Starting phenix.real_space_refine on Thu Jul 31 22:51:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ty1_41710/07_2025/8ty1_41710.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ty1_41710/07_2025/8ty1_41710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ty1_41710/07_2025/8ty1_41710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ty1_41710/07_2025/8ty1_41710.map" model { file = "/net/cci-nas-00/data/ceres_data/8ty1_41710/07_2025/8ty1_41710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ty1_41710/07_2025/8ty1_41710.cif" } resolution = 3.46 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= 0.007 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: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 8618 2.51 5 N 2290 2.21 5 O 2535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13508 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1236, 10004 Classifications: {'peptide': 1236} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 59, 'TRANS': 1176} Chain breaks: 7 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1570 Classifications: {'peptide': 204} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Chain: "C" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1784 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 223} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 9.95, per 1000 atoms: 0.74 Number of scatterers: 13508 At special positions: 0 Unit cell: (81.164, 123.716, 178.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 2535 8.00 N 2290 7.00 C 8618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 180 " distance=2.04 Simple disulfide: pdb=" SG CYS A 249 " - pdb=" SG CYS A 330 " distance=2.03 Simple disulfide: pdb=" SG CYS A 528 " - pdb=" SG CYS A 554 " distance=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 711 " distance=2.03 Simple disulfide: pdb=" SG CYS A1832 " - pdb=" SG CYS A1858 " distance=2.03 Simple disulfide: pdb=" SG CYS A2021 " - pdb=" SG CYS A2169 " distance=2.03 Simple disulfide: pdb=" SG CYS A2174 " - pdb=" SG CYS A2326 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 106 " distance=2.03 Simple disulfide: pdb=" SG CYS C 164 " - pdb=" SG CYS C 220 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG D 1 " - " ASN A 240 " " NAG E 1 " - " ASN A1810 " " NAG F 1 " - " ASN C 28 " Time building additional restraints: 3.78 Conformation dependent library (CDL) restraints added in 1.8 seconds 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3128 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 33 sheets defined 9.3% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 120 through 128 removed outlier: 4.426A pdb=" N GLU A 125 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP A 126 " --> pdb=" O GLU A 123 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP A 127 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 128 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 171 Processing helix chain 'A' and resid 191 through 195 removed outlier: 3.733A pdb=" N GLU A 195 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 538 through 546 removed outlier: 4.228A pdb=" N ALA A 544 " --> pdb=" O GLU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 595 Processing helix chain 'A' and resid 605 through 612 Processing helix chain 'A' and resid 694 through 700 removed outlier: 4.156A pdb=" N ASN A 699 " --> pdb=" O SER A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 1750 through 1755 removed outlier: 3.551A pdb=" N ASN A1753 " --> pdb=" O GLY A1750 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N HIS A1755 " --> pdb=" O LEU A1752 " (cutoff:3.500A) Processing helix chain 'A' and resid 1820 through 1824 Processing helix chain 'A' and resid 1842 through 1847 removed outlier: 3.514A pdb=" N ASP A1846 " --> pdb=" O ASP A1842 " (cutoff:3.500A) Processing helix chain 'A' and resid 1886 through 1888 No H-bonds generated for 'chain 'A' and resid 1886 through 1888' Processing helix chain 'A' and resid 1891 through 1895 removed outlier: 3.618A pdb=" N VAL A1895 " --> pdb=" O THR A1892 " (cutoff:3.500A) Processing helix chain 'A' and resid 1912 through 1915 Processing helix chain 'A' and resid 2002 through 2007 Processing helix chain 'A' and resid 2047 through 2051 removed outlier: 4.084A pdb=" N LEU A2050 " --> pdb=" O ALA A2047 " (cutoff:3.500A) Processing helix chain 'A' and resid 2186 through 2190 Processing helix chain 'A' and resid 2204 through 2208 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 93 through 97 removed outlier: 3.572A pdb=" N ALA B 96 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 130 Processing helix chain 'B' and resid 184 through 191 removed outlier: 4.429A pdb=" N HIS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 75 removed outlier: 4.056A pdb=" N GLN C 75 " --> pdb=" O HIS C 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 72 through 75' Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.970A pdb=" N THR C 101 " --> pdb=" O SER C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 155 removed outlier: 4.108A pdb=" N THR C 155 " --> pdb=" O SER C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 182 Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.596A pdb=" N TYR A 6 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 90 " --> pdb=" O LEU A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.596A pdb=" N TYR A 6 " --> pdb=" O PHE A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 77 removed outlier: 5.763A pdb=" N ILE A 77 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N CYS A 180 " --> pdb=" O ILE A 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 197 through 198 Processing sheet with id=AA5, first strand: chain 'A' and resid 200 through 203 Processing sheet with id=AA6, first strand: chain 'A' and resid 246 through 248 removed outlier: 5.617A pdb=" N LEU A 246 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 422 through 429 Processing sheet with id=AA8, first strand: chain 'A' and resid 476 through 477 removed outlier: 3.905A pdb=" N TYR A 476 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER A 534 " --> pdb=" O TYR A 476 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 613 through 617 removed outlier: 3.901A pdb=" N ILE A 574 " --> pdb=" O TYR A 638 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 658 through 659 removed outlier: 3.700A pdb=" N PHE A 658 " --> pdb=" O GLU A 665 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 665 " --> pdb=" O PHE A 658 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 1695 through 1697 Processing sheet with id=AB3, first strand: chain 'A' and resid 1701 through 1707 Processing sheet with id=AB4, first strand: chain 'A' and resid 1763 through 1765 removed outlier: 6.421A pdb=" N ILE A1763 " --> pdb=" O LEU A1856 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N CYS A1858 " --> pdb=" O ILE A1763 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA A1765 " --> pdb=" O CYS A1858 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1917 through 1921 Processing sheet with id=AB6, first strand: chain 'A' and resid 1933 through 1935 removed outlier: 3.629A pdb=" N TYR A2017 " --> pdb=" O MET A1934 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A2016 " --> pdb=" O GLY A1994 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1975 through 1976 Processing sheet with id=AB8, first strand: chain 'A' and resid 1963 through 1965 Processing sheet with id=AB9, first strand: chain 'A' and resid 2062 through 2064 removed outlier: 6.953A pdb=" N CYS A2169 " --> pdb=" O ILE A2081 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ILE A2081 " --> pdb=" O CYS A2169 " (cutoff:3.500A) removed outlier: 13.348A pdb=" N ILE A2071 " --> pdb=" O THR A2154 " (cutoff:3.500A) removed outlier: 12.184A pdb=" N THR A2154 " --> pdb=" O ILE A2071 " (cutoff:3.500A) removed outlier: 12.503A pdb=" N VAL A2073 " --> pdb=" O HIS A2152 " (cutoff:3.500A) removed outlier: 11.960A pdb=" N HIS A2152 " --> pdb=" O VAL A2073 " (cutoff:3.500A) removed outlier: 11.362A pdb=" N LEU A2075 " --> pdb=" O ARG A2150 " (cutoff:3.500A) removed outlier: 11.952A pdb=" N ARG A2150 " --> pdb=" O LEU A2075 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N ALA A2077 " --> pdb=" O TYR A2148 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TYR A2148 " --> pdb=" O ALA A2077 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN A2100 " --> pdb=" O THR A2154 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TYR A2156 " --> pdb=" O ILE A2098 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE A2098 " --> pdb=" O TYR A2156 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2089 through 2091 Processing sheet with id=AC2, first strand: chain 'A' and resid 2191 through 2192 removed outlier: 3.948A pdb=" N THR A2272 " --> pdb=" O SER A2264 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 2293 through 2296 removed outlier: 4.969A pdb=" N VAL A2240 " --> pdb=" O CYS A2326 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N CYS A2326 " --> pdb=" O VAL A2240 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 2248 through 2250 Processing sheet with id=AC5, first strand: chain 'B' and resid 5 through 7 removed outlier: 12.177A pdb=" N CYS B 23 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 11.253A pdb=" N THR B 75 " --> pdb=" O CYS B 23 " (cutoff:3.500A) removed outlier: 12.400A pdb=" N ALA B 25 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 11.974A pdb=" N THR B 73 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N GLN B 27 " --> pdb=" O ASP B 71 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASP B 71 " --> pdb=" O GLN B 27 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.547A pdb=" N LEU B 11 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.547A pdb=" N LEU B 11 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 91 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 99 " --> pdb=" O GLN B 91 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 116 through 120 Processing sheet with id=AC9, first strand: chain 'B' and resid 150 through 151 removed outlier: 4.371A pdb=" N TRP B 150 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.387A pdb=" N GLU C 10 " --> pdb=" O THR C 134 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA C 109 " --> pdb=" O SER C 43 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N SER C 43 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL C 44 " --> pdb=" O ARG C 60 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG C 60 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP C 46 " --> pdb=" O MET C 58 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET C 58 " --> pdb=" O TRP C 46 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.387A pdb=" N GLU C 10 " --> pdb=" O THR C 134 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N CYS C 106 " --> pdb=" O TRP C 127 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TRP C 127 " --> pdb=" O CYS C 106 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ARG C 108 " --> pdb=" O ASP C 125 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP C 125 " --> pdb=" O ARG C 108 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 144 through 148 removed outlier: 4.033A pdb=" N SER C 144 " --> pdb=" O LYS C 167 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR C 200 " --> pdb=" O ASP C 168 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 144 through 148 removed outlier: 4.033A pdb=" N SER C 144 " --> pdb=" O LYS C 167 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR C 200 " --> pdb=" O ASP C 168 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 174 through 177 340 hydrogen bonds defined for protein. 822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.97 Time building geometry restraints manager: 4.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4283 1.34 - 1.46: 3586 1.46 - 1.59: 5896 1.59 - 1.71: 1 1.71 - 1.83: 103 Bond restraints: 13869 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.568 -0.049 2.00e-02 2.50e+03 5.90e+00 bond pdb=" C1 MAN F 4 " pdb=" C2 MAN F 4 " ideal model delta sigma weight residual 1.526 1.574 -0.048 2.00e-02 2.50e+03 5.84e+00 bond pdb=" CB PRO C 209 " pdb=" CG PRO C 209 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.70e+00 bond pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sigma weight residual 1.417 1.453 -0.036 2.00e-02 2.50e+03 3.28e+00 ... (remaining 13864 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 18287 2.33 - 4.65: 440 4.65 - 6.98: 59 6.98 - 9.30: 22 9.30 - 11.63: 8 Bond angle restraints: 18816 Sorted by residual: angle pdb=" CA PRO C 209 " pdb=" N PRO C 209 " pdb=" CD PRO C 209 " ideal model delta sigma weight residual 112.00 101.99 10.01 1.40e+00 5.10e-01 5.12e+01 angle pdb=" C ASN A1805 " pdb=" CA ASN A1805 " pdb=" CB ASN A1805 " ideal model delta sigma weight residual 116.54 110.18 6.36 1.15e+00 7.56e-01 3.06e+01 angle pdb=" C HIS A2315 " pdb=" N GLN A2316 " pdb=" CA GLN A2316 " ideal model delta sigma weight residual 121.54 131.22 -9.68 1.91e+00 2.74e-01 2.57e+01 angle pdb=" N GLN A2316 " pdb=" CA GLN A2316 " pdb=" CB GLN A2316 " ideal model delta sigma weight residual 110.49 118.97 -8.48 1.69e+00 3.50e-01 2.52e+01 angle pdb=" C VAL A2314 " pdb=" N HIS A2315 " pdb=" CA HIS A2315 " ideal model delta sigma weight residual 121.54 130.14 -8.60 1.91e+00 2.74e-01 2.03e+01 ... (remaining 18811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.52: 7469 23.52 - 47.03: 713 47.03 - 70.55: 105 70.55 - 94.06: 42 94.06 - 117.58: 18 Dihedral angle restraints: 8347 sinusoidal: 3473 harmonic: 4874 Sorted by residual: dihedral pdb=" CB CYS B 136 " pdb=" SG CYS B 136 " pdb=" SG CYS B 196 " pdb=" CB CYS B 196 " ideal model delta sinusoidal sigma weight residual 93.00 154.96 -61.96 1 1.00e+01 1.00e-02 5.09e+01 dihedral pdb=" CB CYS C 164 " pdb=" SG CYS C 164 " pdb=" SG CYS C 220 " pdb=" CB CYS C 220 " ideal model delta sinusoidal sigma weight residual 93.00 151.99 -58.99 1 1.00e+01 1.00e-02 4.65e+01 dihedral pdb=" CA CYS A 180 " pdb=" C CYS A 180 " pdb=" N ARG A 181 " pdb=" CA ARG A 181 " ideal model delta harmonic sigma weight residual -180.00 -148.81 -31.19 0 5.00e+00 4.00e-02 3.89e+01 ... (remaining 8344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1598 0.055 - 0.110: 384 0.110 - 0.164: 81 0.164 - 0.219: 5 0.219 - 0.274: 3 Chirality restraints: 2071 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 2068 not shown) Planarity restraints: 2382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 208 " 0.119 5.00e-02 4.00e+02 1.73e-01 4.78e+01 pdb=" N PRO C 209 " -0.299 5.00e-02 4.00e+02 pdb=" CA PRO C 209 " 0.094 5.00e-02 4.00e+02 pdb=" CD PRO C 209 " 0.085 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 127 " -0.018 2.00e-02 2.50e+03 2.71e-02 1.84e+01 pdb=" CG TRP C 127 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP C 127 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP C 127 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP C 127 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 127 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 127 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 127 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 127 " -0.026 2.00e-02 2.50e+03 pdb=" CH2 TRP C 127 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " -0.025 2.00e-02 2.50e+03 2.40e-02 1.45e+01 pdb=" CG TRP A 139 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " -0.006 2.00e-02 2.50e+03 ... (remaining 2379 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 222 2.58 - 3.16: 11640 3.16 - 3.74: 21330 3.74 - 4.32: 29351 4.32 - 4.90: 47611 Nonbonded interactions: 110154 Sorted by model distance: nonbonded pdb=" OE2 GLU A 111 " pdb=" OH TYR A 115 " model vdw 2.005 3.040 nonbonded pdb=" O ALA A1877 " pdb=" ND2 ASN A1922 " model vdw 2.124 3.120 nonbonded pdb=" OE1 GLN A 135 " pdb=" OH TYR A 137 " model vdw 2.136 3.040 nonbonded pdb=" OG SER A 628 " pdb=" O LYS A 707 " model vdw 2.138 3.040 nonbonded pdb=" OE2 GLU A 389 " pdb=" NH2 ARG A 439 " model vdw 2.139 3.120 ... (remaining 110149 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 37.870 Find NCS groups from input model: 0.150 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:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5852 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 13892 Z= 0.232 Angle : 0.899 11.625 18874 Z= 0.454 Chirality : 0.050 0.274 2071 Planarity : 0.006 0.173 2379 Dihedral : 19.173 117.576 5186 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 22.87 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.53 % Favored : 88.99 % Rotamer: Outliers : 0.68 % Allowed : 27.90 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.57 (0.20), residues: 1653 helix: -1.71 (0.52), residues: 74 sheet: -1.19 (0.22), residues: 491 loop : -2.05 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.004 TRP C 127 HIS 0.009 0.002 HIS A2005 PHE 0.033 0.002 PHE A1785 TYR 0.025 0.002 TYR B 88 ARG 0.010 0.001 ARG B 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 3) link_NAG-ASN : angle 5.34067 ( 9) link_BETA1-4 : bond 0.00558 ( 6) link_BETA1-4 : angle 2.89423 ( 18) link_ALPHA1-3 : bond 0.00426 ( 3) link_ALPHA1-3 : angle 1.71437 ( 9) hydrogen bonds : bond 0.15833 ( 315) hydrogen bonds : angle 8.58911 ( 822) SS BOND : bond 0.00367 ( 11) SS BOND : angle 1.16668 ( 22) covalent geometry : bond 0.00527 (13869) covalent geometry : angle 0.88656 (18816) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 159 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 MET cc_start: 0.7284 (ppp) cc_final: 0.6583 (ttt) REVERT: A 625 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7894 (mp) REVERT: A 666 ASP cc_start: 0.7261 (OUTLIER) cc_final: 0.6903 (t0) REVERT: A 683 GLU cc_start: 0.6371 (mm-30) cc_final: 0.6127 (mm-30) REVERT: A 1711 MET cc_start: 0.3602 (mpp) cc_final: 0.3044 (mpp) REVERT: A 1794 ASP cc_start: 0.5830 (t0) cc_final: 0.4916 (p0) REVERT: A 1797 GLU cc_start: 0.4601 (tp30) cc_final: 0.4215 (tp30) REVERT: A 2180 MET cc_start: 0.7767 (tpt) cc_final: 0.7433 (tpt) REVERT: A 2313 TRP cc_start: 0.4492 (p90) cc_final: 0.4154 (p90) REVERT: C 42 TYR cc_start: 0.4728 (p90) cc_final: 0.4482 (p90) outliers start: 10 outliers final: 4 residues processed: 167 average time/residue: 0.2693 time to fit residues: 67.1361 Evaluate side-chains 154 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain B residue 111 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1870 GLN ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2231 GLN C 1 GLN ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.194473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.153124 restraints weight = 24081.298| |-----------------------------------------------------------------------------| r_work (start): 0.4435 rms_B_bonded: 4.39 r_work: 0.4199 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13892 Z= 0.163 Angle : 0.752 10.368 18874 Z= 0.374 Chirality : 0.048 0.251 2071 Planarity : 0.006 0.109 2379 Dihedral : 12.968 115.053 2078 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.95 % Favored : 90.62 % Rotamer: Outliers : 4.23 % Allowed : 25.24 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.20), residues: 1653 helix: -1.41 (0.56), residues: 75 sheet: -1.28 (0.22), residues: 478 loop : -1.97 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 127 HIS 0.006 0.001 HIS A2005 PHE 0.023 0.002 PHE A1785 TYR 0.020 0.002 TYR B 92 ARG 0.005 0.001 ARG C 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00567 ( 3) link_NAG-ASN : angle 5.16181 ( 9) link_BETA1-4 : bond 0.00923 ( 6) link_BETA1-4 : angle 2.95240 ( 18) link_ALPHA1-3 : bond 0.01130 ( 3) link_ALPHA1-3 : angle 2.42702 ( 9) hydrogen bonds : bond 0.04042 ( 315) hydrogen bonds : angle 7.27141 ( 822) SS BOND : bond 0.00304 ( 11) SS BOND : angle 1.02113 ( 22) covalent geometry : bond 0.00369 (13869) covalent geometry : angle 0.73623 (18816) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 152 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8404 (tmm) cc_final: 0.8026 (tmm) REVERT: A 279 VAL cc_start: 0.2883 (OUTLIER) cc_final: 0.2655 (t) REVERT: A 292 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.5789 (mp) REVERT: A 313 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7665 (mp) REVERT: A 324 HIS cc_start: 0.5800 (m-70) cc_final: 0.5416 (m-70) REVERT: A 1711 MET cc_start: 0.3035 (mpp) cc_final: 0.2645 (mpp) REVERT: A 1794 ASP cc_start: 0.5842 (t0) cc_final: 0.5012 (p0) REVERT: A 2167 MET cc_start: 0.5979 (mmt) cc_final: 0.5592 (mmt) REVERT: A 2180 MET cc_start: 0.7838 (tpt) cc_final: 0.7540 (tpt) REVERT: A 2238 MET cc_start: 0.4552 (mmm) cc_final: 0.4271 (mmm) REVERT: A 2324 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6821 (mt) REVERT: C 1 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.7008 (pt0) REVERT: C 57 TRP cc_start: 0.8267 (OUTLIER) cc_final: 0.7662 (t60) outliers start: 62 outliers final: 29 residues processed: 199 average time/residue: 0.2379 time to fit residues: 71.9329 Evaluate side-chains 172 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2023 THR Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2324 LEU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 1 GLN Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 98 optimal weight: 0.2980 chunk 39 optimal weight: 0.2980 chunk 103 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 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 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1957 HIS ** A1961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2087 GLN ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4952 r_free = 0.4952 target = 0.193916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.150724 restraints weight = 24225.927| |-----------------------------------------------------------------------------| r_work (start): 0.4393 rms_B_bonded: 3.91 r_work: 0.4196 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 13892 Z= 0.197 Angle : 0.756 9.899 18874 Z= 0.378 Chirality : 0.049 0.237 2071 Planarity : 0.005 0.085 2379 Dihedral : 11.745 114.564 2069 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.10 % Favored : 89.47 % Rotamer: Outliers : 5.46 % Allowed : 25.31 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.20), residues: 1653 helix: -1.45 (0.56), residues: 75 sheet: -1.37 (0.22), residues: 479 loop : -2.02 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 127 HIS 0.009 0.001 HIS A2005 PHE 0.028 0.002 PHE A1785 TYR 0.020 0.002 TYR A 159 ARG 0.004 0.000 ARG C 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00664 ( 3) link_NAG-ASN : angle 5.25807 ( 9) link_BETA1-4 : bond 0.00841 ( 6) link_BETA1-4 : angle 2.90648 ( 18) link_ALPHA1-3 : bond 0.01090 ( 3) link_ALPHA1-3 : angle 2.23420 ( 9) hydrogen bonds : bond 0.03862 ( 315) hydrogen bonds : angle 7.24017 ( 822) SS BOND : bond 0.00405 ( 11) SS BOND : angle 1.21876 ( 22) covalent geometry : bond 0.00455 (13869) covalent geometry : angle 0.74043 (18816) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 141 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8397 (tmm) cc_final: 0.8110 (tmm) REVERT: A 279 VAL cc_start: 0.2625 (OUTLIER) cc_final: 0.2396 (t) REVERT: A 292 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.5949 (mp) REVERT: A 324 HIS cc_start: 0.5914 (m-70) cc_final: 0.5474 (m-70) REVERT: A 407 TYR cc_start: 0.5654 (OUTLIER) cc_final: 0.5011 (t80) REVERT: A 645 GLN cc_start: 0.5008 (OUTLIER) cc_final: 0.4525 (mp10) REVERT: A 666 ASP cc_start: 0.7331 (OUTLIER) cc_final: 0.6935 (t0) REVERT: A 1794 ASP cc_start: 0.5821 (t0) cc_final: 0.5026 (p0) REVERT: A 2010 MET cc_start: 0.8069 (tpp) cc_final: 0.7818 (mpp) REVERT: A 2167 MET cc_start: 0.5942 (mmt) cc_final: 0.5558 (mmt) REVERT: A 2180 MET cc_start: 0.7611 (tpt) cc_final: 0.7120 (tpt) REVERT: A 2238 MET cc_start: 0.4933 (mmm) cc_final: 0.4726 (tpp) REVERT: A 2324 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6821 (mt) REVERT: B 110 ARG cc_start: 0.4884 (OUTLIER) cc_final: 0.3272 (ptp-170) REVERT: C 57 TRP cc_start: 0.8267 (OUTLIER) cc_final: 0.7570 (t60) outliers start: 80 outliers final: 49 residues processed: 205 average time/residue: 0.2347 time to fit residues: 72.6516 Evaluate side-chains 190 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 133 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1777 ASN Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1871 VAL Chi-restraints excluded: chain A residue 1882 ILE Chi-restraints excluded: chain A residue 1926 MET Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2023 THR Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2178 LEU Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2324 LEU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 142 TYR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 97 optimal weight: 0.1980 chunk 88 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 149 optimal weight: 0.4980 chunk 107 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1950 ASN ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4968 r_free = 0.4968 target = 0.195301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.153878 restraints weight = 24077.238| |-----------------------------------------------------------------------------| r_work (start): 0.4459 rms_B_bonded: 4.34 r_work: 0.4209 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13892 Z= 0.156 Angle : 0.728 10.684 18874 Z= 0.360 Chirality : 0.047 0.245 2071 Planarity : 0.005 0.075 2379 Dihedral : 10.701 114.048 2069 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.95 % Favored : 90.62 % Rotamer: Outliers : 5.39 % Allowed : 25.44 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.20), residues: 1653 helix: -1.50 (0.55), residues: 81 sheet: -1.34 (0.22), residues: 483 loop : -1.98 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 127 HIS 0.008 0.001 HIS A2005 PHE 0.023 0.002 PHE A1785 TYR 0.022 0.002 TYR A 159 ARG 0.004 0.000 ARG C 48 Details of bonding type rmsd link_NAG-ASN : bond 0.00679 ( 3) link_NAG-ASN : angle 5.54007 ( 9) link_BETA1-4 : bond 0.00842 ( 6) link_BETA1-4 : angle 2.77062 ( 18) link_ALPHA1-3 : bond 0.01152 ( 3) link_ALPHA1-3 : angle 2.30744 ( 9) hydrogen bonds : bond 0.03419 ( 315) hydrogen bonds : angle 7.16619 ( 822) SS BOND : bond 0.00464 ( 11) SS BOND : angle 1.29464 ( 22) covalent geometry : bond 0.00353 (13869) covalent geometry : angle 0.71084 (18816) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 143 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8357 (tmm) cc_final: 0.8122 (tmm) REVERT: A 279 VAL cc_start: 0.2739 (OUTLIER) cc_final: 0.2497 (t) REVERT: A 292 LEU cc_start: 0.6717 (OUTLIER) cc_final: 0.5783 (mp) REVERT: A 302 MET cc_start: 0.4764 (tpt) cc_final: 0.4187 (mmt) REVERT: A 324 HIS cc_start: 0.5752 (m-70) cc_final: 0.5345 (m-70) REVERT: A 407 TYR cc_start: 0.5835 (OUTLIER) cc_final: 0.5148 (t80) REVERT: A 1794 ASP cc_start: 0.5857 (t0) cc_final: 0.5055 (p0) REVERT: A 2010 MET cc_start: 0.8026 (tpp) cc_final: 0.7360 (mpp) REVERT: A 2167 MET cc_start: 0.6009 (mmt) cc_final: 0.5643 (mmt) REVERT: A 2180 MET cc_start: 0.7723 (tpt) cc_final: 0.7325 (tpt) REVERT: A 2324 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6833 (mt) REVERT: B 138 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8787 (pp) REVERT: B 141 PHE cc_start: 0.3978 (p90) cc_final: 0.3225 (p90) REVERT: C 57 TRP cc_start: 0.8221 (OUTLIER) cc_final: 0.7628 (t60) outliers start: 79 outliers final: 47 residues processed: 208 average time/residue: 0.2383 time to fit residues: 74.6608 Evaluate side-chains 188 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 135 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1777 ASN Chi-restraints excluded: chain A residue 1871 VAL Chi-restraints excluded: chain A residue 1882 ILE Chi-restraints excluded: chain A residue 1889 TRP Chi-restraints excluded: chain A residue 1921 ILE Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2023 THR Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain A residue 2324 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 142 TYR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 44 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 78 optimal weight: 0.0370 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 125 optimal weight: 0.0370 chunk 110 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.9338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1861 ASN ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2091 GLN ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** 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 = 0.4971 r_free = 0.4971 target = 0.195170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.153797 restraints weight = 24034.015| |-----------------------------------------------------------------------------| r_work (start): 0.4441 rms_B_bonded: 4.20 r_work: 0.4219 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6177 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13892 Z= 0.158 Angle : 0.722 10.757 18874 Z= 0.356 Chirality : 0.047 0.243 2071 Planarity : 0.005 0.074 2379 Dihedral : 9.874 112.912 2069 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.50 % Favored : 90.08 % Rotamer: Outliers : 6.00 % Allowed : 25.38 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.20), residues: 1653 helix: -1.71 (0.52), residues: 91 sheet: -1.22 (0.23), residues: 472 loop : -2.02 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 209 HIS 0.006 0.001 HIS A2005 PHE 0.024 0.002 PHE A2234 TYR 0.032 0.002 TYR A 159 ARG 0.003 0.000 ARG A 583 Details of bonding type rmsd link_NAG-ASN : bond 0.00756 ( 3) link_NAG-ASN : angle 5.79290 ( 9) link_BETA1-4 : bond 0.00812 ( 6) link_BETA1-4 : angle 2.69393 ( 18) link_ALPHA1-3 : bond 0.01205 ( 3) link_ALPHA1-3 : angle 2.35788 ( 9) hydrogen bonds : bond 0.03361 ( 315) hydrogen bonds : angle 7.03787 ( 822) SS BOND : bond 0.00544 ( 11) SS BOND : angle 0.84743 ( 22) covalent geometry : bond 0.00360 (13869) covalent geometry : angle 0.70478 (18816) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 144 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.5427 (OUTLIER) cc_final: 0.4992 (m-80) REVERT: A 261 MET cc_start: 0.8303 (tmm) cc_final: 0.8047 (tmm) REVERT: A 279 VAL cc_start: 0.2760 (OUTLIER) cc_final: 0.2472 (t) REVERT: A 287 LEU cc_start: 0.4183 (OUTLIER) cc_final: 0.3855 (mt) REVERT: A 292 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.5935 (mp) REVERT: A 302 MET cc_start: 0.4745 (tpt) cc_final: 0.4214 (mmt) REVERT: A 324 HIS cc_start: 0.5825 (m-70) cc_final: 0.5455 (m90) REVERT: A 407 TYR cc_start: 0.5779 (OUTLIER) cc_final: 0.5144 (t80) REVERT: A 665 GLU cc_start: 0.8640 (mp0) cc_final: 0.8312 (mp0) REVERT: A 666 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.6917 (t0) REVERT: A 1711 MET cc_start: 0.3074 (mpp) cc_final: 0.2782 (mpp) REVERT: A 1794 ASP cc_start: 0.5902 (t0) cc_final: 0.5138 (p0) REVERT: A 2033 ARG cc_start: 0.7041 (ptt90) cc_final: 0.6531 (ptp-110) REVERT: A 2167 MET cc_start: 0.6061 (mmt) cc_final: 0.5672 (mmt) REVERT: A 2180 MET cc_start: 0.7543 (tpt) cc_final: 0.7182 (tpt) REVERT: A 2324 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6744 (mt) REVERT: B 138 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8682 (pp) REVERT: B 141 PHE cc_start: 0.3862 (p90) cc_final: 0.3439 (p90) REVERT: C 57 TRP cc_start: 0.8200 (OUTLIER) cc_final: 0.7644 (t60) outliers start: 88 outliers final: 59 residues processed: 215 average time/residue: 0.2361 time to fit residues: 77.9657 Evaluate side-chains 203 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 135 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1777 ASN Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1847 VAL Chi-restraints excluded: chain A residue 1871 VAL Chi-restraints excluded: chain A residue 1882 ILE Chi-restraints excluded: chain A residue 1889 TRP Chi-restraints excluded: chain A residue 1921 ILE Chi-restraints excluded: chain A residue 1926 MET Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1958 PHE Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2023 THR Chi-restraints excluded: chain A residue 2062 TRP Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2127 PHE Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2324 LEU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 118 optimal weight: 0.0870 chunk 59 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 35 optimal weight: 0.0030 chunk 128 optimal weight: 0.0370 chunk 42 optimal weight: 2.9990 overall best weight: 0.5848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 HIS A 645 GLN ** A1745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN C 6 GLN C 221 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4988 r_free = 0.4988 target = 0.197165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.153776 restraints weight = 24242.629| |-----------------------------------------------------------------------------| r_work (start): 0.4435 rms_B_bonded: 4.19 r_work: 0.4231 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13892 Z= 0.130 Angle : 0.702 10.728 18874 Z= 0.345 Chirality : 0.047 0.252 2071 Planarity : 0.005 0.073 2379 Dihedral : 9.119 110.289 2069 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.95 % Favored : 90.68 % Rotamer: Outliers : 5.87 % Allowed : 25.38 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.20), residues: 1653 helix: -1.71 (0.51), residues: 91 sheet: -1.15 (0.22), residues: 488 loop : -1.93 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 209 HIS 0.005 0.001 HIS C 37 PHE 0.018 0.001 PHE A1785 TYR 0.035 0.002 TYR A 159 ARG 0.003 0.000 ARG B 110 Details of bonding type rmsd link_NAG-ASN : bond 0.00698 ( 3) link_NAG-ASN : angle 5.58336 ( 9) link_BETA1-4 : bond 0.00770 ( 6) link_BETA1-4 : angle 2.65809 ( 18) link_ALPHA1-3 : bond 0.01189 ( 3) link_ALPHA1-3 : angle 2.27790 ( 9) hydrogen bonds : bond 0.03112 ( 315) hydrogen bonds : angle 6.82859 ( 822) SS BOND : bond 0.00584 ( 11) SS BOND : angle 1.19522 ( 22) covalent geometry : bond 0.00294 (13869) covalent geometry : angle 0.68486 (18816) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 147 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.4974 (OUTLIER) cc_final: 0.2547 (m-80) REVERT: A 209 TRP cc_start: 0.6498 (t-100) cc_final: 0.5474 (t60) REVERT: A 261 MET cc_start: 0.8270 (tmm) cc_final: 0.8005 (tmm) REVERT: A 279 VAL cc_start: 0.2958 (OUTLIER) cc_final: 0.2674 (t) REVERT: A 287 LEU cc_start: 0.4199 (OUTLIER) cc_final: 0.3841 (mt) REVERT: A 292 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.6059 (mp) REVERT: A 302 MET cc_start: 0.4644 (tpt) cc_final: 0.4405 (tpp) REVERT: A 324 HIS cc_start: 0.5777 (m-70) cc_final: 0.5456 (m90) REVERT: A 407 TYR cc_start: 0.5815 (OUTLIER) cc_final: 0.5202 (t80) REVERT: A 539 MET cc_start: 0.4742 (OUTLIER) cc_final: 0.3484 (tmm) REVERT: A 645 GLN cc_start: 0.4982 (OUTLIER) cc_final: 0.4609 (mp10) REVERT: A 665 GLU cc_start: 0.8133 (mp0) cc_final: 0.7787 (mp0) REVERT: A 1794 ASP cc_start: 0.5860 (t0) cc_final: 0.5092 (p0) REVERT: A 2167 MET cc_start: 0.6220 (mmt) cc_final: 0.5840 (mmt) REVERT: A 2180 MET cc_start: 0.7714 (tpt) cc_final: 0.7411 (tpt) REVERT: A 2238 MET cc_start: 0.5530 (tpt) cc_final: 0.5251 (tpp) REVERT: A 2321 MET cc_start: 0.6311 (mmm) cc_final: 0.5740 (mpp) REVERT: A 2324 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6676 (mt) REVERT: B 138 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8761 (pp) REVERT: C 57 TRP cc_start: 0.8198 (OUTLIER) cc_final: 0.7595 (t60) REVERT: C 108 ARG cc_start: 0.3695 (OUTLIER) cc_final: 0.3486 (ptt180) REVERT: C 164 CYS cc_start: 0.3582 (p) cc_final: 0.3008 (p) outliers start: 86 outliers final: 58 residues processed: 216 average time/residue: 0.2366 time to fit residues: 78.0632 Evaluate side-chains 209 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 140 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1847 VAL Chi-restraints excluded: chain A residue 1882 ILE Chi-restraints excluded: chain A residue 1889 TRP Chi-restraints excluded: chain A residue 1898 ASN Chi-restraints excluded: chain A residue 1926 MET Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2023 THR Chi-restraints excluded: chain A residue 2062 TRP Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2324 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 142 TYR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 153 optimal weight: 20.0000 chunk 156 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 693 HIS ** A1745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.194709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.153902 restraints weight = 24275.518| |-----------------------------------------------------------------------------| r_work (start): 0.4446 rms_B_bonded: 3.84 r_work: 0.4195 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13892 Z= 0.175 Angle : 0.731 10.757 18874 Z= 0.361 Chirality : 0.048 0.289 2071 Planarity : 0.005 0.077 2379 Dihedral : 8.887 107.384 2069 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.92 % Favored : 89.78 % Rotamer: Outliers : 6.28 % Allowed : 25.58 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.20), residues: 1653 helix: -1.72 (0.51), residues: 91 sheet: -1.14 (0.22), residues: 489 loop : -1.99 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 209 HIS 0.008 0.001 HIS A1697 PHE 0.027 0.002 PHE A1785 TYR 0.049 0.002 TYR A 159 ARG 0.003 0.000 ARG A2033 Details of bonding type rmsd link_NAG-ASN : bond 0.00695 ( 3) link_NAG-ASN : angle 5.49788 ( 9) link_BETA1-4 : bond 0.00698 ( 6) link_BETA1-4 : angle 2.70500 ( 18) link_ALPHA1-3 : bond 0.01110 ( 3) link_ALPHA1-3 : angle 2.34018 ( 9) hydrogen bonds : bond 0.03369 ( 315) hydrogen bonds : angle 6.93715 ( 822) SS BOND : bond 0.00456 ( 11) SS BOND : angle 1.04060 ( 22) covalent geometry : bond 0.00403 (13869) covalent geometry : angle 0.71438 (18816) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 141 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.5222 (OUTLIER) cc_final: 0.2903 (m-80) REVERT: A 261 MET cc_start: 0.8331 (tmm) cc_final: 0.8053 (tmm) REVERT: A 275 HIS cc_start: 0.3823 (OUTLIER) cc_final: 0.3055 (t-170) REVERT: A 287 LEU cc_start: 0.4200 (OUTLIER) cc_final: 0.3863 (mt) REVERT: A 292 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.5810 (mp) REVERT: A 324 HIS cc_start: 0.5821 (m-70) cc_final: 0.5457 (m90) REVERT: A 407 TYR cc_start: 0.5965 (OUTLIER) cc_final: 0.5328 (t80) REVERT: A 539 MET cc_start: 0.4827 (OUTLIER) cc_final: 0.3609 (tmm) REVERT: A 665 GLU cc_start: 0.8255 (mp0) cc_final: 0.7884 (mp0) REVERT: A 666 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.7065 (t0) REVERT: A 1794 ASP cc_start: 0.5862 (t0) cc_final: 0.5120 (p0) REVERT: A 1958 PHE cc_start: 0.5504 (OUTLIER) cc_final: 0.4690 (m-80) REVERT: A 2167 MET cc_start: 0.6175 (mmt) cc_final: 0.5801 (mmt) REVERT: A 2180 MET cc_start: 0.7655 (tpt) cc_final: 0.7318 (tpt) REVERT: A 2238 MET cc_start: 0.5590 (tpt) cc_final: 0.5225 (tpp) REVERT: A 2324 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6730 (mt) REVERT: B 138 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8765 (pp) REVERT: C 57 TRP cc_start: 0.8218 (OUTLIER) cc_final: 0.7593 (t60) REVERT: C 164 CYS cc_start: 0.3563 (p) cc_final: 0.2993 (p) outliers start: 92 outliers final: 68 residues processed: 212 average time/residue: 0.3483 time to fit residues: 115.0429 Evaluate side-chains 213 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 134 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1847 VAL Chi-restraints excluded: chain A residue 1882 ILE Chi-restraints excluded: chain A residue 1889 TRP Chi-restraints excluded: chain A residue 1898 ASN Chi-restraints excluded: chain A residue 1926 MET Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1958 PHE Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2023 THR Chi-restraints excluded: chain A residue 2062 TRP Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2324 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 164 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 110 optimal weight: 0.5980 chunk 154 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.196634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.151572 restraints weight = 23750.122| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 3.86 r_work: 0.4202 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6176 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13892 Z= 0.149 Angle : 0.730 10.544 18874 Z= 0.359 Chirality : 0.047 0.278 2071 Planarity : 0.005 0.080 2379 Dihedral : 8.615 104.720 2069 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.32 % Favored : 90.38 % Rotamer: Outliers : 5.80 % Allowed : 26.33 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.20), residues: 1653 helix: -1.64 (0.51), residues: 83 sheet: -1.15 (0.22), residues: 497 loop : -1.93 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 209 HIS 0.009 0.001 HIS A2005 PHE 0.022 0.001 PHE A1785 TYR 0.047 0.002 TYR A 159 ARG 0.003 0.000 ARG A 531 Details of bonding type rmsd link_NAG-ASN : bond 0.00654 ( 3) link_NAG-ASN : angle 5.32255 ( 9) link_BETA1-4 : bond 0.00743 ( 6) link_BETA1-4 : angle 2.72960 ( 18) link_ALPHA1-3 : bond 0.01128 ( 3) link_ALPHA1-3 : angle 2.28791 ( 9) hydrogen bonds : bond 0.03196 ( 315) hydrogen bonds : angle 6.84562 ( 822) SS BOND : bond 0.00388 ( 11) SS BOND : angle 1.23999 ( 22) covalent geometry : bond 0.00342 (13869) covalent geometry : angle 0.71412 (18816) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 140 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.5019 (OUTLIER) cc_final: 0.2309 (m-80) REVERT: A 261 MET cc_start: 0.8359 (tmm) cc_final: 0.8070 (tmm) REVERT: A 275 HIS cc_start: 0.3774 (OUTLIER) cc_final: 0.2983 (t-170) REVERT: A 279 VAL cc_start: 0.2625 (OUTLIER) cc_final: 0.2350 (t) REVERT: A 287 LEU cc_start: 0.4099 (OUTLIER) cc_final: 0.3769 (mt) REVERT: A 292 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.5877 (mp) REVERT: A 302 MET cc_start: 0.4787 (tpt) cc_final: 0.4307 (mmt) REVERT: A 324 HIS cc_start: 0.5848 (m-70) cc_final: 0.5498 (m90) REVERT: A 407 TYR cc_start: 0.6021 (OUTLIER) cc_final: 0.5401 (t80) REVERT: A 539 MET cc_start: 0.4741 (OUTLIER) cc_final: 0.3482 (tmm) REVERT: A 665 GLU cc_start: 0.8202 (mp0) cc_final: 0.7803 (mp0) REVERT: A 1794 ASP cc_start: 0.5856 (t0) cc_final: 0.5142 (p0) REVERT: A 2167 MET cc_start: 0.6227 (mmt) cc_final: 0.5832 (mmt) REVERT: A 2180 MET cc_start: 0.7519 (tpt) cc_final: 0.7213 (tpt) REVERT: A 2321 MET cc_start: 0.5943 (mmm) cc_final: 0.5479 (mpp) REVERT: A 2324 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6773 (mt) REVERT: B 138 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8780 (pp) REVERT: C 57 TRP cc_start: 0.8206 (OUTLIER) cc_final: 0.7643 (t60) REVERT: C 164 CYS cc_start: 0.3373 (p) cc_final: 0.2845 (p) outliers start: 85 outliers final: 67 residues processed: 209 average time/residue: 0.2354 time to fit residues: 74.8202 Evaluate side-chains 216 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 139 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1847 VAL Chi-restraints excluded: chain A residue 1882 ILE Chi-restraints excluded: chain A residue 1889 TRP Chi-restraints excluded: chain A residue 1898 ASN Chi-restraints excluded: chain A residue 1926 MET Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2023 THR Chi-restraints excluded: chain A residue 2062 TRP Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2257 VAL Chi-restraints excluded: chain A residue 2324 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 150 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 165 optimal weight: 0.7980 chunk 136 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.194459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.149980 restraints weight = 24197.935| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 4.03 r_work: 0.4190 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13892 Z= 0.172 Angle : 0.753 13.066 18874 Z= 0.369 Chirality : 0.048 0.269 2071 Planarity : 0.005 0.082 2379 Dihedral : 8.448 101.700 2069 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.04 % Favored : 89.66 % Rotamer: Outliers : 5.87 % Allowed : 26.74 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.20), residues: 1653 helix: -1.88 (0.48), residues: 89 sheet: -1.12 (0.23), residues: 491 loop : -2.01 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 209 HIS 0.011 0.001 HIS A2005 PHE 0.027 0.002 PHE A1785 TYR 0.051 0.002 TYR A 159 ARG 0.012 0.000 ARG C 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00665 ( 3) link_NAG-ASN : angle 5.29793 ( 9) link_BETA1-4 : bond 0.00732 ( 6) link_BETA1-4 : angle 2.79514 ( 18) link_ALPHA1-3 : bond 0.01112 ( 3) link_ALPHA1-3 : angle 2.34090 ( 9) hydrogen bonds : bond 0.03331 ( 315) hydrogen bonds : angle 6.95626 ( 822) SS BOND : bond 0.00438 ( 11) SS BOND : angle 1.14436 ( 22) covalent geometry : bond 0.00399 (13869) covalent geometry : angle 0.73687 (18816) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 139 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.5164 (OUTLIER) cc_final: 0.2627 (m-80) REVERT: A 124 LYS cc_start: 0.6612 (tptp) cc_final: 0.6183 (tppt) REVERT: A 261 MET cc_start: 0.8351 (tmm) cc_final: 0.8041 (tmm) REVERT: A 275 HIS cc_start: 0.3738 (OUTLIER) cc_final: 0.2948 (t-170) REVERT: A 287 LEU cc_start: 0.4189 (OUTLIER) cc_final: 0.3876 (mt) REVERT: A 292 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.5842 (mp) REVERT: A 302 MET cc_start: 0.4701 (tpt) cc_final: 0.4094 (mmt) REVERT: A 407 TYR cc_start: 0.6057 (OUTLIER) cc_final: 0.5419 (t80) REVERT: A 539 MET cc_start: 0.4804 (OUTLIER) cc_final: 0.3623 (tmm) REVERT: A 553 ILE cc_start: 0.6952 (OUTLIER) cc_final: 0.6146 (tp) REVERT: A 665 GLU cc_start: 0.8256 (mp0) cc_final: 0.7997 (mp0) REVERT: A 1794 ASP cc_start: 0.5721 (t0) cc_final: 0.5048 (p0) REVERT: A 1952 ASN cc_start: 0.7882 (t0) cc_final: 0.7201 (t0) REVERT: A 2033 ARG cc_start: 0.7124 (ptt90) cc_final: 0.6611 (ptp-110) REVERT: A 2167 MET cc_start: 0.6127 (mmt) cc_final: 0.5768 (mmt) REVERT: A 2180 MET cc_start: 0.7425 (tpt) cc_final: 0.7109 (tpt) REVERT: A 2238 MET cc_start: 0.5539 (tpt) cc_final: 0.5130 (tpp) REVERT: A 2321 MET cc_start: 0.5842 (mmm) cc_final: 0.5420 (mpp) REVERT: A 2324 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6782 (mt) REVERT: B 88 TYR cc_start: 0.5898 (m-80) cc_final: 0.5519 (m-80) REVERT: B 138 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8731 (pp) REVERT: C 57 TRP cc_start: 0.8209 (OUTLIER) cc_final: 0.7654 (t60) REVERT: C 164 CYS cc_start: 0.3232 (p) cc_final: 0.2741 (p) outliers start: 86 outliers final: 70 residues processed: 204 average time/residue: 0.3986 time to fit residues: 125.1926 Evaluate side-chains 215 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 135 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1777 ASN Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1847 VAL Chi-restraints excluded: chain A residue 1882 ILE Chi-restraints excluded: chain A residue 1889 TRP Chi-restraints excluded: chain A residue 1898 ASN Chi-restraints excluded: chain A residue 1921 ILE Chi-restraints excluded: chain A residue 1926 MET Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2023 THR Chi-restraints excluded: chain A residue 2062 TRP Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2086 THR Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2124 MET Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2257 VAL Chi-restraints excluded: chain A residue 2324 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 152 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 93 optimal weight: 0.0170 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 overall best weight: 0.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4991 r_free = 0.4991 target = 0.196733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.151473 restraints weight = 23663.632| |-----------------------------------------------------------------------------| r_work (start): 0.4415 rms_B_bonded: 4.01 r_work: 0.4228 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6175 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13892 Z= 0.154 Angle : 0.741 11.684 18874 Z= 0.362 Chirality : 0.048 0.265 2071 Planarity : 0.005 0.085 2379 Dihedral : 8.209 98.924 2069 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.74 % Favored : 89.96 % Rotamer: Outliers : 5.73 % Allowed : 26.47 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.20), residues: 1653 helix: -1.91 (0.48), residues: 89 sheet: -1.11 (0.22), residues: 495 loop : -1.96 (0.19), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 209 HIS 0.010 0.001 HIS A2005 PHE 0.023 0.002 PHE A1785 TYR 0.050 0.002 TYR A 159 ARG 0.011 0.000 ARG C 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00659 ( 3) link_NAG-ASN : angle 5.19715 ( 9) link_BETA1-4 : bond 0.00763 ( 6) link_BETA1-4 : angle 2.83306 ( 18) link_ALPHA1-3 : bond 0.01123 ( 3) link_ALPHA1-3 : angle 2.31069 ( 9) hydrogen bonds : bond 0.03229 ( 315) hydrogen bonds : angle 6.86332 ( 822) SS BOND : bond 0.00394 ( 11) SS BOND : angle 1.01686 ( 22) covalent geometry : bond 0.00356 (13869) covalent geometry : angle 0.72538 (18816) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 136 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.5030 (OUTLIER) cc_final: 0.2442 (m-80) REVERT: A 124 LYS cc_start: 0.6597 (tptp) cc_final: 0.6174 (tppt) REVERT: A 261 MET cc_start: 0.8263 (tmm) cc_final: 0.7967 (tmm) REVERT: A 275 HIS cc_start: 0.3739 (OUTLIER) cc_final: 0.2909 (t-170) REVERT: A 279 VAL cc_start: 0.2615 (OUTLIER) cc_final: 0.2346 (t) REVERT: A 287 LEU cc_start: 0.4180 (OUTLIER) cc_final: 0.3849 (mt) REVERT: A 292 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.5751 (mp) REVERT: A 302 MET cc_start: 0.4618 (tpt) cc_final: 0.4293 (tpt) REVERT: A 407 TYR cc_start: 0.6055 (OUTLIER) cc_final: 0.5426 (t80) REVERT: A 539 MET cc_start: 0.4801 (OUTLIER) cc_final: 0.3588 (tmm) REVERT: A 553 ILE cc_start: 0.7030 (OUTLIER) cc_final: 0.6220 (tp) REVERT: A 665 GLU cc_start: 0.8178 (mp0) cc_final: 0.7745 (mp0) REVERT: A 666 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.7026 (t0) REVERT: A 1772 MET cc_start: 0.6555 (tmm) cc_final: 0.6150 (ttp) REVERT: A 1794 ASP cc_start: 0.5800 (t0) cc_final: 0.5093 (p0) REVERT: A 1952 ASN cc_start: 0.7852 (t0) cc_final: 0.7135 (t0) REVERT: A 2033 ARG cc_start: 0.7099 (ptt90) cc_final: 0.6529 (ptp-110) REVERT: A 2167 MET cc_start: 0.6168 (mmt) cc_final: 0.5808 (mmt) REVERT: A 2180 MET cc_start: 0.7766 (tpt) cc_final: 0.7470 (tpt) REVERT: A 2321 MET cc_start: 0.6357 (mmm) cc_final: 0.5804 (mpp) REVERT: A 2324 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6666 (mt) REVERT: B 88 TYR cc_start: 0.5894 (m-80) cc_final: 0.5461 (m-80) REVERT: C 57 TRP cc_start: 0.8254 (OUTLIER) cc_final: 0.7595 (t60) REVERT: C 164 CYS cc_start: 0.3606 (p) cc_final: 0.3029 (p) outliers start: 84 outliers final: 67 residues processed: 202 average time/residue: 0.2378 time to fit residues: 73.1707 Evaluate side-chains 213 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 135 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1777 ASN Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1847 VAL Chi-restraints excluded: chain A residue 1882 ILE Chi-restraints excluded: chain A residue 1889 TRP Chi-restraints excluded: chain A residue 1898 ASN Chi-restraints excluded: chain A residue 1926 MET Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2023 THR Chi-restraints excluded: chain A residue 2062 TRP Chi-restraints excluded: chain A residue 2086 THR Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2124 MET Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2257 VAL Chi-restraints excluded: chain A residue 2324 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 13 optimal weight: 0.6980 chunk 162 optimal weight: 0.0770 chunk 136 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5000 r_free = 0.5000 target = 0.197712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.153650 restraints weight = 23778.693| |-----------------------------------------------------------------------------| r_work (start): 0.4450 rms_B_bonded: 3.98 r_work: 0.4251 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6134 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13892 Z= 0.142 Angle : 0.735 13.794 18874 Z= 0.358 Chirality : 0.047 0.261 2071 Planarity : 0.005 0.083 2379 Dihedral : 7.882 95.698 2069 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.44 % Favored : 90.26 % Rotamer: Outliers : 5.66 % Allowed : 26.74 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.20), residues: 1653 helix: -1.92 (0.48), residues: 89 sheet: -1.05 (0.22), residues: 496 loop : -1.91 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 209 HIS 0.008 0.001 HIS A2005 PHE 0.021 0.001 PHE A1785 TYR 0.020 0.002 TYR B 92 ARG 0.012 0.000 ARG C 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00607 ( 3) link_NAG-ASN : angle 5.07377 ( 9) link_BETA1-4 : bond 0.00744 ( 6) link_BETA1-4 : angle 2.86603 ( 18) link_ALPHA1-3 : bond 0.01233 ( 3) link_ALPHA1-3 : angle 2.25076 ( 9) hydrogen bonds : bond 0.03112 ( 315) hydrogen bonds : angle 6.76746 ( 822) SS BOND : bond 0.00393 ( 11) SS BOND : angle 0.95430 ( 22) covalent geometry : bond 0.00326 (13869) covalent geometry : angle 0.72020 (18816) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9540.47 seconds wall clock time: 172 minutes 41.94 seconds (10361.94 seconds total)