Starting phenix.real_space_refine on Sat Jun 14 23:44:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmp_41397/06_2025/8tmp_41397.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmp_41397/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tmp_41397/06_2025/8tmp_41397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmp_41397/06_2025/8tmp_41397.map" model { file = "/net/cci-nas-00/data/ceres_data/8tmp_41397/06_2025/8tmp_41397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmp_41397/06_2025/8tmp_41397.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.040 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.54, per 1000 atoms: 0.65 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: 4.87 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.95 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: 6.10 Time building geometry restraints manager: 5.50 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: 3.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 42.110 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.550 ------------------------------------------------------------------------------- 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 : 10.73 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (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 TRP 0.029 0.001 TRP B 350 HIS 0.010 0.001 HIS A 257 PHE 0.025 0.001 PHE D 182 TYR 0.021 0.001 TYR C 19 ARG 0.009 0.000 ARG H 90 Details of bonding type rmsd hydrogen bonds : bond 0.10804 ( 984) hydrogen bonds : angle 5.34043 ( 2850) SS BOND : bond 0.00363 ( 2) SS BOND : angle 0.97464 ( 4) covalent geometry : bond 0.00287 (16506) covalent geometry : angle 0.58241 (22380) *********************** 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 : 1.762 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: 0.3074 time to fit residues: 217.3000 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 : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.5980 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 126 GLN B 285 ASN C 95 GLN C 217 ASN ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.179595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.147752 restraints weight = 19233.435| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.28 r_work: 0.3259 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16508 Z= 0.198 Angle : 0.622 11.415 22384 Z= 0.323 Chirality : 0.044 0.170 2543 Planarity : 0.005 0.052 2800 Dihedral : 4.410 19.118 2166 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.05 % Favored : 94.85 % Rotamer: Outliers : 2.20 % Allowed : 10.02 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.19), residues: 1940 helix: 2.22 (0.16), residues: 951 sheet: 0.59 (0.28), residues: 351 loop : -1.85 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 350 HIS 0.013 0.001 HIS A 257 PHE 0.023 0.002 PHE D 182 TYR 0.019 0.002 TYR H 106 ARG 0.007 0.001 ARG C 222 Details of bonding type rmsd hydrogen bonds : bond 0.05427 ( 984) hydrogen bonds : angle 4.59381 ( 2850) SS BOND : bond 0.00017 ( 2) SS BOND : angle 1.47252 ( 4) covalent geometry : bond 0.00471 (16506) covalent geometry : angle 0.62150 (22380) *********************** 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 486 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 446 time to evaluate : 1.994 Fit side-chains revert: symmetry clash REVERT: L 19 ARG cc_start: 0.7868 (mtp-110) cc_final: 0.7491 (mtp-110) REVERT: L 43 LYS cc_start: 0.8412 (mmmm) cc_final: 0.8024 (mptt) REVERT: L 61 SER cc_start: 0.8752 (t) cc_final: 0.8453 (m) REVERT: L 70 THR cc_start: 0.8302 (p) cc_final: 0.8098 (p) REVERT: H 22 ARG cc_start: 0.8024 (ttp-110) cc_final: 0.7494 (ttt180) REVERT: H 42 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8030 (tp40) REVERT: H 65 ASP cc_start: 0.8665 (m-30) cc_final: 0.8446 (m-30) REVERT: H 90 ARG cc_start: 0.7946 (mtm110) cc_final: 0.7421 (mtt-85) REVERT: A 98 LYS cc_start: 0.8673 (pttt) cc_final: 0.8336 (pttp) REVERT: A 177 LEU cc_start: 0.8953 (tp) cc_final: 0.8722 (tp) REVERT: A 186 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7612 (mt-10) REVERT: A 191 GLU cc_start: 0.8497 (tp30) cc_final: 0.8288 (mm-30) REVERT: A 219 VAL cc_start: 0.8704 (t) cc_final: 0.8435 (t) REVERT: A 245 LYS cc_start: 0.7199 (mmtm) cc_final: 0.6574 (mtpp) REVERT: A 266 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7865 (mt-10) REVERT: A 322 ARG cc_start: 0.5547 (mmm160) cc_final: 0.4591 (mmm160) REVERT: B 1 MET cc_start: 0.6809 (tpt) cc_final: 0.6321 (mmt) REVERT: B 48 GLU cc_start: 0.7298 (mm-30) cc_final: 0.7011 (mm-30) REVERT: B 100 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7821 (mm-30) REVERT: B 163 LYS cc_start: 0.8532 (pttt) cc_final: 0.8263 (pttp) REVERT: B 187 LYS cc_start: 0.8072 (mtmt) cc_final: 0.7793 (mtmt) REVERT: B 204 GLU cc_start: 0.6220 (pt0) cc_final: 0.5430 (mm-30) REVERT: B 216 ARG cc_start: 0.7119 (mtm110) cc_final: 0.6433 (mtp85) REVERT: B 222 ARG cc_start: 0.8399 (ttp-110) cc_final: 0.8169 (ttp-110) REVERT: B 244 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6742 (mt-10) REVERT: C 28 GLU cc_start: 0.6068 (tp30) cc_final: 0.5637 (tp30) REVERT: C 70 THR cc_start: 0.7293 (m) cc_final: 0.6874 (t) REVERT: C 116 ASP cc_start: 0.6663 (t0) cc_final: 0.6427 (t0) REVERT: C 137 LEU cc_start: 0.7084 (tt) cc_final: 0.6786 (tt) REVERT: C 202 ARG cc_start: 0.7205 (ptm160) cc_final: 0.6369 (pmt170) REVERT: C 244 GLU cc_start: 0.6867 (tp30) cc_final: 0.6604 (tp30) REVERT: C 245 LYS cc_start: 0.6520 (tptp) cc_final: 0.6230 (ttpp) REVERT: C 269 ARG cc_start: 0.7504 (ttp80) cc_final: 0.6973 (ttp80) REVERT: C 344 TYR cc_start: 0.5307 (t80) cc_final: 0.4518 (t80) REVERT: D 22 LYS cc_start: 0.7859 (pttp) cc_final: 0.7563 (ptmm) REVERT: D 23 TYR cc_start: 0.7621 (m-80) cc_final: 0.7275 (m-80) REVERT: D 27 PHE cc_start: 0.8283 (t80) cc_final: 0.8045 (t80) REVERT: D 37 GLU cc_start: 0.7103 (pp20) cc_final: 0.6847 (pp20) REVERT: D 40 ARG cc_start: 0.6418 (mtp180) cc_final: 0.5907 (mtp85) REVERT: D 120 HIS cc_start: 0.7976 (m-70) cc_final: 0.7581 (m-70) REVERT: D 133 LYS cc_start: 0.8190 (tttt) cc_final: 0.7800 (tptt) REVERT: D 163 LYS cc_start: 0.8762 (mtmt) cc_final: 0.8405 (mtpt) REVERT: D 181 TYR cc_start: 0.8625 (m-80) cc_final: 0.7932 (m-80) REVERT: D 233 SER cc_start: 0.8858 (t) cc_final: 0.8344 (p) REVERT: D 286 LYS cc_start: 0.8271 (tptt) cc_final: 0.7797 (mtpp) REVERT: D 289 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6750 (mm-30) REVERT: D 302 MET cc_start: 0.8474 (tpp) cc_final: 0.8213 (mmm) REVERT: E 121 GLU cc_start: 0.7527 (pt0) cc_final: 0.7045 (pm20) REVERT: E 133 LYS cc_start: 0.7771 (ttmt) cc_final: 0.7455 (tptp) REVERT: E 220 GLU cc_start: 0.7645 (tt0) cc_final: 0.7355 (tp30) REVERT: E 245 LYS cc_start: 0.8581 (ttmm) cc_final: 0.8229 (mtpp) REVERT: E 288 ASN cc_start: 0.8566 (m-40) cc_final: 0.8305 (m-40) REVERT: E 291 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7492 (ttm) outliers start: 40 outliers final: 28 residues processed: 461 average time/residue: 0.3231 time to fit residues: 211.6757 Evaluate side-chains 445 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 415 time to evaluate : 2.491 ------------------------------------------------------------------------------- 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 65 THR Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 184 LEU 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 228 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 342 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 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 144 optimal weight: 1.9990 chunk 138 optimal weight: 0.0970 chunk 51 optimal weight: 2.9990 chunk 113 optimal weight: 0.0270 chunk 96 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.0980 chunk 115 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.2436 ------------------------------------------------------------------------------- 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** C 217 ASN C 314 ASN D 74 GLN E 120 HIS E 285 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.182152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.149824 restraints weight = 19234.986| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.05 r_work: 0.3323 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1804 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= 0.129 Angle : 0.542 9.171 22384 Z= 0.285 Chirality : 0.041 0.184 2543 Planarity : 0.004 0.048 2800 Dihedral : 4.230 16.536 2166 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.97 % Favored : 95.93 % Rotamer: Outliers : 1.98 % Allowed : 14.42 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.20), residues: 1940 helix: 2.45 (0.17), residues: 952 sheet: 0.67 (0.28), residues: 336 loop : -1.85 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 350 HIS 0.008 0.001 HIS A 257 PHE 0.018 0.001 PHE A 79 TYR 0.017 0.001 TYR B 236 ARG 0.006 0.000 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.04863 ( 984) hydrogen bonds : angle 4.38223 ( 2850) SS BOND : bond 0.00203 ( 2) SS BOND : angle 0.84849 ( 4) covalent geometry : bond 0.00276 (16506) covalent geometry : angle 0.54189 (22380) *********************** 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 449 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 413 time to evaluate : 1.770 Fit side-chains revert: symmetry clash REVERT: L 19 ARG cc_start: 0.7824 (mtp-110) cc_final: 0.7505 (mtp-110) REVERT: L 43 LYS cc_start: 0.8374 (mmmm) cc_final: 0.8016 (mptt) REVERT: L 61 SER cc_start: 0.8676 (t) cc_final: 0.8386 (m) REVERT: H 22 ARG cc_start: 0.7895 (ttp-110) cc_final: 0.7246 (ttt180) REVERT: H 65 ASP cc_start: 0.8604 (m-30) cc_final: 0.8385 (m-30) REVERT: H 90 ARG cc_start: 0.7998 (mtm110) cc_final: 0.7581 (mtt-85) REVERT: H 117 ASP cc_start: 0.7664 (m-30) cc_final: 0.7364 (m-30) REVERT: A 96 ARG cc_start: 0.7757 (mmt90) cc_final: 0.7522 (mmt90) REVERT: A 98 LYS cc_start: 0.8615 (pttt) cc_final: 0.8271 (pttp) REVERT: A 145 ASP cc_start: 0.7933 (p0) cc_final: 0.7560 (p0) REVERT: A 177 LEU cc_start: 0.8845 (tp) cc_final: 0.8624 (tp) REVERT: A 186 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7581 (mt-10) REVERT: A 219 VAL cc_start: 0.8685 (t) cc_final: 0.8357 (t) REVERT: A 245 LYS cc_start: 0.7169 (mmtm) cc_final: 0.6574 (mtpp) REVERT: A 252 ARG cc_start: 0.7735 (ttm110) cc_final: 0.7265 (ttp80) REVERT: A 322 ARG cc_start: 0.5523 (mmm160) cc_final: 0.4543 (mmm160) REVERT: B 1 MET cc_start: 0.6859 (tpt) cc_final: 0.6346 (mmt) REVERT: B 100 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7795 (mm-30) REVERT: B 187 LYS cc_start: 0.8024 (mtmt) cc_final: 0.7738 (mtmt) REVERT: B 216 ARG cc_start: 0.7161 (mtm110) cc_final: 0.6398 (mtp85) REVERT: B 237 ARG cc_start: 0.7652 (mtm180) cc_final: 0.7191 (mtp180) REVERT: B 334 MET cc_start: 0.5221 (mmt) cc_final: 0.3909 (ttt) REVERT: C 28 GLU cc_start: 0.6167 (tp30) cc_final: 0.5667 (tp30) REVERT: C 95 GLN cc_start: 0.6192 (OUTLIER) cc_final: 0.4891 (tm-30) REVERT: C 116 ASP cc_start: 0.6811 (t0) cc_final: 0.6562 (t0) REVERT: C 137 LEU cc_start: 0.7088 (tt) cc_final: 0.6782 (tt) REVERT: C 202 ARG cc_start: 0.7150 (ptm160) cc_final: 0.6415 (pmt170) REVERT: C 244 GLU cc_start: 0.6853 (tp30) cc_final: 0.6540 (tp30) REVERT: C 245 LYS cc_start: 0.6639 (tptp) cc_final: 0.6334 (ttpp) REVERT: C 269 ARG cc_start: 0.7535 (ttp80) cc_final: 0.6962 (ttp80) REVERT: C 344 TYR cc_start: 0.5292 (t80) cc_final: 0.4534 (t80) REVERT: D 22 LYS cc_start: 0.7872 (pttp) cc_final: 0.7555 (ptmm) REVERT: D 23 TYR cc_start: 0.7569 (m-80) cc_final: 0.7285 (m-80) REVERT: D 37 GLU cc_start: 0.7070 (pp20) cc_final: 0.6804 (pp20) REVERT: D 40 ARG cc_start: 0.6241 (mtp180) cc_final: 0.5735 (mtp85) REVERT: D 87 LEU cc_start: 0.8388 (mm) cc_final: 0.7972 (mm) REVERT: D 120 HIS cc_start: 0.7925 (m-70) cc_final: 0.7559 (m-70) REVERT: D 133 LYS cc_start: 0.7981 (tttt) cc_final: 0.7640 (tptt) REVERT: D 181 TYR cc_start: 0.8578 (m-80) cc_final: 0.7875 (m-80) REVERT: D 233 SER cc_start: 0.8774 (t) cc_final: 0.8281 (p) REVERT: D 286 LYS cc_start: 0.8255 (tptt) cc_final: 0.7810 (mtpp) REVERT: D 289 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6833 (mm-30) REVERT: D 302 MET cc_start: 0.8424 (tpp) cc_final: 0.8139 (mmm) REVERT: E 89 ASP cc_start: 0.8281 (m-30) cc_final: 0.8066 (m-30) REVERT: E 121 GLU cc_start: 0.7422 (pt0) cc_final: 0.7034 (pm20) REVERT: E 133 LYS cc_start: 0.7686 (ttmt) cc_final: 0.7434 (tptp) REVERT: E 162 ARG cc_start: 0.8079 (mtp180) cc_final: 0.7877 (mtp180) REVERT: E 245 LYS cc_start: 0.8551 (ttmm) cc_final: 0.8197 (mtpp) REVERT: E 291 MET cc_start: 0.7668 (tpp) cc_final: 0.7024 (ttm) outliers start: 36 outliers final: 25 residues processed: 426 average time/residue: 0.3070 time to fit residues: 186.4310 Evaluate side-chains 423 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 397 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain A residue 65 THR 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 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 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 D residue 88 GLU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 143 ILE 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 132 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 63 ASN ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN E 285 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.174880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.142705 restraints weight = 19125.990| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.06 r_work: 0.3216 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 16508 Z= 0.261 Angle : 0.649 11.411 22384 Z= 0.338 Chirality : 0.045 0.188 2543 Planarity : 0.005 0.047 2800 Dihedral : 4.564 20.921 2166 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.95 % Favored : 94.95 % Rotamer: Outliers : 4.13 % Allowed : 15.47 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.19), residues: 1940 helix: 2.03 (0.16), residues: 955 sheet: 0.35 (0.28), residues: 344 loop : -1.96 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 350 HIS 0.013 0.002 HIS A 257 PHE 0.019 0.002 PHE A 345 TYR 0.029 0.002 TYR H 103 ARG 0.009 0.001 ARG B 5 Details of bonding type rmsd hydrogen bonds : bond 0.05969 ( 984) hydrogen bonds : angle 4.61868 ( 2850) SS BOND : bond 0.00230 ( 2) SS BOND : angle 1.13796 ( 4) covalent geometry : bond 0.00631 (16506) covalent geometry : angle 0.64838 (22380) *********************** 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 498 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 423 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 19 ARG cc_start: 0.7966 (mtp-110) cc_final: 0.7673 (mtp-110) REVERT: L 43 LYS cc_start: 0.8397 (mmmm) cc_final: 0.7965 (mptt) REVERT: L 61 SER cc_start: 0.8694 (t) cc_final: 0.8438 (m) REVERT: H 22 ARG cc_start: 0.8007 (ttp-110) cc_final: 0.7532 (ttt180) REVERT: H 42 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8163 (tp40) REVERT: H 65 ASP cc_start: 0.8663 (m-30) cc_final: 0.8458 (m-30) REVERT: H 70 ARG cc_start: 0.8479 (ttp80) cc_final: 0.8133 (ttp80) REVERT: H 85 GLN cc_start: 0.8588 (tp-100) cc_final: 0.8312 (tp40) REVERT: H 90 ARG cc_start: 0.8100 (mtm110) cc_final: 0.7654 (mtt-85) REVERT: A 54 ARG cc_start: 0.5895 (mtm110) cc_final: 0.5630 (mtp-110) REVERT: A 87 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7147 (mm) REVERT: A 98 LYS cc_start: 0.8739 (pttt) cc_final: 0.8377 (pttp) REVERT: A 177 LEU cc_start: 0.9071 (tp) cc_final: 0.8804 (tp) REVERT: A 186 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7719 (mt-10) REVERT: A 219 VAL cc_start: 0.8800 (t) cc_final: 0.8505 (t) REVERT: A 245 LYS cc_start: 0.7250 (mmtm) cc_final: 0.6684 (mtpp) REVERT: A 266 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7780 (mt-10) REVERT: A 291 MET cc_start: 0.8444 (mmm) cc_final: 0.7818 (mmm) REVERT: A 322 ARG cc_start: 0.5627 (mmm160) cc_final: 0.4857 (mmm160) REVERT: B 1 MET cc_start: 0.6810 (tpt) cc_final: 0.6442 (tpt) REVERT: B 9 LYS cc_start: 0.8392 (mtmt) cc_final: 0.7880 (mmtm) REVERT: B 48 GLU cc_start: 0.7431 (mm-30) cc_final: 0.6935 (mm-30) REVERT: B 65 THR cc_start: 0.9246 (OUTLIER) cc_final: 0.9024 (m) REVERT: B 100 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7786 (mm-30) REVERT: B 187 LYS cc_start: 0.8149 (mtmt) cc_final: 0.7877 (mtmt) REVERT: B 204 GLU cc_start: 0.6556 (pt0) cc_final: 0.5782 (mm-30) REVERT: B 216 ARG cc_start: 0.7296 (mtm110) cc_final: 0.6569 (mtp85) REVERT: B 327 TYR cc_start: 0.6060 (t80) cc_final: 0.5786 (t80) REVERT: C 28 GLU cc_start: 0.6300 (tp30) cc_final: 0.5797 (tp30) REVERT: C 35 SER cc_start: 0.6073 (p) cc_final: 0.5671 (m) REVERT: C 36 ILE cc_start: 0.6767 (mp) cc_final: 0.6198 (mp) REVERT: C 70 THR cc_start: 0.7412 (m) cc_final: 0.7044 (t) REVERT: C 116 ASP cc_start: 0.6608 (t0) cc_final: 0.6348 (t0) REVERT: C 127 VAL cc_start: 0.8036 (t) cc_final: 0.7770 (p) REVERT: C 137 LEU cc_start: 0.7304 (tt) cc_final: 0.6917 (tt) REVERT: C 202 ARG cc_start: 0.7161 (ptm160) cc_final: 0.6344 (pmt170) REVERT: C 244 GLU cc_start: 0.6844 (tp30) cc_final: 0.6520 (tp30) REVERT: C 245 LYS cc_start: 0.6825 (tptp) cc_final: 0.6565 (ttpp) REVERT: C 269 ARG cc_start: 0.7565 (ttp80) cc_final: 0.7009 (ttp80) REVERT: C 344 TYR cc_start: 0.5513 (t80) cc_final: 0.4847 (t80) REVERT: D 22 LYS cc_start: 0.7944 (pttp) cc_final: 0.7591 (ptmm) REVERT: D 37 GLU cc_start: 0.7175 (pp20) cc_final: 0.6922 (pp20) REVERT: D 40 ARG cc_start: 0.6433 (mtp180) cc_final: 0.5823 (ttt90) REVERT: D 69 ARG cc_start: 0.7428 (mtp180) cc_final: 0.7157 (mmm-85) REVERT: D 87 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8003 (mm) REVERT: D 120 HIS cc_start: 0.8014 (m-70) cc_final: 0.7629 (m-70) REVERT: D 181 TYR cc_start: 0.8677 (m-80) cc_final: 0.7931 (m-80) REVERT: D 220 GLU cc_start: 0.8291 (tm-30) cc_final: 0.8030 (tm-30) REVERT: D 233 SER cc_start: 0.9028 (t) cc_final: 0.8580 (p) REVERT: D 286 LYS cc_start: 0.8172 (tptt) cc_final: 0.7780 (mtpp) REVERT: D 289 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6886 (mm-30) REVERT: D 302 MET cc_start: 0.8619 (tpp) cc_final: 0.8335 (mmm) REVERT: E 121 GLU cc_start: 0.7648 (pt0) cc_final: 0.7116 (pm20) REVERT: E 133 LYS cc_start: 0.7779 (ttmt) cc_final: 0.7524 (tptp) REVERT: E 245 LYS cc_start: 0.8699 (ttmm) cc_final: 0.8376 (tptp) outliers start: 75 outliers final: 48 residues processed: 450 average time/residue: 0.2978 time to fit residues: 194.7204 Evaluate side-chains 455 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 403 time to evaluate : 1.845 ------------------------------------------------------------------------------- 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 106 GLU 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 94 THR Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 87 LEU 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 65 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 132 THR 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 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 C residue 290 VAL Chi-restraints excluded: chain C residue 305 THR 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 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 282 SER Chi-restraints excluded: chain D residue 284 SER 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 281 SER Chi-restraints excluded: chain E residue 302 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 2 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 100 optimal weight: 0.0170 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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** C 314 ASN D 74 GLN E 120 HIS ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.177806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.146029 restraints weight = 19435.526| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.23 r_work: 0.3248 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2421 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= 0.160 Angle : 0.564 9.947 22384 Z= 0.297 Chirality : 0.042 0.190 2543 Planarity : 0.005 0.044 2800 Dihedral : 4.393 18.237 2166 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.12 % Favored : 95.77 % Rotamer: Outliers : 3.36 % Allowed : 17.67 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.19), residues: 1940 helix: 2.20 (0.16), residues: 957 sheet: 0.33 (0.28), residues: 344 loop : -1.98 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 350 HIS 0.007 0.001 HIS A 83 PHE 0.015 0.002 PHE D 301 TYR 0.018 0.001 TYR H 103 ARG 0.009 0.000 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.05319 ( 984) hydrogen bonds : angle 4.44806 ( 2850) SS BOND : bond 0.00060 ( 2) SS BOND : angle 0.86151 ( 4) covalent geometry : bond 0.00370 (16506) covalent geometry : angle 0.56430 (22380) *********************** 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 464 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 403 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 19 ARG cc_start: 0.7865 (mtp-110) cc_final: 0.7593 (mtp-110) REVERT: L 43 LYS cc_start: 0.8370 (mmmm) cc_final: 0.7961 (mptt) REVERT: L 61 SER cc_start: 0.8689 (t) cc_final: 0.8412 (m) REVERT: H 22 ARG cc_start: 0.7980 (ttp-110) cc_final: 0.7555 (ttt180) REVERT: H 70 ARG cc_start: 0.8472 (ttp80) cc_final: 0.8178 (ttp80) REVERT: H 85 GLN cc_start: 0.8588 (tp-100) cc_final: 0.8330 (tp40) REVERT: H 90 ARG cc_start: 0.8071 (mtm110) cc_final: 0.7688 (mtt-85) REVERT: A 98 LYS cc_start: 0.8702 (pttt) cc_final: 0.8336 (pttp) REVERT: A 145 ASP cc_start: 0.8150 (p0) cc_final: 0.7808 (p0) REVERT: A 177 LEU cc_start: 0.8994 (tp) cc_final: 0.8743 (tp) REVERT: A 186 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7643 (mt-10) REVERT: A 219 VAL cc_start: 0.8709 (t) cc_final: 0.8413 (t) REVERT: A 245 LYS cc_start: 0.7255 (mmtm) cc_final: 0.6659 (mtpp) REVERT: A 322 ARG cc_start: 0.5636 (mmm160) cc_final: 0.4787 (mmm160) REVERT: B 1 MET cc_start: 0.6766 (tpt) cc_final: 0.6393 (tpt) REVERT: B 48 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6889 (mm-30) REVERT: B 65 THR cc_start: 0.9207 (t) cc_final: 0.8995 (m) REVERT: B 100 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7864 (mm-30) REVERT: B 165 ARG cc_start: 0.6977 (mtm-85) cc_final: 0.6693 (mtm-85) REVERT: B 187 LYS cc_start: 0.8036 (mtmt) cc_final: 0.7800 (mtmt) REVERT: B 210 ARG cc_start: 0.7339 (mtp85) cc_final: 0.7034 (mtp85) REVERT: B 216 ARG cc_start: 0.7280 (mtm110) cc_final: 0.6470 (mtp85) REVERT: B 244 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6606 (mt-10) REVERT: B 318 MET cc_start: 0.4137 (mmp) cc_final: 0.3046 (mmp) REVERT: C 28 GLU cc_start: 0.6250 (tp30) cc_final: 0.5625 (tp30) REVERT: C 36 ILE cc_start: 0.6770 (mp) cc_final: 0.6260 (mp) REVERT: C 70 THR cc_start: 0.7342 (m) cc_final: 0.7048 (m) REVERT: C 116 ASP cc_start: 0.6630 (t0) cc_final: 0.6392 (t0) REVERT: C 202 ARG cc_start: 0.7136 (ptm160) cc_final: 0.6357 (pmt170) REVERT: C 244 GLU cc_start: 0.6844 (tp30) cc_final: 0.6503 (tp30) REVERT: C 269 ARG cc_start: 0.7555 (ttp80) cc_final: 0.6999 (ttp80) REVERT: C 344 TYR cc_start: 0.5507 (t80) cc_final: 0.4843 (t80) REVERT: D 22 LYS cc_start: 0.7959 (pttp) cc_final: 0.7612 (ptmm) REVERT: D 37 GLU cc_start: 0.7136 (pp20) cc_final: 0.6918 (pp20) REVERT: D 40 ARG cc_start: 0.6165 (mtp180) cc_final: 0.5635 (ttt90) REVERT: D 87 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7875 (mm) REVERT: D 120 HIS cc_start: 0.7887 (m-70) cc_final: 0.7488 (m-70) REVERT: D 133 LYS cc_start: 0.8305 (tttt) cc_final: 0.7804 (tptt) REVERT: D 181 TYR cc_start: 0.8658 (m-80) cc_final: 0.8023 (m-80) REVERT: D 243 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7525 (mp) REVERT: D 286 LYS cc_start: 0.8179 (tptt) cc_final: 0.7778 (mtpp) REVERT: D 289 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6887 (mm-30) REVERT: D 302 MET cc_start: 0.8616 (tpp) cc_final: 0.8337 (mmm) REVERT: E 121 GLU cc_start: 0.7660 (pt0) cc_final: 0.7152 (pm20) REVERT: E 133 LYS cc_start: 0.7792 (ttmt) cc_final: 0.7500 (tptp) REVERT: E 200 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8054 (mm) REVERT: E 245 LYS cc_start: 0.8713 (ttmm) cc_final: 0.8351 (tptp) REVERT: E 291 MET cc_start: 0.7916 (ttp) cc_final: 0.7681 (mtm) outliers start: 61 outliers final: 40 residues processed: 432 average time/residue: 0.3941 time to fit residues: 247.8717 Evaluate side-chains 437 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 394 time to evaluate : 2.573 ------------------------------------------------------------------------------- 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 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 51 VAL Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 67 ILE 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 236 TYR 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 136 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 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 185 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 282 SER 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 103 GLU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 302 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 82 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 172 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 HIS E 140 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.176910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.144443 restraints weight = 19234.253| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.95 r_work: 0.3257 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16508 Z= 0.184 Angle : 0.591 9.632 22384 Z= 0.307 Chirality : 0.043 0.190 2543 Planarity : 0.005 0.045 2800 Dihedral : 4.389 18.831 2166 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.79 % Favored : 95.10 % Rotamer: Outliers : 3.85 % Allowed : 18.66 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.19), residues: 1940 helix: 2.16 (0.16), residues: 957 sheet: 0.36 (0.28), residues: 346 loop : -2.00 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 350 HIS 0.007 0.001 HIS A 257 PHE 0.021 0.002 PHE C 147 TYR 0.019 0.001 TYR H 106 ARG 0.008 0.001 ARG B 5 Details of bonding type rmsd hydrogen bonds : bond 0.05403 ( 984) hydrogen bonds : angle 4.46450 ( 2850) SS BOND : bond 0.00059 ( 2) SS BOND : angle 1.02093 ( 4) covalent geometry : bond 0.00436 (16506) covalent geometry : angle 0.59077 (22380) *********************** 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 477 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 407 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 19 ARG cc_start: 0.7966 (mtp-110) cc_final: 0.7707 (mtp-110) REVERT: L 43 LYS cc_start: 0.8369 (mmmm) cc_final: 0.7910 (mptt) REVERT: L 61 SER cc_start: 0.8794 (t) cc_final: 0.8521 (m) REVERT: H 22 ARG cc_start: 0.8067 (ttp-110) cc_final: 0.7561 (ttt180) REVERT: H 42 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8267 (tp40) REVERT: H 70 ARG cc_start: 0.8524 (ttp80) cc_final: 0.8249 (ttp80) REVERT: H 85 GLN cc_start: 0.8693 (tp-100) cc_final: 0.8417 (tp40) REVERT: H 90 ARG cc_start: 0.8255 (mtm180) cc_final: 0.7769 (mtt-85) REVERT: A 98 LYS cc_start: 0.8790 (pttt) cc_final: 0.8434 (pttp) REVERT: A 152 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7860 (mm-30) REVERT: A 177 LEU cc_start: 0.9096 (tp) cc_final: 0.8845 (tp) REVERT: A 186 GLU cc_start: 0.8441 (mt-10) cc_final: 0.7933 (mt-10) REVERT: A 219 VAL cc_start: 0.8820 (t) cc_final: 0.8530 (t) REVERT: A 222 ARG cc_start: 0.8660 (ptm160) cc_final: 0.8365 (ptm-80) REVERT: A 245 LYS cc_start: 0.7320 (mmtm) cc_final: 0.6683 (mtpp) REVERT: A 322 ARG cc_start: 0.5732 (mmm160) cc_final: 0.4859 (mmm160) REVERT: A 341 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.6500 (mmm) REVERT: B 1 MET cc_start: 0.6652 (tpt) cc_final: 0.5996 (mmt) REVERT: B 48 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7064 (mm-30) REVERT: B 65 THR cc_start: 0.9243 (OUTLIER) cc_final: 0.9043 (m) REVERT: B 100 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8085 (mm-30) REVERT: B 187 LYS cc_start: 0.8149 (mtmt) cc_final: 0.7938 (mtmt) REVERT: B 216 ARG cc_start: 0.7393 (mtm110) cc_final: 0.6513 (mtp85) REVERT: B 244 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6791 (mt-10) REVERT: B 246 GLU cc_start: 0.7722 (pm20) cc_final: 0.7317 (mm-30) REVERT: B 341 MET cc_start: 0.4794 (mmp) cc_final: 0.4504 (mmm) REVERT: C 28 GLU cc_start: 0.6764 (tp30) cc_final: 0.6209 (tp30) REVERT: C 36 ILE cc_start: 0.7095 (mp) cc_final: 0.6538 (mp) REVERT: C 70 THR cc_start: 0.7450 (m) cc_final: 0.7181 (m) REVERT: C 116 ASP cc_start: 0.6637 (t0) cc_final: 0.6383 (t0) REVERT: C 202 ARG cc_start: 0.7238 (ptm160) cc_final: 0.6333 (pmt170) REVERT: C 269 ARG cc_start: 0.7762 (ttp80) cc_final: 0.7244 (ttp80) REVERT: C 344 TYR cc_start: 0.5489 (t80) cc_final: 0.4738 (t80) REVERT: D 22 LYS cc_start: 0.8052 (pttp) cc_final: 0.7707 (ptmm) REVERT: D 37 GLU cc_start: 0.7304 (pp20) cc_final: 0.7075 (pp20) REVERT: D 40 ARG cc_start: 0.6316 (mtp180) cc_final: 0.5694 (ttt90) REVERT: D 69 ARG cc_start: 0.7417 (mtp180) cc_final: 0.7199 (mmm-85) REVERT: D 87 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8000 (mm) REVERT: D 120 HIS cc_start: 0.7956 (m-70) cc_final: 0.7564 (m-70) REVERT: D 133 LYS cc_start: 0.8434 (tttt) cc_final: 0.7913 (tptt) REVERT: D 181 TYR cc_start: 0.8749 (m-80) cc_final: 0.8073 (m-80) REVERT: D 243 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7671 (mp) REVERT: D 286 LYS cc_start: 0.8318 (tptt) cc_final: 0.7878 (mtpp) REVERT: D 289 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7101 (mm-30) REVERT: D 302 MET cc_start: 0.8730 (tpp) cc_final: 0.8442 (mmm) REVERT: E 121 GLU cc_start: 0.7862 (pt0) cc_final: 0.6737 (tp30) REVERT: E 133 LYS cc_start: 0.7830 (ttmt) cc_final: 0.7506 (tptp) REVERT: E 200 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8158 (mm) REVERT: E 245 LYS cc_start: 0.8726 (ttmm) cc_final: 0.8342 (tptp) REVERT: E 291 MET cc_start: 0.8148 (ttp) cc_final: 0.7770 (ttp) outliers start: 70 outliers final: 50 residues processed: 442 average time/residue: 0.3001 time to fit residues: 191.2231 Evaluate side-chains 458 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 401 time to evaluate : 1.777 ------------------------------------------------------------------------------- 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 67 ILE 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 65 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 186 GLU 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 31 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 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 146 VAL 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 243 ILE Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 282 SER 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 140 GLN Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 200 LEU 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 20 optimal weight: 0.0470 chunk 168 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 27 optimal weight: 0.0980 chunk 161 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 177 optimal weight: 0.6980 chunk 78 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 overall best weight: 0.3678 ------------------------------------------------------------------------------- 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** ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN D 95 GLN E 120 HIS E 140 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.178970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.146871 restraints weight = 19176.680| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.13 r_work: 0.3275 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16508 Z= 0.138 Angle : 0.557 9.401 22384 Z= 0.291 Chirality : 0.042 0.199 2543 Planarity : 0.004 0.045 2800 Dihedral : 4.278 17.554 2166 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.38 % Favored : 95.52 % Rotamer: Outliers : 3.52 % Allowed : 19.37 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.19), residues: 1940 helix: 2.34 (0.16), residues: 955 sheet: 0.44 (0.28), residues: 343 loop : -1.97 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 350 HIS 0.006 0.001 HIS A 83 PHE 0.020 0.001 PHE C 147 TYR 0.016 0.001 TYR B 236 ARG 0.007 0.000 ARG B 165 Details of bonding type rmsd hydrogen bonds : bond 0.05029 ( 984) hydrogen bonds : angle 4.36891 ( 2850) SS BOND : bond 0.00064 ( 2) SS BOND : angle 0.86702 ( 4) covalent geometry : bond 0.00307 (16506) covalent geometry : angle 0.55717 (22380) *********************** 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 466 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 402 time to evaluate : 1.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 43 LYS cc_start: 0.8366 (mmmm) cc_final: 0.7956 (mptt) REVERT: L 61 SER cc_start: 0.8688 (t) cc_final: 0.8398 (m) REVERT: H 22 ARG cc_start: 0.7875 (ttp-110) cc_final: 0.7448 (ttt180) REVERT: H 42 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8204 (tp40) REVERT: H 70 ARG cc_start: 0.8467 (ttp80) cc_final: 0.8135 (ttp80) REVERT: H 85 GLN cc_start: 0.8570 (tp-100) cc_final: 0.8287 (tp40) REVERT: H 90 ARG cc_start: 0.8065 (mtm180) cc_final: 0.7744 (mtt-85) REVERT: A 177 LEU cc_start: 0.8968 (tp) cc_final: 0.8723 (tp) REVERT: A 186 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7695 (mt-10) REVERT: A 219 VAL cc_start: 0.8673 (t) cc_final: 0.8387 (t) REVERT: A 222 ARG cc_start: 0.8554 (ptm160) cc_final: 0.8199 (ptm-80) REVERT: A 245 LYS cc_start: 0.7301 (mmtm) cc_final: 0.6693 (mtpp) REVERT: A 322 ARG cc_start: 0.5641 (mmm160) cc_final: 0.4725 (mmm160) REVERT: A 341 MET cc_start: 0.6667 (OUTLIER) cc_final: 0.6394 (mmm) REVERT: B 1 MET cc_start: 0.6683 (tpt) cc_final: 0.6021 (mmt) REVERT: B 48 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6872 (mm-30) REVERT: B 65 THR cc_start: 0.9191 (t) cc_final: 0.8979 (m) REVERT: B 100 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7829 (mm-30) REVERT: B 165 ARG cc_start: 0.6757 (mtm-85) cc_final: 0.6434 (mtm-85) REVERT: B 204 GLU cc_start: 0.6464 (pt0) cc_final: 0.5639 (mm-30) REVERT: B 216 ARG cc_start: 0.7282 (mtm110) cc_final: 0.6442 (mtp85) REVERT: B 220 GLU cc_start: 0.6727 (mm-30) cc_final: 0.6524 (mm-30) REVERT: B 244 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6619 (mt-10) REVERT: B 318 MET cc_start: 0.3912 (mmp) cc_final: 0.2894 (mmt) REVERT: C 28 GLU cc_start: 0.6374 (tp30) cc_final: 0.5864 (tp30) REVERT: C 36 ILE cc_start: 0.6745 (mp) cc_final: 0.6233 (mp) REVERT: C 70 THR cc_start: 0.7362 (m) cc_final: 0.7082 (m) REVERT: C 107 PHE cc_start: 0.6798 (OUTLIER) cc_final: 0.6087 (t80) REVERT: C 116 ASP cc_start: 0.6640 (t0) cc_final: 0.6400 (t0) REVERT: C 202 ARG cc_start: 0.7102 (ptm160) cc_final: 0.6341 (pmt170) REVERT: C 344 TYR cc_start: 0.5324 (t80) cc_final: 0.4634 (t80) REVERT: D 22 LYS cc_start: 0.7969 (pttp) cc_final: 0.7618 (ptmm) REVERT: D 37 GLU cc_start: 0.7114 (pp20) cc_final: 0.6874 (pp20) REVERT: D 40 ARG cc_start: 0.6121 (mtp180) cc_final: 0.5521 (ttt90) REVERT: D 120 HIS cc_start: 0.7856 (m-70) cc_final: 0.7442 (m-70) REVERT: D 133 LYS cc_start: 0.8157 (tttt) cc_final: 0.7697 (tptt) REVERT: D 181 TYR cc_start: 0.8637 (m-80) cc_final: 0.8015 (m-80) REVERT: D 243 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7514 (mp) REVERT: D 286 LYS cc_start: 0.8162 (tptt) cc_final: 0.7787 (mtpp) REVERT: D 289 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6810 (mm-30) REVERT: D 302 MET cc_start: 0.8535 (tpp) cc_final: 0.8252 (mmm) REVERT: E 121 GLU cc_start: 0.7628 (pt0) cc_final: 0.6697 (tp30) REVERT: E 133 LYS cc_start: 0.7781 (ttmt) cc_final: 0.7490 (tptp) REVERT: E 200 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7896 (mm) REVERT: E 245 LYS cc_start: 0.8671 (ttmm) cc_final: 0.8360 (tptp) REVERT: E 291 MET cc_start: 0.7926 (ttp) cc_final: 0.7558 (ttp) outliers start: 64 outliers final: 48 residues processed: 432 average time/residue: 0.2931 time to fit residues: 184.4590 Evaluate side-chains 442 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 389 time to evaluate : 1.795 ------------------------------------------------------------------------------- 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 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 266 GLU 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 236 TYR 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 87 LEU 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 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 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 184 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 282 SER 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 103 GLU Chi-restraints excluded: chain E residue 183 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 36 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 182 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** ** A 140 GLN ** 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 = 0.3842 r_free = 0.3842 target = 0.176867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.144995 restraints weight = 19208.207| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.09 r_work: 0.3231 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2722 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= 0.203 Angle : 0.610 10.704 22384 Z= 0.318 Chirality : 0.044 0.199 2543 Planarity : 0.005 0.047 2800 Dihedral : 4.410 19.189 2166 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.85 % Favored : 95.05 % Rotamer: Outliers : 3.74 % Allowed : 19.65 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.19), residues: 1940 helix: 2.10 (0.16), residues: 958 sheet: 0.42 (0.28), residues: 345 loop : -2.01 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 350 HIS 0.008 0.001 HIS A 257 PHE 0.019 0.002 PHE D 301 TYR 0.021 0.002 TYR H 106 ARG 0.010 0.001 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.05483 ( 984) hydrogen bonds : angle 4.48973 ( 2850) SS BOND : bond 0.00117 ( 2) SS BOND : angle 1.21533 ( 4) covalent geometry : bond 0.00485 (16506) covalent geometry : angle 0.60950 (22380) *********************** 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 465 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 397 time to evaluate : 2.585 Fit side-chains REVERT: L 43 LYS cc_start: 0.8393 (mmmm) cc_final: 0.7981 (mptt) REVERT: L 61 SER cc_start: 0.8696 (t) cc_final: 0.8419 (m) REVERT: H 22 ARG cc_start: 0.7979 (ttp-110) cc_final: 0.7402 (ttt180) REVERT: H 42 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8188 (tp40) REVERT: H 70 ARG cc_start: 0.8494 (ttp80) cc_final: 0.8159 (ttp80) REVERT: H 90 ARG cc_start: 0.8038 (mtm180) cc_final: 0.7687 (mtt-85) REVERT: A 152 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7707 (mm-30) REVERT: A 156 TYR cc_start: 0.7446 (m-10) cc_final: 0.7087 (m-10) REVERT: A 177 LEU cc_start: 0.9057 (tp) cc_final: 0.8808 (tp) REVERT: A 219 VAL cc_start: 0.8763 (t) cc_final: 0.8468 (t) REVERT: A 222 ARG cc_start: 0.8562 (ptm160) cc_final: 0.8248 (ptm-80) REVERT: A 245 LYS cc_start: 0.7280 (mmtm) cc_final: 0.6696 (mtpp) REVERT: A 322 ARG cc_start: 0.5721 (mmm160) cc_final: 0.4771 (mmm160) REVERT: B 1 MET cc_start: 0.6572 (tpt) cc_final: 0.5862 (mmt) REVERT: B 48 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6926 (mm-30) REVERT: B 100 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7802 (mm-30) REVERT: B 165 ARG cc_start: 0.6898 (mtm-85) cc_final: 0.6570 (mtm-85) REVERT: B 204 GLU cc_start: 0.6604 (pt0) cc_final: 0.5733 (mm-30) REVERT: B 216 ARG cc_start: 0.7385 (mtm110) cc_final: 0.6611 (mtp85) REVERT: B 244 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6548 (mt-10) REVERT: B 341 MET cc_start: 0.4685 (mmp) cc_final: 0.4442 (mmm) REVERT: C 28 GLU cc_start: 0.6431 (tp30) cc_final: 0.5957 (tp30) REVERT: C 70 THR cc_start: 0.7441 (m) cc_final: 0.7180 (m) REVERT: C 107 PHE cc_start: 0.6750 (OUTLIER) cc_final: 0.6036 (t80) REVERT: C 116 ASP cc_start: 0.6684 (t0) cc_final: 0.6436 (t0) REVERT: C 152 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6774 (mm-30) REVERT: C 202 ARG cc_start: 0.7140 (ptm160) cc_final: 0.6321 (pmt170) REVERT: C 344 TYR cc_start: 0.5519 (t80) cc_final: 0.4837 (t80) REVERT: D 22 LYS cc_start: 0.7995 (pttp) cc_final: 0.7651 (ptmm) REVERT: D 37 GLU cc_start: 0.7176 (pp20) cc_final: 0.6931 (pp20) REVERT: D 40 ARG cc_start: 0.6305 (mtp180) cc_final: 0.5713 (ttt90) REVERT: D 87 LEU cc_start: 0.8409 (mm) cc_final: 0.8114 (mm) REVERT: D 120 HIS cc_start: 0.7964 (m-70) cc_final: 0.7530 (m-70) REVERT: D 133 LYS cc_start: 0.8309 (tttt) cc_final: 0.7860 (tptt) REVERT: D 181 TYR cc_start: 0.8670 (m-80) cc_final: 0.8085 (m-80) REVERT: D 220 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7993 (tm-30) REVERT: D 243 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7561 (mp) REVERT: D 286 LYS cc_start: 0.8207 (tptt) cc_final: 0.7787 (mtpp) REVERT: D 302 MET cc_start: 0.8634 (tpp) cc_final: 0.8328 (mmm) REVERT: E 121 GLU cc_start: 0.7722 (pt0) cc_final: 0.6724 (tp30) REVERT: E 133 LYS cc_start: 0.7827 (ttmt) cc_final: 0.7517 (tptp) REVERT: E 200 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8112 (mm) REVERT: E 245 LYS cc_start: 0.8717 (ttmm) cc_final: 0.8386 (tptp) outliers start: 68 outliers final: 55 residues processed: 429 average time/residue: 0.3437 time to fit residues: 215.9322 Evaluate side-chains 454 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 393 time to evaluate : 1.826 ------------------------------------------------------------------------------- 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 50 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 31 VAL 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 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 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 243 ILE Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 282 SER 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 1 optimal weight: 2.9990 chunk 123 optimal weight: 0.0170 chunk 171 optimal weight: 0.1980 chunk 95 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 44 optimal weight: 0.0040 chunk 109 optimal weight: 0.8980 overall best weight: 0.4230 ------------------------------------------------------------------------------- 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 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN 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 = 0.3867 r_free = 0.3867 target = 0.179269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.147138 restraints weight = 19165.519| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.07 r_work: 0.3269 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- 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 = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2731 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= 0.144 Angle : 0.571 11.395 22384 Z= 0.298 Chirality : 0.042 0.213 2543 Planarity : 0.005 0.045 2800 Dihedral : 4.300 17.779 2166 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.18 % Favored : 95.72 % Rotamer: Outliers : 3.52 % Allowed : 19.81 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.19), residues: 1940 helix: 2.27 (0.16), residues: 956 sheet: 0.46 (0.28), residues: 343 loop : -1.96 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 350 HIS 0.006 0.001 HIS A 83 PHE 0.016 0.001 PHE C 147 TYR 0.016 0.001 TYR B 236 ARG 0.008 0.001 ARG B 5 Details of bonding type rmsd hydrogen bonds : bond 0.05042 ( 984) hydrogen bonds : angle 4.38206 ( 2850) SS BOND : bond 0.00074 ( 2) SS BOND : angle 0.86390 ( 4) covalent geometry : bond 0.00324 (16506) covalent geometry : angle 0.57074 (22380) *********************** 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 459 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 395 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 43 LYS cc_start: 0.8375 (mmmm) cc_final: 0.7964 (mptt) REVERT: L 61 SER cc_start: 0.8680 (t) cc_final: 0.8390 (m) REVERT: H 22 ARG cc_start: 0.7816 (ttp-110) cc_final: 0.7302 (ttt180) REVERT: H 42 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8197 (tp40) REVERT: H 70 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8126 (ttp80) REVERT: H 90 ARG cc_start: 0.8042 (mtm180) cc_final: 0.7709 (mtt-85) REVERT: A 79 PHE cc_start: 0.6096 (t80) cc_final: 0.5854 (t80) REVERT: A 152 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7652 (mm-30) REVERT: A 177 LEU cc_start: 0.8988 (tp) cc_final: 0.8739 (tp) REVERT: A 186 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7705 (mt-10) REVERT: A 219 VAL cc_start: 0.8681 (t) cc_final: 0.8389 (t) REVERT: A 222 ARG cc_start: 0.8533 (ptm160) cc_final: 0.8227 (ptm-80) REVERT: A 245 LYS cc_start: 0.7289 (mmtm) cc_final: 0.6783 (ttmm) REVERT: A 322 ARG cc_start: 0.5625 (mmm160) cc_final: 0.4658 (mmm160) REVERT: B 1 MET cc_start: 0.6540 (tpt) cc_final: 0.5834 (mmt) REVERT: B 48 GLU cc_start: 0.7372 (mm-30) cc_final: 0.6912 (mm-30) REVERT: B 100 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7753 (mm-30) REVERT: B 204 GLU cc_start: 0.6468 (pt0) cc_final: 0.5557 (mm-30) REVERT: B 216 ARG cc_start: 0.7368 (mtm110) cc_final: 0.6580 (mtp85) REVERT: B 244 GLU cc_start: 0.6923 (mm-30) cc_final: 0.6676 (mt-10) REVERT: C 28 GLU cc_start: 0.6395 (tp30) cc_final: 0.5927 (tp30) REVERT: C 36 ILE cc_start: 0.6902 (mp) cc_final: 0.6546 (mp) REVERT: C 70 THR cc_start: 0.7329 (m) cc_final: 0.7027 (m) REVERT: C 107 PHE cc_start: 0.6754 (OUTLIER) cc_final: 0.6121 (t80) REVERT: C 116 ASP cc_start: 0.6684 (t0) cc_final: 0.6440 (t0) REVERT: C 127 VAL cc_start: 0.7738 (t) cc_final: 0.7512 (p) REVERT: C 202 ARG cc_start: 0.7036 (ptm160) cc_final: 0.6228 (pmt170) REVERT: C 344 TYR cc_start: 0.5479 (t80) cc_final: 0.4811 (t80) REVERT: D 22 LYS cc_start: 0.7972 (pttp) cc_final: 0.7633 (ptmm) REVERT: D 37 GLU cc_start: 0.7129 (pp20) cc_final: 0.6886 (pp20) REVERT: D 40 ARG cc_start: 0.6092 (mtp180) cc_final: 0.5485 (ttt90) REVERT: D 87 LEU cc_start: 0.8429 (mm) cc_final: 0.8154 (mm) REVERT: D 120 HIS cc_start: 0.7887 (m-70) cc_final: 0.7434 (m-70) REVERT: D 133 LYS cc_start: 0.8249 (tttt) cc_final: 0.7785 (tptt) REVERT: D 181 TYR cc_start: 0.8601 (m-80) cc_final: 0.8103 (m-80) REVERT: D 243 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7464 (mp) REVERT: D 286 LYS cc_start: 0.8182 (tptt) cc_final: 0.7788 (mtpp) REVERT: D 302 MET cc_start: 0.8535 (tpp) cc_final: 0.8301 (mmm) REVERT: E 121 GLU cc_start: 0.7654 (pt0) cc_final: 0.7091 (pm20) REVERT: E 133 LYS cc_start: 0.7789 (ttmt) cc_final: 0.7491 (tptp) REVERT: E 200 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7877 (mm) REVERT: E 245 LYS cc_start: 0.8684 (ttmm) cc_final: 0.8354 (tptp) outliers start: 64 outliers final: 48 residues processed: 428 average time/residue: 0.2938 time to fit residues: 183.0879 Evaluate side-chains 441 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 388 time to evaluate : 1.807 ------------------------------------------------------------------------------- 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 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 236 TYR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 107 PHE 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 239 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 281 SER 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 184 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 208 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 111 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 120 optimal weight: 0.0050 chunk 35 optimal weight: 0.0770 chunk 180 optimal weight: 0.5980 chunk 78 optimal weight: 0.0970 chunk 185 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.2750 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.180748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.148867 restraints weight = 19218.610| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.20 r_work: 0.3287 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2713 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= 0.130 Angle : 0.570 10.236 22384 Z= 0.296 Chirality : 0.042 0.216 2543 Planarity : 0.005 0.046 2800 Dihedral : 4.197 16.979 2166 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.02 % Favored : 95.88 % Rotamer: Outliers : 2.86 % Allowed : 20.69 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.20), residues: 1940 helix: 2.33 (0.17), residues: 955 sheet: 0.68 (0.28), residues: 340 loop : -1.94 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 350 HIS 0.005 0.001 HIS A 83 PHE 0.015 0.001 PHE C 147 TYR 0.018 0.001 TYR B 236 ARG 0.009 0.001 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.04776 ( 984) hydrogen bonds : angle 4.30381 ( 2850) SS BOND : bond 0.00151 ( 2) SS BOND : angle 0.94154 ( 4) covalent geometry : bond 0.00283 (16506) covalent geometry : angle 0.57013 (22380) ********************** 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 436 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 384 time to evaluate : 1.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 43 LYS cc_start: 0.8368 (mmmm) cc_final: 0.7966 (mptt) REVERT: L 61 SER cc_start: 0.8661 (t) cc_final: 0.8366 (m) REVERT: H 22 ARG cc_start: 0.7779 (ttp-110) cc_final: 0.7418 (ttt180) REVERT: H 42 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8230 (tp40) REVERT: H 70 ARG cc_start: 0.8430 (ttp80) cc_final: 0.8123 (ttp80) REVERT: H 85 GLN cc_start: 0.8537 (tp-100) cc_final: 0.8267 (tp40) REVERT: H 90 ARG cc_start: 0.8058 (mtm180) cc_final: 0.7800 (mtt-85) REVERT: A 141 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7462 (mt-10) REVERT: A 152 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7658 (mm-30) REVERT: A 177 LEU cc_start: 0.8923 (tp) cc_final: 0.8699 (tp) REVERT: A 186 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7672 (mt-10) REVERT: A 219 VAL cc_start: 0.8651 (t) cc_final: 0.8357 (t) REVERT: A 222 ARG cc_start: 0.8524 (ptm160) cc_final: 0.8073 (ptm160) REVERT: A 245 LYS cc_start: 0.7359 (mmtm) cc_final: 0.6873 (ttmm) REVERT: A 291 MET cc_start: 0.8137 (mmm) cc_final: 0.7686 (mmm) REVERT: A 322 ARG cc_start: 0.5637 (mmm160) cc_final: 0.4667 (mmm160) REVERT: A 341 MET cc_start: 0.6714 (tpt) cc_final: 0.6450 (mmm) REVERT: B 1 MET cc_start: 0.6537 (tpt) cc_final: 0.5833 (mmt) REVERT: B 48 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6924 (mm-30) REVERT: B 75 ARG cc_start: 0.8368 (tpt90) cc_final: 0.8122 (mmm160) REVERT: B 100 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7760 (mm-30) REVERT: B 185 LEU cc_start: 0.8048 (mt) cc_final: 0.7582 (mt) REVERT: B 204 GLU cc_start: 0.6352 (pt0) cc_final: 0.5470 (mm-30) REVERT: B 216 ARG cc_start: 0.7389 (mtm110) cc_final: 0.6583 (mtp85) REVERT: C 28 GLU cc_start: 0.6263 (tp30) cc_final: 0.5854 (tp30) REVERT: C 36 ILE cc_start: 0.6885 (mp) cc_final: 0.6537 (mp) REVERT: C 70 THR cc_start: 0.7332 (m) cc_final: 0.6864 (m) REVERT: C 96 ARG cc_start: 0.6696 (ttm110) cc_final: 0.6485 (ttm110) REVERT: C 107 PHE cc_start: 0.6751 (OUTLIER) cc_final: 0.6160 (t80) REVERT: C 116 ASP cc_start: 0.6685 (t0) cc_final: 0.6389 (t0) REVERT: C 127 VAL cc_start: 0.7744 (t) cc_final: 0.7542 (p) REVERT: C 202 ARG cc_start: 0.7011 (ptm160) cc_final: 0.6204 (pmt170) REVERT: C 344 TYR cc_start: 0.5521 (t80) cc_final: 0.4882 (t80) REVERT: D 22 LYS cc_start: 0.7943 (pttp) cc_final: 0.7608 (ptmm) REVERT: D 37 GLU cc_start: 0.7093 (pp20) cc_final: 0.6828 (pp20) REVERT: D 40 ARG cc_start: 0.6059 (mtp180) cc_final: 0.5467 (ttt90) REVERT: D 120 HIS cc_start: 0.7862 (m-70) cc_final: 0.7403 (m-70) REVERT: D 133 LYS cc_start: 0.8114 (tttt) cc_final: 0.7662 (tptt) REVERT: D 181 TYR cc_start: 0.8588 (m-80) cc_final: 0.8160 (m-80) REVERT: D 186 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7470 (mt-10) REVERT: D 286 LYS cc_start: 0.8273 (tptt) cc_final: 0.7855 (mtpp) REVERT: D 291 MET cc_start: 0.8535 (mmm) cc_final: 0.8107 (mmt) REVERT: D 302 MET cc_start: 0.8406 (tpp) cc_final: 0.8170 (mmm) REVERT: E 121 GLU cc_start: 0.7603 (pt0) cc_final: 0.7059 (pm20) REVERT: E 133 LYS cc_start: 0.7702 (ttmt) cc_final: 0.7423 (tptp) REVERT: E 245 LYS cc_start: 0.8669 (ttmm) cc_final: 0.8339 (tptp) outliers start: 52 outliers final: 46 residues processed: 411 average time/residue: 0.3219 time to fit residues: 195.9608 Evaluate side-chains 425 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 376 time to evaluate : 1.795 ------------------------------------------------------------------------------- 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 152 GLU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 266 GLU 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 186 GLU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 107 PHE 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 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 184 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 282 SER 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 194 VAL Chi-restraints excluded: chain E residue 230 GLU 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 8 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 158 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 134 optimal weight: 0.6980 chunk 184 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** ** A 140 GLN ** 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 = 0.3856 r_free = 0.3856 target = 0.178405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.146173 restraints weight = 19126.317| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.18 r_work: 0.3261 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2798 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= 0.172 Angle : 0.596 9.872 22384 Z= 0.309 Chirality : 0.043 0.209 2543 Planarity : 0.005 0.046 2800 Dihedral : 4.296 18.178 2166 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.64 % Favored : 95.26 % Rotamer: Outliers : 3.03 % Allowed : 20.69 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.19), residues: 1940 helix: 2.22 (0.16), residues: 957 sheet: 0.66 (0.28), residues: 340 loop : -1.98 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 350 HIS 0.006 0.001 HIS A 257 PHE 0.020 0.002 PHE E 39 TYR 0.024 0.001 TYR D 279 ARG 0.009 0.001 ARG L 19 Details of bonding type rmsd hydrogen bonds : bond 0.05135 ( 984) hydrogen bonds : angle 4.36835 ( 2850) SS BOND : bond 0.00095 ( 2) SS BOND : angle 1.12500 ( 4) covalent geometry : bond 0.00404 (16506) covalent geometry : angle 0.59557 (22380) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10024.16 seconds wall clock time: 176 minutes 10.18 seconds (10570.18 seconds total)