.3274 (pp20) REVERT: K 368 HIS cc_start: 0.2119 (m-70) cc_final: 0.1818 (m-70) outliers start: 39 outliers final: 28 residues processed: 159 average time/residue: 0.2531 time to fit residues: 64.1448 Evaluate side-chains 153 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 122 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 848 TRP Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1621 GLU Chi-restraints excluded: chain A residue 1662 ASP Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1831 THR Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 370 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 170 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 129 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 HIS ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 HIS ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 GLN ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1202 ASN A1543 GLN ** A1891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 15893 Z= 0.368 Angle : 0.760 16.413 21722 Z= 0.383 Chirality : 0.045 0.245 2459 Planarity : 0.005 0.056 2656 Dihedral : 12.343 84.481 2633 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 23.08 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.40 % Favored : 92.26 % Rotamer: Outliers : 2.86 % Allowed : 15.98 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.19), residues: 1783 helix: 0.39 (0.17), residues: 811 sheet: -0.82 (0.40), residues: 176 loop : -1.50 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 848 HIS 0.011 0.002 HIS A1096 PHE 0.018 0.003 PHE K 367 TYR 0.031 0.002 TYR A1148 ARG 0.007 0.001 ARG A1207 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 123 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.5659 (mpp) cc_final: 0.5390 (mpp) REVERT: A 1593 LEU cc_start: 0.1467 (OUTLIER) cc_final: 0.0204 (mt) REVERT: A 1664 PHE cc_start: 0.5523 (OUTLIER) cc_final: 0.4804 (m-10) REVERT: A 1669 ASP cc_start: 0.4690 (OUTLIER) cc_final: 0.3536 (p0) REVERT: A 1917 GLU cc_start: 0.5503 (mm-30) cc_final: 0.4137 (mm-30) REVERT: A 2151 MET cc_start: 0.6981 (mpp) cc_final: 0.6464 (mpp) REVERT: K 164 GLU cc_start: 0.3828 (OUTLIER) cc_final: 0.2953 (pp20) REVERT: K 368 HIS cc_start: 0.1968 (m-70) cc_final: 0.1669 (m-70) outliers start: 46 outliers final: 37 residues processed: 156 average time/residue: 0.2572 time to fit residues: 62.8168 Evaluate side-chains 151 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 110 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 318 HIS Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 1016 ILE Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1196 HIS Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1274 ILE Chi-restraints excluded: chain A residue 1543 GLN Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1621 GLU Chi-restraints excluded: chain A residue 1662 ASP Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1831 THR Chi-restraints excluded: chain A residue 1903 ILE Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 436 VAL Chi-restraints excluded: chain K residue 438 HIS Chi-restraints excluded: chain K residue 461 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 34 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 GLN ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1736 ASN ** A1891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6069 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15893 Z= 0.206 Angle : 0.627 11.977 21722 Z= 0.315 Chirality : 0.041 0.211 2459 Planarity : 0.004 0.061 2656 Dihedral : 12.220 90.829 2633 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.67 % Favored : 92.99 % Rotamer: Outliers : 2.61 % Allowed : 16.85 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % 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: -0.45 (0.20), residues: 1783 helix: 0.81 (0.18), residues: 808 sheet: -0.88 (0.40), residues: 173 loop : -1.32 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A1834 HIS 0.009 0.001 HIS K 360 PHE 0.018 0.001 PHE K 367 TYR 0.031 0.002 TYR A1148 ARG 0.005 0.000 ARG A2222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 125 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.6448 (tpp) cc_final: 0.6140 (tmm) REVERT: A 338 LEU cc_start: 0.7716 (tp) cc_final: 0.7226 (pp) REVERT: A 1593 LEU cc_start: 0.1462 (OUTLIER) cc_final: 0.0293 (mt) REVERT: A 1664 PHE cc_start: 0.5175 (OUTLIER) cc_final: 0.4384 (m-10) REVERT: A 1669 ASP cc_start: 0.4625 (OUTLIER) cc_final: 0.3416 (p0) REVERT: A 1929 TRP cc_start: 0.7647 (t60) cc_final: 0.7149 (t60) REVERT: A 2151 MET cc_start: 0.6828 (mpp) cc_final: 0.6431 (mpp) REVERT: K 164 GLU cc_start: 0.3682 (OUTLIER) cc_final: 0.3285 (pp20) REVERT: K 368 HIS cc_start: 0.1826 (m-70) cc_final: 0.1592 (m-70) outliers start: 42 outliers final: 34 residues processed: 155 average time/residue: 0.2841 time to fit residues: 70.2107 Evaluate side-chains 154 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 116 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1196 HIS Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1274 ILE Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1621 GLU Chi-restraints excluded: chain A residue 1662 ASP Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1831 THR Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 436 VAL Chi-restraints excluded: chain K residue 438 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 168 optimal weight: 9.9990 chunk 98 optimal weight: 0.3980 chunk 71 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 163 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2053 GLN ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6069 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15893 Z= 0.211 Angle : 0.632 11.771 21722 Z= 0.316 Chirality : 0.041 0.218 2459 Planarity : 0.004 0.061 2656 Dihedral : 12.156 91.601 2633 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.12 % Favored : 92.54 % Rotamer: Outliers : 2.80 % Allowed : 17.54 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % 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: -0.36 (0.20), residues: 1783 helix: 0.90 (0.18), residues: 808 sheet: -0.82 (0.39), residues: 172 loop : -1.28 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1834 HIS 0.006 0.001 HIS A 112 PHE 0.018 0.001 PHE K 367 TYR 0.028 0.002 TYR A1148 ARG 0.004 0.000 ARG A2222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 120 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.3911 (mmp-170) cc_final: 0.3414 (mmp80) REVERT: A 100 MET cc_start: 0.6539 (tpp) cc_final: 0.6314 (tmm) REVERT: A 338 LEU cc_start: 0.7550 (tp) cc_final: 0.7164 (pp) REVERT: A 510 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7220 (tm-30) REVERT: A 1593 LEU cc_start: 0.1400 (OUTLIER) cc_final: 0.0220 (mt) REVERT: A 1664 PHE cc_start: 0.5123 (OUTLIER) cc_final: 0.4341 (m-10) REVERT: A 1669 ASP cc_start: 0.4456 (OUTLIER) cc_final: 0.3237 (p0) REVERT: A 1929 TRP cc_start: 0.7638 (t60) cc_final: 0.7141 (t60) REVERT: A 2151 MET cc_start: 0.6866 (mpp) cc_final: 0.6440 (mpp) REVERT: K 164 GLU cc_start: 0.3684 (OUTLIER) cc_final: 0.3282 (pp20) REVERT: K 368 HIS cc_start: 0.2131 (m-70) cc_final: 0.1730 (m-70) outliers start: 45 outliers final: 38 residues processed: 150 average time/residue: 0.2569 time to fit residues: 61.1987 Evaluate side-chains 158 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 116 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 876 ASP Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1196 HIS Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1274 ILE Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1621 GLU Chi-restraints excluded: chain A residue 1662 ASP Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1758 THR Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1831 THR Chi-restraints excluded: chain A residue 1903 ILE Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2053 GLN Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 436 VAL Chi-restraints excluded: chain K residue 438 HIS Chi-restraints excluded: chain K residue 461 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 173 optimal weight: 10.0000 chunk 106 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 120 optimal weight: 0.4980 chunk 182 optimal weight: 0.9980 chunk 167 optimal weight: 8.9990 chunk 145 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 89 optimal weight: 0.5980 chunk 115 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1147 GLN A1543 GLN ** A1891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2053 GLN ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5986 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15893 Z= 0.168 Angle : 0.608 11.505 21722 Z= 0.304 Chirality : 0.040 0.215 2459 Planarity : 0.004 0.061 2656 Dihedral : 12.079 93.941 2633 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.66 % Favored : 94.00 % Rotamer: Outliers : 2.49 % Allowed : 17.97 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.99 % 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: -0.10 (0.20), residues: 1783 helix: 1.10 (0.18), residues: 808 sheet: -0.74 (0.39), residues: 172 loop : -1.12 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1834 HIS 0.007 0.001 HIS A 112 PHE 0.018 0.001 PHE K 367 TYR 0.033 0.002 TYR A1148 ARG 0.004 0.000 ARG A2222 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 121 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.7291 (m) cc_final: 0.7038 (m) REVERT: A 63 ARG cc_start: 0.3964 (mmp-170) cc_final: 0.3545 (mtp85) REVERT: A 338 LEU cc_start: 0.7549 (tp) cc_final: 0.7190 (pp) REVERT: A 510 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7240 (tm-30) REVERT: A 1593 LEU cc_start: 0.1470 (OUTLIER) cc_final: 0.0356 (mt) REVERT: A 1664 PHE cc_start: 0.5058 (OUTLIER) cc_final: 0.4270 (m-10) REVERT: A 1669 ASP cc_start: 0.4283 (OUTLIER) cc_final: 0.3128 (p0) REVERT: A 1929 TRP cc_start: 0.7526 (t60) cc_final: 0.7025 (t60) REVERT: A 2151 MET cc_start: 0.6807 (mpp) cc_final: 0.6434 (mpp) REVERT: K 164 GLU cc_start: 0.3588 (OUTLIER) cc_final: 0.3156 (pp20) REVERT: K 368 HIS cc_start: 0.2066 (m-70) cc_final: 0.1710 (m-70) outliers start: 40 outliers final: 33 residues processed: 149 average time/residue: 0.2451 time to fit residues: 58.2659 Evaluate side-chains 151 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 114 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 876 ASP Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1274 ILE Chi-restraints excluded: chain A residue 1543 GLN Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain A residue 1664 PHE Chi-restraints excluded: chain A residue 1669 ASP Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1831 THR Chi-restraints excluded: chain A residue 1989 LEU Chi-restraints excluded: chain A residue 2004 PHE Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2117 LEU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 436 VAL Chi-restraints excluded: chain K residue 438 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 chunk 133 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 145 optimal weight: 0.9990 chunk 60 optimal weight: 0.0060 chunk 149 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.0270 chunk 127 optimal weight: 0.9980 overall best weight: 0.6056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1543 GLN ** A1891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2053 GLN A2108 HIS ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.165766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.138722 restraints weight = 43053.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.138692 restraints weight = 36556.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.139775 restraints weight = 31087.900| |-----------------------------------------------------------------------------| r_work (final): 0.4458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5969 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 15893 Z= 0.268 Angle : 0.804 59.200 21722 Z= 0.444 Chirality : 0.046 1.032 2459 Planarity : 0.004 0.061 2656 Dihedral : 12.084 93.936 2633 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.72 % Favored : 93.94 % Rotamer: Outliers : 2.55 % Allowed : 18.10 % Favored : 79.35 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.99 % 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: -0.10 (0.20), residues: 1783 helix: 1.11 (0.18), residues: 808 sheet: -0.73 (0.39), residues: 172 loop : -1.11 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1834 HIS 0.006 0.001 HIS A 112 PHE 0.018 0.001 PHE K 367 TYR 0.027 0.001 TYR A1542 ARG 0.006 0.000 ARG A 602 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3018.69 seconds wall clock time: 56 minutes 34.26 seconds (3394.26 seconds total)