Starting phenix.real_space_refine on Sun Aug 24 03:34:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmp_41397/08_2025/8tmp_41397.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmp_41397/08_2025/8tmp_41397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tmp_41397/08_2025/8tmp_41397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmp_41397/08_2025/8tmp_41397.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tmp_41397/08_2025/8tmp_41397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmp_41397/08_2025/8tmp_41397.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 793 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 2 5.21 5 S 59 5.16 5 C 10484 2.51 5 N 2628 2.21 5 O 2968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16141 Number of models: 1 Model: "" Number of chains: 9 Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 803 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "H" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 969 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "A" Number of atoms: 2804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2804 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain: "B" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2925 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain: "C" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2812 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 13, 'TRANS': 322} Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2909 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 15, 'TRANS': 333} Chain: "E" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2917 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 15, 'TRANS': 334} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.96, per 1000 atoms: 0.25 Number of scatterers: 16141 At special positions: 0 Unit cell: (121.182, 144.568, 138.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 59 16.00 Mg 2 11.99 O 2968 8.00 N 2628 7.00 C 10484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 442.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3746 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 11 sheets defined 52.5% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'H' and resid 31 through 34 Processing helix chain 'A' and resid 46 through 51 removed outlier: 3.992A pdb=" N VAL A 50 " --> pdb=" O ASP A 46 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 46 through 51' Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 69 through 81 removed outlier: 4.005A pdb=" N VAL A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 removed outlier: 4.027A pdb=" N LEU A 87 " --> pdb=" O HIS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 157 Processing helix chain 'A' and resid 165 through 202 removed outlier: 3.896A pdb=" N GLU A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 237 Proline residue: A 227 - end of helix Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 247 through 281 removed outlier: 3.872A pdb=" N ASP A 253 " --> pdb=" O PRO A 249 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL A 254 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR A 255 " --> pdb=" O PHE A 251 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 299 Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 325 through 348 removed outlier: 3.580A pdb=" N LYS A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 54 removed outlier: 3.561A pdb=" N SER B 49 " --> pdb=" O ASP B 46 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU B 51 " --> pdb=" O GLU B 48 " (cutoff:3.500A) Proline residue: B 52 - end of helix Processing helix chain 'B' and resid 69 through 80 removed outlier: 3.701A pdb=" N VAL B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 117 through 120 Processing helix chain 'B' and resid 147 through 157 Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.696A pdb=" N LYS B 163 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 164 " --> pdb=" O ILE B 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 160 through 164' Processing helix chain 'B' and resid 165 through 202 removed outlier: 3.543A pdb=" N VAL B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 237 removed outlier: 3.592A pdb=" N VAL B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Proline residue: B 227 - end of helix Processing helix chain 'B' and resid 247 through 311 removed outlier: 3.600A pdb=" N PHE B 251 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG B 252 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASP B 253 " --> pdb=" O PRO B 249 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL B 254 " --> pdb=" O TYR B 250 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 326 through 348 Processing helix chain 'C' and resid 69 through 80 removed outlier: 3.967A pdb=" N VAL C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 86 through 92 removed outlier: 3.557A pdb=" N ASN C 92 " --> pdb=" O GLU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 removed outlier: 3.806A pdb=" N ARG C 151 " --> pdb=" O PHE C 147 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU C 152 " --> pdb=" O ASP C 148 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 153 " --> pdb=" O PRO C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 164 removed outlier: 4.011A pdb=" N LYS C 164 " --> pdb=" O ILE C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 202 removed outlier: 3.633A pdb=" N LEU C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 238 Proline residue: C 227 - end of helix removed outlier: 3.613A pdb=" N ASP C 238 " --> pdb=" O SER C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 311 removed outlier: 3.558A pdb=" N ASP C 253 " --> pdb=" O PRO C 249 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 254 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP C 277 " --> pdb=" O SER C 273 " (cutoff:3.500A) Proline residue: C 303 - end of helix Processing helix chain 'C' and resid 326 through 349 removed outlier: 3.603A pdb=" N GLY C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS C 348 " --> pdb=" O TYR C 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 54 Proline residue: D 52 - end of helix Processing helix chain 'D' and resid 69 through 80 removed outlier: 3.996A pdb=" N VAL D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'D' and resid 147 through 157 Processing helix chain 'D' and resid 165 through 202 removed outlier: 3.606A pdb=" N LEU D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 239 removed outlier: 4.277A pdb=" N VAL D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLN D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR D 224 " --> pdb=" O GLU D 220 " (cutoff:3.500A) Proline residue: D 227 - end of helix removed outlier: 3.620A pdb=" N VAL D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 312 removed outlier: 3.555A pdb=" N PHE D 251 " --> pdb=" O THR D 247 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) Proline residue: D 303 - end of helix Processing helix chain 'D' and resid 325 through 345 Processing helix chain 'E' and resid 46 through 56 removed outlier: 3.646A pdb=" N SER E 49 " --> pdb=" O ASP E 46 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU E 51 " --> pdb=" O GLU E 48 " (cutoff:3.500A) Proline residue: E 52 - end of helix removed outlier: 3.925A pdb=" N ASP E 55 " --> pdb=" O PRO E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 81 removed outlier: 3.788A pdb=" N VAL E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 92 Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 165 through 202 removed outlier: 3.525A pdb=" N LEU E 169 " --> pdb=" O ARG E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 237 removed outlier: 3.568A pdb=" N VAL E 208 " --> pdb=" O GLU E 204 " (cutoff:3.500A) Proline residue: E 227 - end of helix removed outlier: 3.819A pdb=" N GLU E 230 " --> pdb=" O TRP E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 313 removed outlier: 3.934A pdb=" N LEU E 276 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP E 277 " --> pdb=" O SER E 273 " (cutoff:3.500A) Proline residue: E 303 - end of helix Processing helix chain 'E' and resid 325 through 346 removed outlier: 3.821A pdb=" N VAL E 329 " --> pdb=" O TRP E 325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AA2, first strand: chain 'L' and resid 11 through 13 removed outlier: 7.032A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 11 through 13 removed outlier: 7.032A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.595A pdb=" N LEU H 21 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 14 through 15 removed outlier: 3.660A pdb=" N SER H 36 " --> pdb=" O SER H 102 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 14 through 15 removed outlier: 6.556A pdb=" N CYS H 99 " --> pdb=" O TRP H 119 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TRP H 119 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG H 101 " --> pdb=" O ASP H 117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 39 through 44 removed outlier: 4.444A pdb=" N GLU A 121 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASP A 116 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 44 removed outlier: 6.615A pdb=" N THR B 60 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N MET B 138 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE B 62 " --> pdb=" O MET B 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 39 through 44 removed outlier: 3.563A pdb=" N LYS C 98 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 42 through 44 removed outlier: 5.893A pdb=" N THR D 60 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N MET D 138 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE D 62 " --> pdb=" O MET D 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 39 through 44 removed outlier: 6.661A pdb=" N THR E 60 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N MET E 138 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE E 62 " --> pdb=" O MET E 138 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLN E 140 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE E 64 " --> pdb=" O GLN E 140 " (cutoff:3.500A) 991 hydrogen bonds defined for protein. 2850 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: 2.34 Time building geometry restraints manager: 1.54 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: 4999 1.34 - 1.46: 2375 1.46 - 1.57: 9023 1.57 - 1.69: 0 1.69 - 1.81: 109 Bond restraints: 16506 Sorted by residual: bond pdb=" C LEU B 51 " pdb=" N PRO B 52 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.08e-02 8.57e+03 2.83e+00 bond pdb=" C LEU E 51 " pdb=" N PRO E 52 " ideal model delta sigma weight residual 1.337 1.351 -0.015 9.80e-03 1.04e+04 2.25e+00 bond pdb=" CB MET B 291 " pdb=" CG MET B 291 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.12e+00 bond pdb=" SD MET C 291 " pdb=" CE MET C 291 " ideal model delta sigma weight residual 1.791 1.758 0.033 2.50e-02 1.60e+03 1.73e+00 bond pdb=" CB PRO C 59 " pdb=" CG PRO C 59 " ideal model delta sigma weight residual 1.492 1.556 -0.064 5.00e-02 4.00e+02 1.62e+00 ... (remaining 16501 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 22146 2.34 - 4.68: 202 4.68 - 7.02: 27 7.02 - 9.36: 2 9.36 - 11.70: 3 Bond angle restraints: 22380 Sorted by residual: angle pdb=" CB MET B 291 " pdb=" CG MET B 291 " pdb=" SD MET B 291 " ideal model delta sigma weight residual 112.70 101.00 11.70 3.00e+00 1.11e-01 1.52e+01 angle pdb=" CB MET C 291 " pdb=" CG MET C 291 " pdb=" SD MET C 291 " ideal model delta sigma weight residual 112.70 103.04 9.66 3.00e+00 1.11e-01 1.04e+01 angle pdb=" C ARG B 237 " pdb=" N ASP B 238 " pdb=" CA ASP B 238 " ideal model delta sigma weight residual 121.54 127.67 -6.13 1.91e+00 2.74e-01 1.03e+01 angle pdb=" C PHE C 147 " pdb=" N ASP C 148 " pdb=" CA ASP C 148 " ideal model delta sigma weight residual 120.06 123.69 -3.63 1.19e+00 7.06e-01 9.29e+00 angle pdb=" C LEU B 235 " pdb=" N TYR B 236 " pdb=" CA TYR B 236 " ideal model delta sigma weight residual 122.38 117.12 5.26 1.81e+00 3.05e-01 8.45e+00 ... (remaining 22375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 8815 18.00 - 36.00: 918 36.00 - 54.00: 161 54.00 - 72.00: 16 72.00 - 90.00: 15 Dihedral angle restraints: 9925 sinusoidal: 4130 harmonic: 5795 Sorted by residual: dihedral pdb=" CA MET B 318 " pdb=" C MET B 318 " pdb=" N PRO B 319 " pdb=" CA PRO B 319 " ideal model delta harmonic sigma weight residual 180.00 160.26 19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA LYS B 349 " pdb=" C LYS B 349 " pdb=" N TRP B 350 " pdb=" CA TRP B 350 " ideal model delta harmonic sigma weight residual 180.00 160.40 19.60 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA LEU E 321 " pdb=" C LEU E 321 " pdb=" N ARG E 322 " pdb=" CA ARG E 322 " ideal model delta harmonic sigma weight residual -180.00 -162.70 -17.30 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 9922 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1518 0.030 - 0.059: 647 0.059 - 0.089: 243 0.089 - 0.118: 110 0.118 - 0.148: 25 Chirality restraints: 2543 Sorted by residual: chirality pdb=" CA PRO C 84 " pdb=" N PRO C 84 " pdb=" C PRO C 84 " pdb=" CB PRO C 84 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA ILE L 22 " pdb=" N ILE L 22 " pdb=" C ILE L 22 " pdb=" CB ILE L 22 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA TYR D 327 " pdb=" N TYR D 327 " pdb=" C TYR D 327 " pdb=" CB TYR D 327 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.50e-01 ... (remaining 2540 not shown) Planarity restraints: 2800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 318 " -0.046 5.00e-02 4.00e+02 7.07e-02 8.00e+00 pdb=" N PRO D 319 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO D 319 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 319 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 58 " -0.035 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO C 59 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 59 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 59 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 202 " -0.031 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO C 203 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 203 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 203 " -0.027 5.00e-02 4.00e+02 ... (remaining 2797 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 897 2.73 - 3.27: 16487 3.27 - 3.82: 26863 3.82 - 4.36: 31015 4.36 - 4.90: 54631 Nonbonded interactions: 129893 Sorted by model distance: nonbonded pdb=" O LYS C 111 " pdb=" OH TYR C 181 " model vdw 2.189 3.040 nonbonded pdb=" O PRO A 319 " pdb=" NE1 TRP A 323 " model vdw 2.224 3.120 nonbonded pdb=" O GLU C 88 " pdb=" ND2 ASN C 92 " model vdw 2.239 3.120 nonbonded pdb=" OE2 GLU D 186 " pdb=" N SER E 7 " model vdw 2.251 3.120 nonbonded pdb=" OH TYR C 115 " pdb=" OE1 GLU C 191 " model vdw 2.255 3.040 ... (remaining 129888 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 'A' and resid 16 through 350) selection = (chain 'B' and resid 16 through 350) selection = (chain 'C' and resid 16 through 350) selection = (chain 'D' and resid 16 through 350) selection = (chain 'E' and resid 16 through 350) } 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=0.49 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: 4.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.490 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 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 : 0.003 0.064 16508 Z= 0.135 Angle : 0.583 11.698 22384 Z= 0.306 Chirality : 0.041 0.148 2543 Planarity : 0.005 0.071 2800 Dihedral : 14.779 89.996 6173 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.64 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.20), residues: 1940 helix: 2.35 (0.17), residues: 949 sheet: 0.45 (0.28), residues: 360 loop : -1.80 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 90 TYR 0.021 0.001 TYR C 19 PHE 0.025 0.001 PHE D 182 TRP 0.029 0.001 TRP B 350 HIS 0.010 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00287 (16506) covalent geometry : angle 0.58241 (22380) SS BOND : bond 0.00363 ( 2) SS BOND : angle 0.97464 ( 4) hydrogen bonds : bond 0.10804 ( 984) hydrogen bonds : angle 5.34043 ( 2850) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 496 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 4 GLN cc_start: 0.7521 (tt0) cc_final: 0.7094 (tt0) REVERT: L 19 ARG cc_start: 0.7550 (mtp-110) cc_final: 0.7303 (mtp-110) REVERT: L 29 SER cc_start: 0.8964 (m) cc_final: 0.8697 (m) REVERT: L 43 LYS cc_start: 0.8046 (mmmm) cc_final: 0.7518 (mptt) REVERT: L 61 SER cc_start: 0.8599 (t) cc_final: 0.8303 (m) REVERT: L 70 THR cc_start: 0.7763 (p) cc_final: 0.7535 (p) REVERT: H 22 ARG cc_start: 0.8052 (ttp-110) cc_final: 0.7439 (ttt180) REVERT: H 65 ASP cc_start: 0.8109 (m-30) cc_final: 0.7838 (m-30) REVERT: H 79 LYS cc_start: 0.7991 (mmtp) cc_final: 0.7609 (mttp) REVERT: A 186 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7094 (mt-10) REVERT: A 192 ILE cc_start: 0.8047 (mt) cc_final: 0.7760 (tt) REVERT: A 219 VAL cc_start: 0.8301 (t) cc_final: 0.8083 (t) REVERT: A 230 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6769 (mt-10) REVERT: A 245 LYS cc_start: 0.7054 (mmtm) cc_final: 0.6440 (mtpp) REVERT: A 291 MET cc_start: 0.7677 (mmm) cc_final: 0.7455 (mmm) REVERT: A 310 ILE cc_start: 0.7607 (mm) cc_final: 0.7384 (mm) REVERT: A 322 ARG cc_start: 0.5478 (mmm160) cc_final: 0.4542 (mmm160) REVERT: B 1 MET cc_start: 0.6460 (tpt) cc_final: 0.6086 (mmt) REVERT: B 9 LYS cc_start: 0.7951 (mtmt) cc_final: 0.7477 (mmtm) REVERT: B 48 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6561 (mm-30) REVERT: B 100 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7330 (mm-30) REVERT: B 123 GLU cc_start: 0.7137 (mp0) cc_final: 0.6707 (mm-30) REVERT: B 163 LYS cc_start: 0.8376 (pttt) cc_final: 0.8169 (pttp) REVERT: B 187 LYS cc_start: 0.7924 (mtmt) cc_final: 0.7599 (mtmt) REVERT: B 204 GLU cc_start: 0.5902 (pt0) cc_final: 0.5208 (mm-30) REVERT: B 222 ARG cc_start: 0.8214 (ttp-170) cc_final: 0.7945 (ttp-110) REVERT: B 237 ARG cc_start: 0.7323 (mtm180) cc_final: 0.6831 (mtp180) REVERT: B 318 MET cc_start: 0.4122 (mmp) cc_final: 0.3216 (mmp) REVERT: B 334 MET cc_start: 0.4752 (mmt) cc_final: 0.3817 (tmm) REVERT: C 116 ASP cc_start: 0.6422 (t0) cc_final: 0.6178 (t0) REVERT: C 147 PHE cc_start: 0.8127 (m-80) cc_final: 0.7871 (m-80) REVERT: C 152 GLU cc_start: 0.7305 (mp0) cc_final: 0.7015 (mp0) REVERT: C 167 ASP cc_start: 0.7869 (m-30) cc_final: 0.7623 (m-30) REVERT: C 202 ARG cc_start: 0.6929 (ptm160) cc_final: 0.6568 (ppt170) REVERT: C 244 GLU cc_start: 0.6749 (tp30) cc_final: 0.6538 (tp30) REVERT: C 245 LYS cc_start: 0.6473 (tptp) cc_final: 0.6133 (ttpp) REVERT: C 269 ARG cc_start: 0.6765 (ttp80) cc_final: 0.6415 (ttp80) REVERT: C 291 MET cc_start: 0.6668 (mmp) cc_final: 0.6382 (mmp) REVERT: D 22 LYS cc_start: 0.7740 (pttp) cc_final: 0.7379 (ptmm) REVERT: D 23 TYR cc_start: 0.7506 (m-80) cc_final: 0.7102 (m-80) REVERT: D 37 GLU cc_start: 0.6667 (pp20) cc_final: 0.6461 (pp20) REVERT: D 40 ARG cc_start: 0.5487 (mtp180) cc_final: 0.5058 (mtp85) REVERT: D 75 ARG cc_start: 0.6441 (tpt90) cc_final: 0.5991 (tpt90) REVERT: D 90 ILE cc_start: 0.8375 (mt) cc_final: 0.8064 (mt) REVERT: D 120 HIS cc_start: 0.7401 (m-70) cc_final: 0.6978 (m-70) REVERT: D 133 LYS cc_start: 0.7858 (tttt) cc_final: 0.7644 (ttmt) REVERT: D 156 TYR cc_start: 0.7418 (m-10) cc_final: 0.7211 (m-10) REVERT: D 163 LYS cc_start: 0.8555 (mtmt) cc_final: 0.8142 (mtpt) REVERT: D 181 TYR cc_start: 0.8266 (m-80) cc_final: 0.7545 (m-80) REVERT: D 183 VAL cc_start: 0.8007 (p) cc_final: 0.7733 (m) REVERT: D 197 GLU cc_start: 0.6050 (mt-10) cc_final: 0.5798 (mt-10) REVERT: D 220 GLU cc_start: 0.7772 (tm-30) cc_final: 0.6613 (mm-30) REVERT: D 226 TRP cc_start: 0.8235 (m100) cc_final: 0.7817 (m100) REVERT: D 233 SER cc_start: 0.8464 (t) cc_final: 0.7883 (p) REVERT: D 286 LYS cc_start: 0.7639 (tptt) cc_final: 0.7347 (mtpp) REVERT: D 289 GLU cc_start: 0.6413 (mm-30) cc_final: 0.5929 (mm-30) REVERT: D 302 MET cc_start: 0.8184 (tpp) cc_final: 0.7980 (mmm) REVERT: E 54 ARG cc_start: 0.8069 (ptm160) cc_final: 0.7741 (ptt180) REVERT: E 89 ASP cc_start: 0.8119 (m-30) cc_final: 0.7832 (m-30) REVERT: E 121 GLU cc_start: 0.7008 (pt0) cc_final: 0.6639 (pm20) REVERT: E 133 LYS cc_start: 0.7795 (ttmt) cc_final: 0.7449 (tptp) REVERT: E 162 ARG cc_start: 0.7836 (mtp180) cc_final: 0.7413 (mtp180) REVERT: E 220 GLU cc_start: 0.7176 (tt0) cc_final: 0.6957 (tp30) REVERT: E 245 LYS cc_start: 0.8368 (ttmm) cc_final: 0.8052 (mtpp) REVERT: E 283 VAL cc_start: 0.8503 (t) cc_final: 0.8281 (t) REVERT: E 291 MET cc_start: 0.6865 (tpp) cc_final: 0.5767 (ttm) outliers start: 0 outliers final: 0 residues processed: 496 average time/residue: 0.1280 time to fit residues: 91.2425 Evaluate side-chains 414 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN C 95 GLN C 217 ASN E 285 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.175915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.144362 restraints weight = 19231.422| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.26 r_work: 0.3206 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 16508 Z= 0.276 Angle : 0.691 12.143 22384 Z= 0.359 Chirality : 0.046 0.169 2543 Planarity : 0.006 0.055 2800 Dihedral : 4.669 21.851 2166 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.05 % Favored : 94.85 % Rotamer: Outliers : 2.81 % Allowed : 10.35 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.19), residues: 1940 helix: 1.93 (0.16), residues: 951 sheet: 0.46 (0.28), residues: 349 loop : -1.95 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 222 TYR 0.019 0.002 TYR H 106 PHE 0.027 0.002 PHE D 182 TRP 0.024 0.002 TRP B 350 HIS 0.017 0.002 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00671 (16506) covalent geometry : angle 0.69040 (22380) SS BOND : bond 0.00244 ( 2) SS BOND : angle 1.59607 ( 4) hydrogen bonds : bond 0.06144 ( 984) hydrogen bonds : angle 4.78922 ( 2850) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 444 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 43 LYS cc_start: 0.8430 (mmmm) cc_final: 0.8030 (mptt) REVERT: L 61 SER cc_start: 0.8802 (t) cc_final: 0.8530 (m) REVERT: H 22 ARG cc_start: 0.8085 (ttp-110) cc_final: 0.7544 (ttt180) REVERT: H 42 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7920 (tp40) REVERT: H 118 TYR cc_start: 0.9001 (m-80) cc_final: 0.8787 (m-80) REVERT: A 98 LYS cc_start: 0.8704 (pttt) cc_final: 0.8392 (pttp) REVERT: A 177 LEU cc_start: 0.9079 (tp) cc_final: 0.8818 (tp) REVERT: A 186 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7659 (mt-10) REVERT: A 191 GLU cc_start: 0.8527 (tp30) cc_final: 0.8320 (mm-30) REVERT: A 219 VAL cc_start: 0.8768 (t) cc_final: 0.8512 (t) REVERT: A 231 VAL cc_start: 0.9091 (t) cc_final: 0.8809 (t) REVERT: A 245 LYS cc_start: 0.7235 (mmtm) cc_final: 0.6626 (mtpp) REVERT: A 266 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7912 (mt-10) REVERT: A 291 MET cc_start: 0.8316 (mmm) cc_final: 0.7852 (mmm) REVERT: A 322 ARG cc_start: 0.5536 (mmm160) cc_final: 0.4841 (mmm160) REVERT: B 1 MET cc_start: 0.6831 (tpt) cc_final: 0.6300 (mmt) REVERT: B 48 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7200 (mm-30) REVERT: B 65 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.9020 (m) REVERT: B 163 LYS cc_start: 0.8527 (pttt) cc_final: 0.8240 (pttp) REVERT: B 187 LYS cc_start: 0.8227 (mtmt) cc_final: 0.7956 (mtmt) REVERT: B 204 GLU cc_start: 0.6427 (pt0) cc_final: 0.5717 (mm-30) REVERT: B 216 ARG cc_start: 0.7204 (mtm110) cc_final: 0.6558 (mtp85) REVERT: B 244 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6700 (mt-10) REVERT: C 28 GLU cc_start: 0.6166 (tp30) cc_final: 0.5718 (tp30) REVERT: C 35 SER cc_start: 0.6111 (p) cc_final: 0.5769 (m) REVERT: C 36 ILE cc_start: 0.6749 (mp) cc_final: 0.6206 (mp) REVERT: C 70 THR cc_start: 0.7369 (m) cc_final: 0.6994 (t) REVERT: C 116 ASP cc_start: 0.6648 (t0) cc_final: 0.6407 (t0) REVERT: C 137 LEU cc_start: 0.7223 (tt) cc_final: 0.6890 (tt) REVERT: C 202 ARG cc_start: 0.7215 (ptm160) cc_final: 0.6355 (pmt170) REVERT: C 244 GLU cc_start: 0.6910 (tp30) cc_final: 0.6655 (tp30) REVERT: C 245 LYS cc_start: 0.6679 (tptp) cc_final: 0.6389 (ttpp) REVERT: C 269 ARG cc_start: 0.7601 (ttp80) cc_final: 0.7077 (ttp80) REVERT: C 344 TYR cc_start: 0.5392 (t80) cc_final: 0.4642 (t80) REVERT: D 22 LYS cc_start: 0.7917 (pttp) cc_final: 0.7615 (ptmm) REVERT: D 23 TYR cc_start: 0.7677 (m-80) cc_final: 0.7315 (m-80) REVERT: D 37 GLU cc_start: 0.7179 (pp20) cc_final: 0.6908 (pp20) REVERT: D 40 ARG cc_start: 0.6480 (mtp180) cc_final: 0.5960 (mtp85) REVERT: D 75 ARG cc_start: 0.6394 (tpt90) cc_final: 0.6152 (tpt90) REVERT: D 120 HIS cc_start: 0.8077 (m-70) cc_final: 0.7527 (m-70) REVERT: D 181 TYR cc_start: 0.8671 (m-80) cc_final: 0.7973 (m-80) REVERT: D 233 SER cc_start: 0.8932 (t) cc_final: 0.8442 (p) REVERT: D 286 LYS cc_start: 0.8184 (tptt) cc_final: 0.7778 (mtpp) REVERT: D 289 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6898 (mm-30) REVERT: E 89 ASP cc_start: 0.8517 (m-30) cc_final: 0.8313 (m-30) REVERT: E 121 GLU cc_start: 0.7611 (pt0) cc_final: 0.7038 (pm20) REVERT: E 133 LYS cc_start: 0.7827 (ttmt) cc_final: 0.7506 (tptp) REVERT: E 245 LYS cc_start: 0.8700 (ttmm) cc_final: 0.8389 (tptp) REVERT: E 288 ASN cc_start: 0.8700 (m-40) cc_final: 0.8380 (m-40) REVERT: E 291 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7790 (ttm) outliers start: 51 outliers final: 35 residues processed: 465 average time/residue: 0.1368 time to fit residues: 91.6123 Evaluate side-chains 445 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 407 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 342 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 146 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 chunk 160 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 172 optimal weight: 0.0470 chunk 56 optimal weight: 0.5980 chunk 164 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN C 314 ASN E 120 HIS E 285 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.178988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.147076 restraints weight = 19349.325| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.15 r_work: 0.3263 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16508 Z= 0.145 Angle : 0.558 9.762 22384 Z= 0.294 Chirality : 0.042 0.183 2543 Planarity : 0.005 0.048 2800 Dihedral : 4.409 17.804 2166 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.33 % Favored : 95.57 % Rotamer: Outliers : 2.37 % Allowed : 14.75 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.19), residues: 1940 helix: 2.29 (0.16), residues: 951 sheet: 0.51 (0.28), residues: 350 loop : -1.93 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 5 TYR 0.017 0.001 TYR B 236 PHE 0.014 0.001 PHE B 301 TRP 0.014 0.001 TRP B 350 HIS 0.008 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00324 (16506) covalent geometry : angle 0.55754 (22380) SS BOND : bond 0.00148 ( 2) SS BOND : angle 0.95031 ( 4) hydrogen bonds : bond 0.05248 ( 984) hydrogen bonds : angle 4.50449 ( 2850) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 426 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 43 LYS cc_start: 0.8393 (mmmm) cc_final: 0.7994 (mptt) REVERT: L 61 SER cc_start: 0.8697 (t) cc_final: 0.8414 (m) REVERT: H 22 ARG cc_start: 0.7909 (ttp-110) cc_final: 0.7460 (ttt180) REVERT: H 79 LYS cc_start: 0.8187 (mttm) cc_final: 0.7827 (mttp) REVERT: H 90 ARG cc_start: 0.7972 (mtm180) cc_final: 0.7572 (mtt-85) REVERT: A 96 ARG cc_start: 0.7799 (mmt90) cc_final: 0.7548 (mmt90) REVERT: A 98 LYS cc_start: 0.8656 (pttt) cc_final: 0.8302 (pttp) REVERT: A 177 LEU cc_start: 0.8946 (tp) cc_final: 0.8699 (tp) REVERT: A 186 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7615 (mt-10) REVERT: A 219 VAL cc_start: 0.8689 (t) cc_final: 0.8429 (t) REVERT: A 245 LYS cc_start: 0.7220 (mmtm) cc_final: 0.6632 (mtpp) REVERT: A 253 ASP cc_start: 0.8132 (m-30) cc_final: 0.7907 (m-30) REVERT: A 266 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7867 (mt-10) REVERT: A 269 ARG cc_start: 0.8256 (ttm-80) cc_final: 0.7803 (ttm170) REVERT: A 291 MET cc_start: 0.8389 (mmm) cc_final: 0.8099 (mmp) REVERT: A 322 ARG cc_start: 0.5570 (mmm160) cc_final: 0.4547 (mmm160) REVERT: B 1 MET cc_start: 0.6904 (tpt) cc_final: 0.6360 (mmt) REVERT: B 48 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7199 (mm-30) REVERT: B 100 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7827 (mm-30) REVERT: B 187 LYS cc_start: 0.8078 (mtmt) cc_final: 0.7801 (mtmt) REVERT: B 210 ARG cc_start: 0.7308 (mtp85) cc_final: 0.6974 (mtp85) REVERT: B 216 ARG cc_start: 0.7226 (mtm110) cc_final: 0.6493 (mtp85) REVERT: B 334 MET cc_start: 0.5231 (mmt) cc_final: 0.4002 (ttt) REVERT: C 28 GLU cc_start: 0.6214 (tp30) cc_final: 0.5707 (tp30) REVERT: C 36 ILE cc_start: 0.6703 (mp) cc_final: 0.6202 (mp) REVERT: C 70 THR cc_start: 0.7327 (m) cc_final: 0.6803 (t) REVERT: C 95 GLN cc_start: 0.6406 (OUTLIER) cc_final: 0.5038 (tm-30) REVERT: C 116 ASP cc_start: 0.6663 (t0) cc_final: 0.6409 (t0) REVERT: C 137 LEU cc_start: 0.7205 (tt) cc_final: 0.6864 (tt) REVERT: C 147 PHE cc_start: 0.8380 (m-80) cc_final: 0.8144 (m-80) REVERT: C 202 ARG cc_start: 0.7156 (ptm160) cc_final: 0.6375 (pmt170) REVERT: C 244 GLU cc_start: 0.6815 (tp30) cc_final: 0.6489 (tp30) REVERT: C 269 ARG cc_start: 0.7531 (ttp80) cc_final: 0.6967 (ttp80) REVERT: C 344 TYR cc_start: 0.5391 (t80) cc_final: 0.4639 (t80) REVERT: D 22 LYS cc_start: 0.7899 (pttp) cc_final: 0.7548 (ptmm) REVERT: D 37 GLU cc_start: 0.7120 (pp20) cc_final: 0.6851 (pp20) REVERT: D 40 ARG cc_start: 0.6273 (mtp180) cc_final: 0.5669 (ttt90) REVERT: D 120 HIS cc_start: 0.7896 (m-70) cc_final: 0.7524 (m-70) REVERT: D 133 LYS cc_start: 0.8115 (tttt) cc_final: 0.7659 (tptt) REVERT: D 181 TYR cc_start: 0.8628 (m-80) cc_final: 0.7910 (m-80) REVERT: D 233 SER cc_start: 0.8844 (t) cc_final: 0.8397 (p) REVERT: D 286 LYS cc_start: 0.8130 (tptt) cc_final: 0.7737 (mtpp) REVERT: D 289 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6907 (mm-30) REVERT: D 302 MET cc_start: 0.8495 (tpp) cc_final: 0.8222 (mmm) REVERT: E 89 ASP cc_start: 0.8427 (m-30) cc_final: 0.8212 (m-30) REVERT: E 121 GLU cc_start: 0.7476 (pt0) cc_final: 0.6946 (pm20) REVERT: E 133 LYS cc_start: 0.7761 (ttmt) cc_final: 0.7476 (tptp) REVERT: E 245 LYS cc_start: 0.8646 (ttmm) cc_final: 0.8311 (tptp) outliers start: 43 outliers final: 29 residues processed: 444 average time/residue: 0.1316 time to fit residues: 84.6882 Evaluate side-chains 442 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 412 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain C residue 95 GLN Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 302 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 36 optimal weight: 0.0570 chunk 88 optimal weight: 0.6980 overall best weight: 0.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN D 74 GLN E 120 HIS E 140 GLN E 285 ASN E 288 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.177299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.145460 restraints weight = 19317.686| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.28 r_work: 0.3230 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16508 Z= 0.175 Angle : 0.569 9.913 22384 Z= 0.298 Chirality : 0.042 0.183 2543 Planarity : 0.005 0.046 2800 Dihedral : 4.379 18.523 2166 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.69 % Favored : 95.21 % Rotamer: Outliers : 3.85 % Allowed : 16.02 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.19), residues: 1940 helix: 2.24 (0.16), residues: 955 sheet: 0.46 (0.28), residues: 350 loop : -1.92 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 5 TYR 0.018 0.001 TYR H 106 PHE 0.018 0.002 PHE D 301 TRP 0.013 0.001 TRP C 226 HIS 0.009 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00410 (16506) covalent geometry : angle 0.56834 (22380) SS BOND : bond 0.00019 ( 2) SS BOND : angle 1.20746 ( 4) hydrogen bonds : bond 0.05335 ( 984) hydrogen bonds : angle 4.44297 ( 2850) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 417 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 43 LYS cc_start: 0.8363 (mmmm) cc_final: 0.7966 (mptt) REVERT: L 61 SER cc_start: 0.8693 (t) cc_final: 0.8419 (m) REVERT: H 22 ARG cc_start: 0.8010 (ttp-110) cc_final: 0.7552 (ttt180) REVERT: H 90 ARG cc_start: 0.8043 (mtm180) cc_final: 0.7732 (mtt-85) REVERT: A 54 ARG cc_start: 0.6166 (mtm110) cc_final: 0.5917 (mtp-110) REVERT: A 96 ARG cc_start: 0.7838 (mmt90) cc_final: 0.7633 (mmt90) REVERT: A 98 LYS cc_start: 0.8687 (pttt) cc_final: 0.8347 (pttp) REVERT: A 177 LEU cc_start: 0.9007 (tp) cc_final: 0.8759 (tp) REVERT: A 186 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7643 (mt-10) REVERT: A 219 VAL cc_start: 0.8751 (t) cc_final: 0.8433 (t) REVERT: A 245 LYS cc_start: 0.7248 (mmtm) cc_final: 0.6649 (mtpp) REVERT: A 291 MET cc_start: 0.8475 (mmm) cc_final: 0.8206 (mmm) REVERT: A 322 ARG cc_start: 0.5639 (mmm160) cc_final: 0.4588 (mmm160) REVERT: A 341 MET cc_start: 0.6500 (OUTLIER) cc_final: 0.6158 (mmm) REVERT: B 1 MET cc_start: 0.6794 (tpt) cc_final: 0.6421 (tpt) REVERT: B 48 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7218 (mm-30) REVERT: B 100 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7832 (mm-30) REVERT: B 187 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7884 (mtmt) REVERT: B 216 ARG cc_start: 0.7307 (mtm110) cc_final: 0.6539 (mtp85) REVERT: B 244 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6734 (mt-10) REVERT: C 28 GLU cc_start: 0.6255 (tp30) cc_final: 0.5750 (tp30) REVERT: C 36 ILE cc_start: 0.6753 (mp) cc_final: 0.6245 (mp) REVERT: C 70 THR cc_start: 0.7329 (m) cc_final: 0.7036 (m) REVERT: C 116 ASP cc_start: 0.6616 (t0) cc_final: 0.6373 (t0) REVERT: C 137 LEU cc_start: 0.7200 (tt) cc_final: 0.6861 (tt) REVERT: C 202 ARG cc_start: 0.7179 (ptm160) cc_final: 0.6381 (pmt170) REVERT: C 244 GLU cc_start: 0.6708 (tp30) cc_final: 0.6409 (tp30) REVERT: C 269 ARG cc_start: 0.7584 (ttp80) cc_final: 0.7031 (ttp80) REVERT: C 344 TYR cc_start: 0.5486 (t80) cc_final: 0.4813 (t80) REVERT: D 22 LYS cc_start: 0.7949 (pttp) cc_final: 0.7599 (ptmm) REVERT: D 37 GLU cc_start: 0.7134 (pp20) cc_final: 0.6885 (pp20) REVERT: D 40 ARG cc_start: 0.6319 (mtp180) cc_final: 0.5778 (ttt90) REVERT: D 87 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.7916 (mm) REVERT: D 120 HIS cc_start: 0.7947 (m-70) cc_final: 0.7563 (m-70) REVERT: D 133 LYS cc_start: 0.8151 (tttt) cc_final: 0.7686 (tptt) REVERT: D 181 TYR cc_start: 0.8664 (m-80) cc_final: 0.7934 (m-80) REVERT: D 233 SER cc_start: 0.8873 (t) cc_final: 0.8407 (p) REVERT: D 286 LYS cc_start: 0.8188 (tptt) cc_final: 0.7799 (mtpp) REVERT: D 289 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6866 (mm-30) REVERT: D 302 MET cc_start: 0.8544 (tpp) cc_final: 0.8266 (mmm) REVERT: D 341 MET cc_start: 0.4213 (mtp) cc_final: 0.3337 (mtm) REVERT: E 121 GLU cc_start: 0.7537 (pt0) cc_final: 0.7039 (pm20) REVERT: E 133 LYS cc_start: 0.7800 (ttmt) cc_final: 0.7506 (tptp) REVERT: E 245 LYS cc_start: 0.8663 (ttmm) cc_final: 0.8344 (tptp) REVERT: E 291 MET cc_start: 0.8026 (ttp) cc_final: 0.7820 (mtm) outliers start: 70 outliers final: 51 residues processed: 444 average time/residue: 0.1242 time to fit residues: 80.2088 Evaluate side-chains 456 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 403 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 342 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 14 optimal weight: 0.4980 chunk 174 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 HIS E 285 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.177992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.146092 restraints weight = 19236.505| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.20 r_work: 0.3246 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16508 Z= 0.167 Angle : 0.563 9.867 22384 Z= 0.294 Chirality : 0.042 0.192 2543 Planarity : 0.005 0.044 2800 Dihedral : 4.355 18.348 2166 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.48 % Favored : 95.41 % Rotamer: Outliers : 4.13 % Allowed : 17.56 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.19), residues: 1940 helix: 2.27 (0.16), residues: 955 sheet: 0.45 (0.28), residues: 341 loop : -1.92 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 19 TYR 0.017 0.001 TYR B 236 PHE 0.021 0.002 PHE C 147 TRP 0.014 0.001 TRP B 350 HIS 0.008 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00392 (16506) covalent geometry : angle 0.56286 (22380) SS BOND : bond 0.00076 ( 2) SS BOND : angle 0.88532 ( 4) hydrogen bonds : bond 0.05252 ( 984) hydrogen bonds : angle 4.39771 ( 2850) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 407 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 43 LYS cc_start: 0.8361 (mmmm) cc_final: 0.7948 (mptt) REVERT: L 61 SER cc_start: 0.8708 (t) cc_final: 0.8436 (m) REVERT: H 22 ARG cc_start: 0.7980 (ttp-110) cc_final: 0.7530 (ttt180) REVERT: H 42 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8173 (tp40) REVERT: H 90 ARG cc_start: 0.8056 (mtm180) cc_final: 0.7735 (mtt-85) REVERT: A 98 LYS cc_start: 0.8717 (pttt) cc_final: 0.8344 (pttp) REVERT: A 126 GLN cc_start: 0.8421 (tm-30) cc_final: 0.8202 (tm-30) REVERT: A 145 ASP cc_start: 0.8105 (p0) cc_final: 0.7753 (p0) REVERT: A 152 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7731 (mm-30) REVERT: A 177 LEU cc_start: 0.8999 (tp) cc_final: 0.8743 (tp) REVERT: A 186 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7706 (mt-10) REVERT: A 191 GLU cc_start: 0.8567 (tp30) cc_final: 0.8295 (mm-30) REVERT: A 219 VAL cc_start: 0.8709 (t) cc_final: 0.8420 (t) REVERT: A 245 LYS cc_start: 0.7257 (mmtm) cc_final: 0.6682 (mtpp) REVERT: A 322 ARG cc_start: 0.5631 (mmm160) cc_final: 0.4760 (mmm160) REVERT: B 1 MET cc_start: 0.6732 (tpt) cc_final: 0.6351 (tpt) REVERT: B 48 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7218 (mm-30) REVERT: B 100 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7814 (mm-30) REVERT: B 187 LYS cc_start: 0.8088 (mtmt) cc_final: 0.7847 (mtmt) REVERT: B 216 ARG cc_start: 0.7298 (mtm110) cc_final: 0.6473 (mtp85) REVERT: B 244 GLU cc_start: 0.7319 (mt-10) cc_final: 0.6767 (mt-10) REVERT: C 28 GLU cc_start: 0.6236 (tp30) cc_final: 0.5582 (tp30) REVERT: C 36 ILE cc_start: 0.6762 (mp) cc_final: 0.6260 (mp) REVERT: C 70 THR cc_start: 0.7280 (m) cc_final: 0.7017 (m) REVERT: C 116 ASP cc_start: 0.6605 (t0) cc_final: 0.6368 (t0) REVERT: C 137 LEU cc_start: 0.7210 (tt) cc_final: 0.6832 (tt) REVERT: C 202 ARG cc_start: 0.7157 (ptm160) cc_final: 0.6351 (pmt170) REVERT: C 269 ARG cc_start: 0.7551 (ttp80) cc_final: 0.7016 (ttp80) REVERT: C 344 TYR cc_start: 0.5522 (t80) cc_final: 0.4838 (t80) REVERT: D 22 LYS cc_start: 0.7982 (pttp) cc_final: 0.7629 (ptmm) REVERT: D 37 GLU cc_start: 0.7111 (pp20) cc_final: 0.6874 (pp20) REVERT: D 40 ARG cc_start: 0.6250 (mtp180) cc_final: 0.5723 (ttt90) REVERT: D 87 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7875 (mm) REVERT: D 120 HIS cc_start: 0.7898 (m-70) cc_final: 0.7496 (m-70) REVERT: D 133 LYS cc_start: 0.8131 (tttt) cc_final: 0.7667 (tptt) REVERT: D 181 TYR cc_start: 0.8648 (m-80) cc_final: 0.7956 (m-80) REVERT: D 233 SER cc_start: 0.8863 (t) cc_final: 0.8391 (p) REVERT: D 286 LYS cc_start: 0.8184 (tptt) cc_final: 0.7799 (mtpp) REVERT: D 289 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6863 (mm-30) REVERT: D 302 MET cc_start: 0.8619 (tpp) cc_final: 0.8322 (mmm) REVERT: E 121 GLU cc_start: 0.7648 (pt0) cc_final: 0.7100 (pm20) REVERT: E 133 LYS cc_start: 0.7788 (ttmt) cc_final: 0.7507 (tptp) REVERT: E 200 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8100 (mm) REVERT: E 245 LYS cc_start: 0.8659 (ttmm) cc_final: 0.8350 (tptp) outliers start: 75 outliers final: 57 residues processed: 445 average time/residue: 0.1399 time to fit residues: 89.9487 Evaluate side-chains 461 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 400 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 342 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 129 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 156 optimal weight: 0.8980 chunk 118 optimal weight: 0.5980 chunk 145 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 79 optimal weight: 0.0000 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN E 120 HIS E 285 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.178422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.146821 restraints weight = 19283.204| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.24 r_work: 0.3247 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16508 Z= 0.153 Angle : 0.556 9.141 22384 Z= 0.290 Chirality : 0.042 0.191 2543 Planarity : 0.005 0.059 2800 Dihedral : 4.297 17.965 2166 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.64 % Favored : 95.26 % Rotamer: Outliers : 4.13 % Allowed : 18.00 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.19), residues: 1940 helix: 2.33 (0.16), residues: 955 sheet: 0.51 (0.28), residues: 339 loop : -1.91 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 19 TYR 0.017 0.001 TYR B 236 PHE 0.020 0.002 PHE D 27 TRP 0.014 0.001 TRP B 350 HIS 0.006 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00353 (16506) covalent geometry : angle 0.55635 (22380) SS BOND : bond 0.00063 ( 2) SS BOND : angle 0.87002 ( 4) hydrogen bonds : bond 0.05121 ( 984) hydrogen bonds : angle 4.36416 ( 2850) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 405 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 43 LYS cc_start: 0.8355 (mmmm) cc_final: 0.7942 (mptt) REVERT: L 61 SER cc_start: 0.8720 (t) cc_final: 0.8445 (m) REVERT: H 22 ARG cc_start: 0.7953 (ttp-110) cc_final: 0.7489 (ttt180) REVERT: H 42 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8199 (tp40) REVERT: H 90 ARG cc_start: 0.8089 (mtm180) cc_final: 0.7791 (mtt-85) REVERT: A 98 LYS cc_start: 0.8714 (pttt) cc_final: 0.8330 (pttp) REVERT: A 126 GLN cc_start: 0.8398 (tm-30) cc_final: 0.8178 (tm-30) REVERT: A 145 ASP cc_start: 0.8070 (p0) cc_final: 0.7659 (p0) REVERT: A 177 LEU cc_start: 0.8988 (tp) cc_final: 0.8747 (tp) REVERT: A 186 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7712 (mt-10) REVERT: A 191 GLU cc_start: 0.8481 (tp30) cc_final: 0.8164 (mm-30) REVERT: A 219 VAL cc_start: 0.8693 (t) cc_final: 0.8410 (t) REVERT: A 235 LEU cc_start: 0.8640 (mt) cc_final: 0.8386 (mt) REVERT: A 245 LYS cc_start: 0.7324 (mmtm) cc_final: 0.6847 (ttmm) REVERT: A 322 ARG cc_start: 0.5652 (mmm160) cc_final: 0.4749 (mmm160) REVERT: A 341 MET cc_start: 0.6608 (OUTLIER) cc_final: 0.6297 (mmm) REVERT: B 1 MET cc_start: 0.6712 (tpt) cc_final: 0.6045 (mmt) REVERT: B 48 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7238 (mm-30) REVERT: B 100 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7885 (mm-30) REVERT: B 216 ARG cc_start: 0.7304 (mtm110) cc_final: 0.6452 (mtp85) REVERT: B 244 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6741 (mt-10) REVERT: C 28 GLU cc_start: 0.6532 (tp30) cc_final: 0.6018 (tp30) REVERT: C 36 ILE cc_start: 0.6986 (mp) cc_final: 0.6473 (mp) REVERT: C 70 THR cc_start: 0.7301 (OUTLIER) cc_final: 0.7037 (m) REVERT: C 116 ASP cc_start: 0.6637 (t0) cc_final: 0.6392 (t0) REVERT: C 202 ARG cc_start: 0.7141 (ptm160) cc_final: 0.6323 (pmt170) REVERT: C 269 ARG cc_start: 0.7552 (ttp80) cc_final: 0.7004 (ttp80) REVERT: C 344 TYR cc_start: 0.5376 (t80) cc_final: 0.4688 (t80) REVERT: D 22 LYS cc_start: 0.7989 (pttp) cc_final: 0.7627 (ptmm) REVERT: D 37 GLU cc_start: 0.7108 (pp20) cc_final: 0.6869 (pp20) REVERT: D 40 ARG cc_start: 0.6188 (mtp180) cc_final: 0.5686 (ttt90) REVERT: D 120 HIS cc_start: 0.7885 (m-70) cc_final: 0.7480 (m-70) REVERT: D 133 LYS cc_start: 0.8124 (tttt) cc_final: 0.7657 (tptt) REVERT: D 181 TYR cc_start: 0.8689 (m-80) cc_final: 0.8088 (m-80) REVERT: D 233 SER cc_start: 0.8829 (t) cc_final: 0.8389 (p) REVERT: D 243 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7529 (mp) REVERT: D 286 LYS cc_start: 0.8187 (tptt) cc_final: 0.7792 (mtpp) REVERT: D 289 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6879 (mm-30) REVERT: D 302 MET cc_start: 0.8552 (tpp) cc_final: 0.8297 (mmm) REVERT: D 341 MET cc_start: 0.4085 (mtp) cc_final: 0.3379 (mtm) REVERT: E 121 GLU cc_start: 0.7659 (pt0) cc_final: 0.7107 (pm20) REVERT: E 133 LYS cc_start: 0.7785 (ttmt) cc_final: 0.7499 (tptp) REVERT: E 200 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8019 (mm) REVERT: E 245 LYS cc_start: 0.8661 (ttmm) cc_final: 0.8350 (tptp) outliers start: 75 outliers final: 53 residues processed: 440 average time/residue: 0.1436 time to fit residues: 91.7177 Evaluate side-chains 455 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 397 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 302 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 146 optimal weight: 0.5980 chunk 168 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 HIS E 120 HIS E 288 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.176530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.144299 restraints weight = 19083.385| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.15 r_work: 0.3229 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16508 Z= 0.196 Angle : 0.594 10.089 22384 Z= 0.309 Chirality : 0.043 0.200 2543 Planarity : 0.005 0.061 2800 Dihedral : 4.429 19.159 2166 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.95 % Favored : 94.95 % Rotamer: Outliers : 4.18 % Allowed : 18.93 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.19), residues: 1940 helix: 2.16 (0.16), residues: 957 sheet: 0.42 (0.28), residues: 339 loop : -1.95 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 19 TYR 0.021 0.002 TYR H 106 PHE 0.021 0.002 PHE D 27 TRP 0.018 0.001 TRP A 350 HIS 0.008 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00466 (16506) covalent geometry : angle 0.59425 (22380) SS BOND : bond 0.00076 ( 2) SS BOND : angle 1.00966 ( 4) hydrogen bonds : bond 0.05475 ( 984) hydrogen bonds : angle 4.46629 ( 2850) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 413 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 43 LYS cc_start: 0.8357 (mmmm) cc_final: 0.7953 (mptt) REVERT: L 61 SER cc_start: 0.8713 (t) cc_final: 0.8431 (m) REVERT: H 22 ARG cc_start: 0.8020 (ttp-110) cc_final: 0.7519 (ttt180) REVERT: H 42 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8165 (tp40) REVERT: H 90 ARG cc_start: 0.8072 (mtm180) cc_final: 0.7788 (mtt-85) REVERT: A 126 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8235 (tm-30) REVERT: A 152 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7759 (mm-30) REVERT: A 177 LEU cc_start: 0.9051 (tp) cc_final: 0.8816 (tp) REVERT: A 219 VAL cc_start: 0.8723 (t) cc_final: 0.8423 (t) REVERT: A 235 LEU cc_start: 0.8680 (mt) cc_final: 0.8431 (mt) REVERT: A 245 LYS cc_start: 0.7339 (mmtm) cc_final: 0.6742 (mtpp) REVERT: A 322 ARG cc_start: 0.5692 (mmm160) cc_final: 0.4742 (mmm160) REVERT: B 1 MET cc_start: 0.6600 (tpt) cc_final: 0.5907 (mmt) REVERT: B 100 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7859 (mm-30) REVERT: B 138 MET cc_start: 0.8897 (ttm) cc_final: 0.8697 (ttm) REVERT: B 216 ARG cc_start: 0.7380 (mtm110) cc_final: 0.6598 (mtp85) REVERT: B 220 GLU cc_start: 0.6717 (mm-30) cc_final: 0.6497 (mm-30) REVERT: B 244 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6709 (mt-10) REVERT: B 341 MET cc_start: 0.4685 (mmp) cc_final: 0.4440 (mmm) REVERT: C 28 GLU cc_start: 0.6460 (tp30) cc_final: 0.6009 (tp30) REVERT: C 70 THR cc_start: 0.7308 (OUTLIER) cc_final: 0.6994 (m) REVERT: C 107 PHE cc_start: 0.6726 (OUTLIER) cc_final: 0.6036 (t80) REVERT: C 110 LEU cc_start: 0.8211 (mp) cc_final: 0.7864 (mt) REVERT: C 116 ASP cc_start: 0.6611 (t0) cc_final: 0.6362 (t0) REVERT: C 127 VAL cc_start: 0.7842 (t) cc_final: 0.7457 (p) REVERT: C 148 ASP cc_start: 0.7705 (p0) cc_final: 0.7376 (p0) REVERT: C 152 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6738 (mp0) REVERT: C 202 ARG cc_start: 0.7158 (ptm160) cc_final: 0.6330 (pmt170) REVERT: C 344 TYR cc_start: 0.5507 (t80) cc_final: 0.4890 (t80) REVERT: D 22 LYS cc_start: 0.8010 (pttp) cc_final: 0.7678 (ptmm) REVERT: D 37 GLU cc_start: 0.7146 (pp20) cc_final: 0.6896 (pp20) REVERT: D 40 ARG cc_start: 0.6344 (mtp180) cc_final: 0.5783 (ttt90) REVERT: D 87 LEU cc_start: 0.8411 (mm) cc_final: 0.8117 (mm) REVERT: D 120 HIS cc_start: 0.7944 (m-70) cc_final: 0.7535 (m-70) REVERT: D 133 LYS cc_start: 0.8266 (tttt) cc_final: 0.7816 (tptt) REVERT: D 181 TYR cc_start: 0.8682 (m-80) cc_final: 0.8116 (m-80) REVERT: D 220 GLU cc_start: 0.8255 (tm-30) cc_final: 0.8028 (tm-30) REVERT: D 243 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7561 (mp) REVERT: D 286 LYS cc_start: 0.8204 (tptt) cc_final: 0.7787 (mtpp) REVERT: D 289 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6905 (mm-30) REVERT: D 302 MET cc_start: 0.8501 (tpp) cc_final: 0.8265 (mmm) REVERT: E 121 GLU cc_start: 0.7705 (pt0) cc_final: 0.7119 (pm20) REVERT: E 133 LYS cc_start: 0.7811 (ttmt) cc_final: 0.7516 (tptp) REVERT: E 200 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8105 (mm) REVERT: E 245 LYS cc_start: 0.8700 (ttmm) cc_final: 0.8374 (tptp) outliers start: 76 outliers final: 60 residues processed: 453 average time/residue: 0.1275 time to fit residues: 84.5077 Evaluate side-chains 466 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 399 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 342 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 4 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 171 optimal weight: 0.0870 chunk 132 optimal weight: 0.9990 chunk 144 optimal weight: 0.6980 chunk 151 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 162 optimal weight: 0.0970 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN E 120 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.178420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.146222 restraints weight = 19223.044| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.17 r_work: 0.3249 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16508 Z= 0.152 Angle : 0.565 9.184 22384 Z= 0.294 Chirality : 0.042 0.199 2543 Planarity : 0.005 0.062 2800 Dihedral : 4.324 18.204 2166 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.59 % Favored : 95.31 % Rotamer: Outliers : 4.35 % Allowed : 19.26 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.19), residues: 1940 helix: 2.27 (0.16), residues: 957 sheet: 0.48 (0.28), residues: 338 loop : -1.90 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 19 TYR 0.017 0.001 TYR B 236 PHE 0.022 0.001 PHE D 27 TRP 0.017 0.001 TRP A 350 HIS 0.006 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00348 (16506) covalent geometry : angle 0.56484 (22380) SS BOND : bond 0.00036 ( 2) SS BOND : angle 0.87096 ( 4) hydrogen bonds : bond 0.05157 ( 984) hydrogen bonds : angle 4.38562 ( 2850) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 393 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 43 LYS cc_start: 0.8375 (mmmm) cc_final: 0.7983 (mptt) REVERT: L 61 SER cc_start: 0.8705 (t) cc_final: 0.8426 (m) REVERT: H 22 ARG cc_start: 0.7938 (ttp-110) cc_final: 0.7460 (ttt180) REVERT: H 42 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8193 (tp40) REVERT: H 90 ARG cc_start: 0.8018 (mtm180) cc_final: 0.7750 (mtt-85) REVERT: A 126 GLN cc_start: 0.8396 (tm-30) cc_final: 0.8179 (tm-30) REVERT: A 145 ASP cc_start: 0.8090 (p0) cc_final: 0.7672 (p0) REVERT: A 177 LEU cc_start: 0.9013 (tp) cc_final: 0.8757 (tp) REVERT: A 186 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7714 (mt-10) REVERT: A 219 VAL cc_start: 0.8693 (t) cc_final: 0.8389 (t) REVERT: A 245 LYS cc_start: 0.7333 (mmtm) cc_final: 0.6805 (ttmm) REVERT: A 291 MET cc_start: 0.8411 (mmm) cc_final: 0.7676 (mmm) REVERT: A 322 ARG cc_start: 0.5688 (mmm160) cc_final: 0.4717 (mmm160) REVERT: B 1 MET cc_start: 0.6581 (tpt) cc_final: 0.5849 (mmt) REVERT: B 100 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7878 (mm-30) REVERT: B 185 LEU cc_start: 0.8208 (mt) cc_final: 0.7910 (mt) REVERT: B 216 ARG cc_start: 0.7391 (mtm110) cc_final: 0.6569 (mtp85) REVERT: B 220 GLU cc_start: 0.6784 (mm-30) cc_final: 0.6579 (mm-30) REVERT: B 244 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6699 (mt-10) REVERT: B 318 MET cc_start: 0.3913 (mmp) cc_final: 0.2940 (mmt) REVERT: B 341 MET cc_start: 0.4681 (mmp) cc_final: 0.4466 (mmm) REVERT: C 28 GLU cc_start: 0.6499 (tp30) cc_final: 0.6033 (tp30) REVERT: C 70 THR cc_start: 0.7317 (OUTLIER) cc_final: 0.6997 (m) REVERT: C 107 PHE cc_start: 0.6730 (OUTLIER) cc_final: 0.6041 (t80) REVERT: C 116 ASP cc_start: 0.6675 (t0) cc_final: 0.6446 (t0) REVERT: C 123 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6696 (tt0) REVERT: C 127 VAL cc_start: 0.7885 (t) cc_final: 0.7515 (p) REVERT: C 202 ARG cc_start: 0.7090 (ptm160) cc_final: 0.6211 (pmt170) REVERT: C 344 TYR cc_start: 0.5477 (t80) cc_final: 0.4875 (t80) REVERT: D 22 LYS cc_start: 0.7992 (pttp) cc_final: 0.7659 (ptmm) REVERT: D 37 GLU cc_start: 0.7147 (pp20) cc_final: 0.6905 (pp20) REVERT: D 40 ARG cc_start: 0.6179 (mtp180) cc_final: 0.5577 (ttt90) REVERT: D 87 LEU cc_start: 0.8447 (mm) cc_final: 0.8197 (mm) REVERT: D 120 HIS cc_start: 0.7899 (m-70) cc_final: 0.7461 (m-70) REVERT: D 133 LYS cc_start: 0.8229 (tttt) cc_final: 0.7786 (tptt) REVERT: D 181 TYR cc_start: 0.8639 (m-80) cc_final: 0.8143 (m-80) REVERT: D 243 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7514 (mp) REVERT: D 286 LYS cc_start: 0.8188 (tptt) cc_final: 0.7784 (mtpp) REVERT: D 302 MET cc_start: 0.8472 (tpp) cc_final: 0.8236 (mmm) REVERT: E 38 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7030 (pm20) REVERT: E 121 GLU cc_start: 0.7682 (pt0) cc_final: 0.7098 (pm20) REVERT: E 133 LYS cc_start: 0.7804 (ttmt) cc_final: 0.7507 (tptp) REVERT: E 200 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7923 (mm) REVERT: E 245 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8352 (tptp) outliers start: 79 outliers final: 61 residues processed: 435 average time/residue: 0.1340 time to fit residues: 85.8129 Evaluate side-chains 453 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 385 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 342 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 3 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 167 optimal weight: 0.3980 chunk 138 optimal weight: 0.0270 chunk 40 optimal weight: 0.4980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.178795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.146248 restraints weight = 19108.847| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.08 r_work: 0.3264 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16508 Z= 0.148 Angle : 0.563 9.278 22384 Z= 0.293 Chirality : 0.042 0.204 2543 Planarity : 0.005 0.061 2800 Dihedral : 4.295 17.979 2166 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.48 % Favored : 95.41 % Rotamer: Outliers : 4.07 % Allowed : 19.70 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.19), residues: 1940 helix: 2.29 (0.16), residues: 957 sheet: 0.53 (0.28), residues: 338 loop : -1.89 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 19 TYR 0.019 0.001 TYR D 279 PHE 0.023 0.001 PHE D 27 TRP 0.018 0.001 TRP A 350 HIS 0.005 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00338 (16506) covalent geometry : angle 0.56262 (22380) SS BOND : bond 0.00034 ( 2) SS BOND : angle 0.95875 ( 4) hydrogen bonds : bond 0.05056 ( 984) hydrogen bonds : angle 4.35043 ( 2850) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 386 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 43 LYS cc_start: 0.8378 (mmmm) cc_final: 0.7980 (mptt) REVERT: L 61 SER cc_start: 0.8689 (t) cc_final: 0.8410 (m) REVERT: H 22 ARG cc_start: 0.7913 (ttp-110) cc_final: 0.7445 (ttt180) REVERT: H 42 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8202 (tp40) REVERT: H 90 ARG cc_start: 0.8008 (mtm180) cc_final: 0.7740 (mtt-85) REVERT: A 145 ASP cc_start: 0.8072 (p0) cc_final: 0.7673 (p0) REVERT: A 177 LEU cc_start: 0.8991 (tp) cc_final: 0.8741 (tp) REVERT: A 186 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7689 (mt-10) REVERT: A 219 VAL cc_start: 0.8675 (t) cc_final: 0.8374 (t) REVERT: A 245 LYS cc_start: 0.7359 (mmtm) cc_final: 0.6870 (ttmm) REVERT: A 291 MET cc_start: 0.8421 (mmm) cc_final: 0.7726 (mmm) REVERT: A 322 ARG cc_start: 0.5708 (mmm160) cc_final: 0.4701 (mmm160) REVERT: B 1 MET cc_start: 0.6568 (tpt) cc_final: 0.5857 (mmt) REVERT: B 100 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7785 (mm-30) REVERT: B 185 LEU cc_start: 0.8137 (mt) cc_final: 0.7827 (mt) REVERT: B 191 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6263 (tp30) REVERT: B 216 ARG cc_start: 0.7410 (mtm110) cc_final: 0.6617 (mtp85) REVERT: B 220 GLU cc_start: 0.6775 (mm-30) cc_final: 0.6568 (mm-30) REVERT: B 244 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6718 (mt-10) REVERT: C 28 GLU cc_start: 0.6306 (tp30) cc_final: 0.5890 (tp30) REVERT: C 70 THR cc_start: 0.7287 (OUTLIER) cc_final: 0.6831 (m) REVERT: C 107 PHE cc_start: 0.6695 (OUTLIER) cc_final: 0.6043 (t80) REVERT: C 127 VAL cc_start: 0.7847 (t) cc_final: 0.7439 (p) REVERT: C 152 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6758 (mm-30) REVERT: C 202 ARG cc_start: 0.7067 (ptm160) cc_final: 0.6234 (pmt170) REVERT: C 344 TYR cc_start: 0.5560 (t80) cc_final: 0.4965 (t80) REVERT: D 22 LYS cc_start: 0.7983 (pttp) cc_final: 0.7640 (ptmm) REVERT: D 37 GLU cc_start: 0.7126 (pp20) cc_final: 0.6885 (pp20) REVERT: D 40 ARG cc_start: 0.6142 (mtp180) cc_final: 0.5573 (ttt90) REVERT: D 120 HIS cc_start: 0.7902 (m-70) cc_final: 0.7451 (m-70) REVERT: D 133 LYS cc_start: 0.8235 (tttt) cc_final: 0.7772 (tptt) REVERT: D 181 TYR cc_start: 0.8604 (m-80) cc_final: 0.8188 (m-80) REVERT: D 243 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7455 (mp) REVERT: D 286 LYS cc_start: 0.8280 (tptt) cc_final: 0.7853 (mtpp) REVERT: D 302 MET cc_start: 0.8522 (tpp) cc_final: 0.8269 (mmm) REVERT: D 341 MET cc_start: 0.4096 (mtp) cc_final: 0.3390 (mtm) REVERT: E 38 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7105 (pm20) REVERT: E 121 GLU cc_start: 0.7650 (pt0) cc_final: 0.7098 (pm20) REVERT: E 133 LYS cc_start: 0.7798 (ttmt) cc_final: 0.7489 (tptp) REVERT: E 200 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7933 (mm) REVERT: E 245 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8355 (tptp) outliers start: 74 outliers final: 62 residues processed: 424 average time/residue: 0.1378 time to fit residues: 85.1022 Evaluate side-chains 447 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 377 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 302 MET Chi-restraints excluded: chain E residue 342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 107 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 147 optimal weight: 0.0870 chunk 11 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 112 optimal weight: 0.0970 chunk 42 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 20 optimal weight: 0.0980 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.180587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.148591 restraints weight = 19162.182| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.19 r_work: 0.3275 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16508 Z= 0.132 Angle : 0.557 9.384 22384 Z= 0.288 Chirality : 0.041 0.211 2543 Planarity : 0.005 0.059 2800 Dihedral : 4.216 17.334 2166 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.18 % Favored : 95.72 % Rotamer: Outliers : 3.58 % Allowed : 20.58 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.20), residues: 1940 helix: 2.38 (0.17), residues: 956 sheet: 0.62 (0.28), residues: 344 loop : -1.88 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 19 TYR 0.019 0.001 TYR D 279 PHE 0.024 0.001 PHE D 27 TRP 0.016 0.001 TRP A 350 HIS 0.005 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00292 (16506) covalent geometry : angle 0.55656 (22380) SS BOND : bond 0.00113 ( 2) SS BOND : angle 0.93479 ( 4) hydrogen bonds : bond 0.04812 ( 984) hydrogen bonds : angle 4.28196 ( 2850) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 382 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 43 LYS cc_start: 0.8372 (mmmm) cc_final: 0.7987 (mptt) REVERT: L 61 SER cc_start: 0.8674 (t) cc_final: 0.8392 (m) REVERT: H 22 ARG cc_start: 0.7878 (ttp-110) cc_final: 0.7398 (ttt180) REVERT: H 42 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8220 (tp40) REVERT: H 90 ARG cc_start: 0.8009 (mtm180) cc_final: 0.7714 (mtt-85) REVERT: A 145 ASP cc_start: 0.8048 (p0) cc_final: 0.7649 (p0) REVERT: A 177 LEU cc_start: 0.8942 (tp) cc_final: 0.8716 (tp) REVERT: A 186 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7688 (mt-10) REVERT: A 219 VAL cc_start: 0.8652 (t) cc_final: 0.8366 (t) REVERT: A 245 LYS cc_start: 0.7402 (mmtm) cc_final: 0.6909 (ttmm) REVERT: A 322 ARG cc_start: 0.5678 (mmm160) cc_final: 0.4698 (mmm160) REVERT: B 1 MET cc_start: 0.6566 (tpt) cc_final: 0.5860 (mmt) REVERT: B 100 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7798 (mm-30) REVERT: B 191 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6342 (tp30) REVERT: B 210 ARG cc_start: 0.7614 (mtp85) cc_final: 0.7398 (mtp85) REVERT: B 216 ARG cc_start: 0.7387 (mtm110) cc_final: 0.6551 (mtp85) REVERT: B 220 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6573 (mm-30) REVERT: B 244 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6666 (mt-10) REVERT: B 318 MET cc_start: 0.3805 (mmp) cc_final: 0.2945 (mmt) REVERT: C 28 GLU cc_start: 0.6149 (tp30) cc_final: 0.5792 (tp30) REVERT: C 36 ILE cc_start: 0.6893 (mp) cc_final: 0.6536 (mp) REVERT: C 70 THR cc_start: 0.7312 (OUTLIER) cc_final: 0.6855 (m) REVERT: C 107 PHE cc_start: 0.6715 (OUTLIER) cc_final: 0.6090 (t80) REVERT: C 116 ASP cc_start: 0.6660 (t0) cc_final: 0.6365 (t0) REVERT: C 127 VAL cc_start: 0.7863 (t) cc_final: 0.7472 (p) REVERT: C 152 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6781 (mm-30) REVERT: C 202 ARG cc_start: 0.7047 (ptm160) cc_final: 0.6213 (pmt170) REVERT: C 344 TYR cc_start: 0.5585 (t80) cc_final: 0.4992 (t80) REVERT: D 22 LYS cc_start: 0.7963 (pttp) cc_final: 0.7629 (ptmm) REVERT: D 37 GLU cc_start: 0.7122 (pp20) cc_final: 0.6849 (pp20) REVERT: D 40 ARG cc_start: 0.6108 (mtp180) cc_final: 0.5538 (ttt90) REVERT: D 87 LEU cc_start: 0.8487 (mm) cc_final: 0.8252 (mm) REVERT: D 120 HIS cc_start: 0.7878 (m-70) cc_final: 0.7425 (m-70) REVERT: D 133 LYS cc_start: 0.8110 (tttt) cc_final: 0.7644 (tptt) REVERT: D 181 TYR cc_start: 0.8590 (m-80) cc_final: 0.8235 (m-80) REVERT: D 243 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7375 (mp) REVERT: D 286 LYS cc_start: 0.8267 (tptt) cc_final: 0.7854 (mtpp) REVERT: D 302 MET cc_start: 0.8493 (tpp) cc_final: 0.8242 (mmm) REVERT: D 341 MET cc_start: 0.4103 (mtp) cc_final: 0.3388 (mtm) REVERT: E 38 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7109 (pm20) REVERT: E 121 GLU cc_start: 0.7630 (pt0) cc_final: 0.7069 (pm20) REVERT: E 133 LYS cc_start: 0.7721 (ttmt) cc_final: 0.7435 (tptp) REVERT: E 245 LYS cc_start: 0.8669 (ttmm) cc_final: 0.8348 (tptp) outliers start: 65 outliers final: 51 residues processed: 417 average time/residue: 0.1360 time to fit residues: 83.3522 Evaluate side-chains 432 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 374 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 302 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 30 optimal weight: 0.0040 chunk 162 optimal weight: 0.0060 chunk 189 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 154 optimal weight: 0.6980 overall best weight: 0.4208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.179554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.147006 restraints weight = 19152.924| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.18 r_work: 0.3269 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16508 Z= 0.140 Angle : 0.565 9.398 22384 Z= 0.292 Chirality : 0.042 0.214 2543 Planarity : 0.005 0.059 2800 Dihedral : 4.198 17.438 2166 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.33 % Favored : 95.62 % Rotamer: Outliers : 3.52 % Allowed : 20.75 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.20), residues: 1940 helix: 2.41 (0.17), residues: 949 sheet: 0.64 (0.28), residues: 344 loop : -1.84 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 19 TYR 0.018 0.001 TYR D 279 PHE 0.026 0.001 PHE A 79 TRP 0.023 0.001 TRP A 350 HIS 0.005 0.001 HIS A 83 Details of bonding type rmsd covalent geometry : bond 0.00318 (16506) covalent geometry : angle 0.56538 (22380) SS BOND : bond 0.00041 ( 2) SS BOND : angle 1.01494 ( 4) hydrogen bonds : bond 0.04842 ( 984) hydrogen bonds : angle 4.26717 ( 2850) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4215.38 seconds wall clock time: 73 minutes 4.09 seconds (4384.09 seconds total)