Starting phenix.real_space_refine on Thu Nov 16 13:06:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dga_27420/11_2023/8dga_27420_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dga_27420/11_2023/8dga_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_27420/11_2023/8dga_27420.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dga_27420/11_2023/8dga_27420.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dga_27420/11_2023/8dga_27420_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dga_27420/11_2023/8dga_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-1.21rc1-5144/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: 8.64, per 1000 atoms: 0.56 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: 6.61 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: 8.36 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: 6.83 Time building geometry restraints manager: 6.92 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: 8682 17.90 - 35.80: 759 35.80 - 53.70: 120 53.70 - 71.59: 16 71.59 - 89.49: 9 Dihedral angle restraints: 9586 sinusoidal: 4261 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 9583 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: 4.380 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: 18.620 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 48.180 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.800 ------------------------------------------------------------------------------- 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 : 13.534 89.493 6126 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 *********************** 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 : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 184 average time/residue: 0.2960 time to fit residues: 80.1785 Evaluate side-chains 119 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.615 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3927 ------------------------------------------------------------------------------- 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: 0.9980 chunk 138 optimal weight: 0.8980 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: 0.7980 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 197 GLN ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 HIS 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5876 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15893 Z= 0.183 Angle : 0.632 14.958 21722 Z= 0.319 Chirality : 0.042 0.237 2459 Planarity : 0.005 0.059 2656 Dihedral : 8.075 95.322 2475 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.55 % Favored : 94.11 % Rotamer: Outliers : 1.18 % Allowed : 7.90 % Favored : 90.92 % 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: -1.24 (0.19), residues: 1783 helix: -0.13 (0.17), residues: 821 sheet: -0.80 (0.39), residues: 167 loop : -1.52 (0.22), residues: 795 *********************** 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: 19 poor density : 148 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 159 average time/residue: 0.2624 time to fit residues: 65.0305 Evaluate side-chains 131 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 1.772 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1498 time to fit residues: 5.5159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 166 optimal weight: 0.2980 chunk 179 optimal weight: 8.9990 chunk 148 optimal weight: 0.6980 chunk 165 optimal weight: 0.8980 chunk 56 optimal weight: 0.4980 chunk 133 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 HIS A 341 HIS ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2079 HIS ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5882 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15893 Z= 0.168 Angle : 0.594 12.874 21722 Z= 0.300 Chirality : 0.040 0.211 2459 Planarity : 0.004 0.055 2656 Dihedral : 7.687 97.523 2475 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.78 % Favored : 93.89 % Rotamer: Outliers : 0.87 % Allowed : 10.39 % Favored : 88.74 % 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: -0.77 (0.20), residues: 1783 helix: 0.39 (0.18), residues: 821 sheet: -0.63 (0.40), residues: 172 loop : -1.42 (0.22), residues: 790 *********************** 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 162 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 148 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 156 average time/residue: 0.2490 time to fit residues: 61.9928 Evaluate side-chains 129 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 123 time to evaluate : 1.719 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1495 time to fit residues: 3.9461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 164 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 111 optimal weight: 0.1980 chunk 167 optimal weight: 0.9990 chunk 176 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 158 optimal weight: 0.5980 chunk 47 optimal weight: 0.0370 overall best weight: 0.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS A 341 HIS A 770 GLN ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 368 HIS ** 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: 0.5864 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15893 Z= 0.160 Angle : 0.563 11.058 21722 Z= 0.286 Chirality : 0.040 0.205 2459 Planarity : 0.004 0.052 2656 Dihedral : 7.383 99.525 2475 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.66 % Favored : 94.00 % Rotamer: Outliers : 1.31 % Allowed : 12.19 % Favored : 86.50 % 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: -0.47 (0.20), residues: 1783 helix: 0.75 (0.18), residues: 811 sheet: -0.66 (0.39), residues: 179 loop : -1.32 (0.22), residues: 793 *********************** 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 172 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 151 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 164 average time/residue: 0.2773 time to fit residues: 74.4924 Evaluate side-chains 139 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 1.652 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1586 time to fit residues: 5.7970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 147 optimal weight: 1.9990 chunk 100 optimal weight: 0.0770 chunk 2 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 158 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- 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 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1543 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 15893 Z= 0.280 Angle : 0.657 9.286 21722 Z= 0.335 Chirality : 0.043 0.316 2459 Planarity : 0.005 0.055 2656 Dihedral : 7.543 96.322 2475 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.79 % Favored : 92.88 % Rotamer: Outliers : 1.80 % Allowed : 13.87 % Favored : 84.33 % 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: -0.63 (0.20), residues: 1783 helix: 0.59 (0.18), residues: 804 sheet: -0.66 (0.40), residues: 179 loop : -1.40 (0.22), residues: 800 *********************** 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: 29 poor density : 140 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 16 residues processed: 158 average time/residue: 0.2797 time to fit residues: 69.6120 Evaluate side-chains 141 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 2.654 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1920 time to fit residues: 8.7626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 59 optimal weight: 0.7980 chunk 159 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 177 optimal weight: 8.9990 chunk 146 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 GLN ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 GLN ** A 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1833 HIS ** K 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6031 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15893 Z= 0.220 Angle : 0.619 8.794 21722 Z= 0.312 Chirality : 0.042 0.219 2459 Planarity : 0.004 0.061 2656 Dihedral : 7.427 97.879 2475 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.79 % Favored : 92.88 % Rotamer: Outliers : 0.87 % Allowed : 16.36 % Favored : 82.77 % 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: -0.43 (0.20), residues: 1783 helix: 0.79 (0.18), residues: 808 sheet: -0.68 (0.40), residues: 179 loop : -1.30 (0.23), residues: 796 *********************** 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 145 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 144 average time/residue: 0.2665 time to fit residues: 59.9649 Evaluate side-chains 131 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 1.741 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1499 time to fit residues: 5.0941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 170 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 100 optimal weight: 0.4980 chunk 129 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 176 optimal weight: 10.0000 chunk 110 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1543 GLN ** K 368 HIS ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6063 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15893 Z= 0.235 Angle : 0.631 9.759 21722 Z= 0.318 Chirality : 0.042 0.208 2459 Planarity : 0.004 0.060 2656 Dihedral : 7.441 95.359 2475 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.79 % Favored : 92.88 % Rotamer: Outliers : 1.37 % Allowed : 16.79 % Favored : 81.84 % 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: 0.82 (0.18), residues: 812 sheet: -0.77 (0.39), residues: 177 loop : -1.35 (0.23), residues: 794 *********************** 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 153 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 141 average time/residue: 0.2662 time to fit residues: 59.1949 Evaluate side-chains 133 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 1.691 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1435 time to fit residues: 6.1429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 112 optimal weight: 0.0050 chunk 120 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1543 GLN ** A1891 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6009 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15893 Z= 0.190 Angle : 0.611 15.095 21722 Z= 0.304 Chirality : 0.041 0.215 2459 Planarity : 0.004 0.062 2656 Dihedral : 7.308 95.333 2475 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.51 % Favored : 93.16 % Rotamer: Outliers : 0.68 % Allowed : 17.29 % Favored : 82.03 % 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: -0.26 (0.20), residues: 1783 helix: 0.98 (0.18), residues: 812 sheet: -0.72 (0.40), residues: 177 loop : -1.24 (0.23), residues: 794 *********************** 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 136 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 132 average time/residue: 0.2721 time to fit residues: 55.4632 Evaluate side-chains 122 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 1.618 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1656 time to fit residues: 4.3961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 129 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 155 optimal weight: 0.4980 chunk 163 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1147 GLN ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 moved from start: 0.3307 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= 0.173 Angle : 0.608 12.374 21722 Z= 0.302 Chirality : 0.042 0.395 2459 Planarity : 0.004 0.060 2656 Dihedral : 7.200 94.892 2475 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.39 % Favored : 93.27 % Rotamer: Outliers : 0.50 % Allowed : 18.22 % Favored : 81.28 % 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: -0.13 (0.20), residues: 1783 helix: 1.08 (0.18), residues: 814 sheet: -0.63 (0.40), residues: 176 loop : -1.18 (0.23), residues: 793 *********************** 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 135 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 130 average time/residue: 0.2758 time to fit residues: 55.7217 Evaluate side-chains 127 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 122 time to evaluate : 1.801 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1553 time to fit residues: 3.9102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 173 optimal weight: 8.9990 chunk 106 optimal weight: 0.0770 chunk 82 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 112 optimal weight: 0.0170 chunk 89 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 HIS ** A 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1543 GLN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5930 moved from start: 0.3491 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= 0.160 Angle : 0.598 12.071 21722 Z= 0.295 Chirality : 0.041 0.324 2459 Planarity : 0.004 0.061 2656 Dihedral : 7.064 94.886 2475 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.55 % Favored : 94.11 % Rotamer: Outliers : 0.31 % Allowed : 18.47 % Favored : 81.22 % 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: 0.01 (0.20), residues: 1783 helix: 1.20 (0.18), residues: 816 sheet: -0.58 (0.41), residues: 172 loop : -1.11 (0.23), residues: 795 ********************** 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 136 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 134 average time/residue: 0.3064 time to fit residues: 63.7891 Evaluate side-chains 124 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 121 time to evaluate : 1.797 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1860 time to fit residues: 3.5383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 145 optimal weight: 0.6980 chunk 60 optimal weight: 0.3980 chunk 149 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ** A 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1553 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.166937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.139592 restraints weight = 43104.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.138924 restraints weight = 34764.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.140189 restraints weight = 28735.901| |-----------------------------------------------------------------------------| r_work (final): 0.4467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5959 moved from start: 0.3604 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 : 0.620 12.885 21722 Z= 0.304 Chirality : 0.041 0.324 2459 Planarity : 0.004 0.056 2656 Dihedral : 7.006 92.777 2475 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.17 % Favored : 93.49 % Rotamer: Outliers : 0.44 % Allowed : 18.84 % Favored : 80.72 % 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: 0.05 (0.21), residues: 1783 helix: 1.22 (0.18), residues: 816 sheet: -0.50 (0.41), residues: 172 loop : -1.08 (0.23), residues: 795 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3036.38 seconds wall clock time: 58 minutes 4.42 seconds (3484.42 seconds total)