Starting phenix.real_space_refine on Mon May 12 11:59:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xzj_38798/05_2025/8xzj_38798.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xzj_38798/05_2025/8xzj_38798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xzj_38798/05_2025/8xzj_38798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xzj_38798/05_2025/8xzj_38798.map" model { file = "/net/cci-nas-00/data/ceres_data/8xzj_38798/05_2025/8xzj_38798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xzj_38798/05_2025/8xzj_38798.cif" } resolution = 3.0 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= 0.002 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 73 5.16 5 C 5804 2.51 5 N 1536 2.21 5 O 1693 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9106 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2410 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 291} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1756 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "L" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 112 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 3, 'TRANS': 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NAL:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.30, per 1000 atoms: 0.58 Number of scatterers: 9106 At special positions: 0 Unit cell: (100.44, 132.06, 114.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 73 16.00 O 1693 8.00 N 1536 7.00 C 5804 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 281 " distance=2.16 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.11 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.02 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 6 " 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: 2.33 Conformation dependent library (CDL) restraints added in 1.0 seconds 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 15 sheets defined 39.2% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'R' and resid 26 through 55 Proline residue: R 32 - end of helix Processing helix chain 'R' and resid 64 through 78 Processing helix chain 'R' and resid 81 through 91 removed outlier: 3.848A pdb=" N TRP R 85 " --> pdb=" O THR R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 132 removed outlier: 4.346A pdb=" N PHE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 3.855A pdb=" N LEU R 142 " --> pdb=" O ALA R 138 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG R 143 " --> pdb=" O ARG R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 161 Processing helix chain 'R' and resid 161 through 167 removed outlier: 3.843A pdb=" N MET R 165 " --> pdb=" O ALA R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 210 Processing helix chain 'R' and resid 210 through 216 removed outlier: 3.705A pdb=" N THR R 215 " --> pdb=" O VAL R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 232 removed outlier: 3.697A pdb=" N GLY R 230 " --> pdb=" O GLN R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 274 Proline residue: R 263 - end of helix removed outlier: 4.199A pdb=" N THR R 269 " --> pdb=" O HIS R 265 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU R 270 " --> pdb=" O LEU R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 311 Proline residue: R 292 - end of helix removed outlier: 3.728A pdb=" N SER R 298 " --> pdb=" O CYS R 294 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR R 299 " --> pdb=" O THR R 295 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL R 300 " --> pdb=" O CYS R 296 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN R 301 " --> pdb=" O ILE R 297 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER R 302 " --> pdb=" O SER R 298 " (cutoff:3.500A) Proline residue: R 306 - end of helix removed outlier: 3.704A pdb=" N ALA R 310 " --> pdb=" O PRO R 306 " (cutoff:3.500A) Processing helix chain 'R' and resid 313 through 325 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.520A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 5.023A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 4.231A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.207A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.873A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.137A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 208 through 212 Processing sheet with id=AA1, first strand: chain 'R' and resid 168 through 172 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.451A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.623A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.542A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.839A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.278A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.610A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.515A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.621A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.991A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.991A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.427A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 134 through 136 removed outlier: 4.055A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.90 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2196 1.33 - 1.45: 1991 1.45 - 1.57: 5015 1.57 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 9307 Sorted by residual: bond pdb=" N ARG L 2 " pdb=" CA ARG L 2 " ideal model delta sigma weight residual 1.461 1.493 -0.032 9.20e-03 1.18e+04 1.24e+01 bond pdb=" N PRO S 224 " pdb=" CD PRO S 224 " ideal model delta sigma weight residual 1.474 1.428 0.046 1.40e-02 5.10e+03 1.06e+01 bond pdb=" N VAL R 79 " pdb=" CA VAL R 79 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.09e-02 8.42e+03 1.05e+01 bond pdb=" N VAL R 80 " pdb=" CA VAL R 80 " ideal model delta sigma weight residual 1.460 1.497 -0.038 1.21e-02 6.83e+03 9.65e+00 bond pdb=" C4A NAL L 11 " pdb=" C8A NAL L 11 " ideal model delta sigma weight residual 1.419 1.480 -0.061 2.00e-02 2.50e+03 9.34e+00 ... (remaining 9302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 11898 1.94 - 3.88: 648 3.88 - 5.82: 53 5.82 - 7.75: 12 7.75 - 9.69: 2 Bond angle restraints: 12613 Sorted by residual: angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 113.23 103.54 9.69 1.24e+00 6.50e-01 6.11e+01 angle pdb=" C ASP R 313 " pdb=" N PRO R 314 " pdb=" CA PRO R 314 " ideal model delta sigma weight residual 119.32 126.59 -7.27 1.14e+00 7.69e-01 4.07e+01 angle pdb=" N LEU R 266 " pdb=" CA LEU R 266 " pdb=" C LEU R 266 " ideal model delta sigma weight residual 113.97 107.43 6.54 1.28e+00 6.10e-01 2.61e+01 angle pdb=" N GLN R 226 " pdb=" CA GLN R 226 " pdb=" C GLN R 226 " ideal model delta sigma weight residual 113.97 107.48 6.49 1.28e+00 6.10e-01 2.57e+01 angle pdb=" N LEU R 308 " pdb=" CA LEU R 308 " pdb=" C LEU R 308 " ideal model delta sigma weight residual 111.36 116.79 -5.43 1.09e+00 8.42e-01 2.48e+01 ... (remaining 12608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 5235 17.12 - 34.24: 178 34.24 - 51.35: 61 51.35 - 68.47: 19 68.47 - 85.59: 6 Dihedral angle restraints: 5499 sinusoidal: 2130 harmonic: 3369 Sorted by residual: dihedral pdb=" CB CYS L 1 " pdb=" SG CYS L 1 " pdb=" SG CYS L 6 " pdb=" CB CYS L 6 " ideal model delta sinusoidal sigma weight residual 93.00 176.96 -83.96 1 1.00e+01 1.00e-02 8.59e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 152.48 27.52 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CD ARG R 91 " pdb=" NE ARG R 91 " pdb=" CZ ARG R 91 " pdb=" NH1 ARG R 91 " ideal model delta sinusoidal sigma weight residual 0.00 -41.70 41.70 1 1.00e+01 1.00e-02 2.43e+01 ... (remaining 5496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 916 0.047 - 0.094: 303 0.094 - 0.141: 135 0.141 - 0.188: 58 0.188 - 0.235: 12 Chirality restraints: 1424 Sorted by residual: chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA VAL A 50 " pdb=" N VAL A 50 " pdb=" C VAL A 50 " pdb=" CB VAL A 50 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA VAL R 300 " pdb=" N VAL R 300 " pdb=" C VAL R 300 " pdb=" CB VAL R 300 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1421 not shown) Planarity restraints: 1588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 91 " 0.723 9.50e-02 1.11e+02 3.24e-01 6.39e+01 pdb=" NE ARG R 91 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG R 91 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG R 91 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG R 91 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS L 8 " 0.022 2.00e-02 2.50e+03 4.50e-02 2.03e+01 pdb=" C LYS L 8 " -0.078 2.00e-02 2.50e+03 pdb=" O LYS L 8 " 0.029 2.00e-02 2.50e+03 pdb=" N GLY L 9 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 75 " 0.015 2.00e-02 2.50e+03 3.10e-02 9.59e+00 pdb=" C GLN B 75 " -0.054 2.00e-02 2.50e+03 pdb=" O GLN B 75 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP B 76 " 0.018 2.00e-02 2.50e+03 ... (remaining 1585 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1984 2.78 - 3.31: 8657 3.31 - 3.84: 15376 3.84 - 4.37: 19249 4.37 - 4.90: 32319 Nonbonded interactions: 77585 Sorted by model distance: nonbonded pdb=" CD1 ILE R 68 " pdb=" O TYR R 309 " model vdw 2.252 3.460 nonbonded pdb=" O PRO R 280 " pdb=" N ASP R 282 " model vdw 2.272 3.120 nonbonded pdb=" OD1 ASP R 23 " pdb=" NZ LYS L 8 " model vdw 2.287 3.120 nonbonded pdb=" OD2 ASP R 75 " pdb=" ND2 ASN R 305 " model vdw 2.330 3.120 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.348 3.040 ... (remaining 77580 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.450 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 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 : 0.011 0.132 9312 Z= 0.634 Angle : 0.967 12.631 12623 Z= 0.667 Chirality : 0.064 0.235 1424 Planarity : 0.010 0.324 1588 Dihedral : 11.329 85.590 3312 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.84 % Favored : 97.89 % Rotamer: Outliers : 2.72 % Allowed : 2.32 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.24), residues: 1139 helix: 0.19 (0.24), residues: 400 sheet: 0.82 (0.29), residues: 288 loop : 0.09 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 95 HIS 0.009 0.001 HIS B 91 PHE 0.024 0.001 PHE B 199 TYR 0.034 0.002 TYR B 105 ARG 0.013 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.18179 ( 457) hydrogen bonds : angle 7.50522 ( 1272) SS BOND : bond 0.06887 ( 5) SS BOND : angle 7.42354 ( 10) covalent geometry : bond 0.01056 ( 9307) covalent geometry : angle 0.94483 (12613) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 218 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: R 78 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7687 (t80) REVERT: R 293 TYR cc_start: 0.6553 (m-80) cc_final: 0.6161 (m-80) REVERT: A 32 ARG cc_start: 0.7145 (mtm-85) cc_final: 0.6692 (mtm180) REVERT: A 186 GLU cc_start: 0.6466 (mt-10) cc_final: 0.6221 (mt-10) REVERT: B 156 GLN cc_start: 0.8012 (mt0) cc_final: 0.7779 (mt0) REVERT: B 176 GLN cc_start: 0.8320 (mt0) cc_final: 0.8024 (mt0) REVERT: B 219 ARG cc_start: 0.7075 (mtt-85) cc_final: 0.6774 (mtm110) REVERT: B 294 CYS cc_start: 0.7664 (m) cc_final: 0.7318 (m) REVERT: B 325 MET cc_start: 0.8126 (mmt) cc_final: 0.7790 (mmm) REVERT: G 59 ASN cc_start: 0.7839 (t0) cc_final: 0.7583 (t0) REVERT: S 23 SER cc_start: 0.8030 (t) cc_final: 0.7778 (m) REVERT: S 85 SER cc_start: 0.8182 (m) cc_final: 0.7971 (p) REVERT: S 87 ARG cc_start: 0.7123 (mtt180) cc_final: 0.6829 (mtt-85) REVERT: L 8 LYS cc_start: 0.6864 (OUTLIER) cc_final: 0.6644 (pttm) outliers start: 27 outliers final: 8 residues processed: 240 average time/residue: 1.2597 time to fit residues: 321.2651 Evaluate side-chains 143 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 78 PHE Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain L residue 8 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN B 75 GLN B 91 HIS B 293 ASN S 39 GLN S 130 GLN S 159 ASN S 167 GLN S 182 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.122736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.098453 restraints weight = 14641.827| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.76 r_work: 0.3253 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9312 Z= 0.146 Angle : 0.588 7.791 12623 Z= 0.313 Chirality : 0.043 0.147 1424 Planarity : 0.004 0.054 1588 Dihedral : 6.249 59.078 1281 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.76 % Favored : 98.07 % Rotamer: Outliers : 3.23 % Allowed : 10.79 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.15 (0.25), residues: 1139 helix: 1.54 (0.26), residues: 410 sheet: 0.75 (0.30), residues: 264 loop : 0.18 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.004 0.001 HIS G 44 PHE 0.025 0.002 PHE R 110 TYR 0.015 0.002 TYR R 114 ARG 0.007 0.000 ARG R 143 Details of bonding type rmsd hydrogen bonds : bond 0.04405 ( 457) hydrogen bonds : angle 4.93454 ( 1272) SS BOND : bond 0.00313 ( 5) SS BOND : angle 1.93447 ( 10) covalent geometry : bond 0.00323 ( 9307) covalent geometry : angle 0.58617 (12613) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.972 Fit side-chains REVERT: R 36 MET cc_start: 0.6032 (tpt) cc_final: 0.3103 (tmm) REVERT: R 41 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6768 (mt) REVERT: R 162 MET cc_start: 0.7627 (ptt) cc_final: 0.7291 (ptt) REVERT: R 183 MET cc_start: 0.4049 (OUTLIER) cc_final: 0.3844 (mtt) REVERT: R 272 MET cc_start: 0.6670 (mtm) cc_final: 0.5881 (ptt) REVERT: R 293 TYR cc_start: 0.6618 (m-80) cc_final: 0.6092 (m-80) REVERT: A 253 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8069 (mm) REVERT: A 274 PHE cc_start: 0.7043 (t80) cc_final: 0.6608 (t80) REVERT: B 19 ARG cc_start: 0.7679 (ttp-110) cc_final: 0.6862 (tpp-160) REVERT: B 212 ASP cc_start: 0.8097 (t0) cc_final: 0.7853 (t0) REVERT: B 217 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8277 (pmt) REVERT: B 219 ARG cc_start: 0.7691 (mtt-85) cc_final: 0.7317 (mtm110) REVERT: B 254 ASP cc_start: 0.7393 (t70) cc_final: 0.7127 (t0) REVERT: B 325 MET cc_start: 0.8472 (mmt) cc_final: 0.7801 (mmm) REVERT: G 59 ASN cc_start: 0.7964 (t0) cc_final: 0.7731 (t0) REVERT: S 87 ARG cc_start: 0.7596 (mtt180) cc_final: 0.7359 (mtt90) REVERT: L 8 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.6774 (pttm) outliers start: 32 outliers final: 11 residues processed: 167 average time/residue: 1.2825 time to fit residues: 227.8582 Evaluate side-chains 142 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 183 MET Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain L residue 8 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 72 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 112 ASN R 180 GLN A 188 HIS B 75 GLN B 176 GLN B 293 ASN B 340 ASN S 159 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.118911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.094552 restraints weight = 14655.733| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.69 r_work: 0.3185 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9312 Z= 0.223 Angle : 0.634 8.615 12623 Z= 0.332 Chirality : 0.045 0.152 1424 Planarity : 0.005 0.051 1588 Dihedral : 5.722 52.760 1270 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.37 % Favored : 97.54 % Rotamer: Outliers : 4.23 % Allowed : 11.90 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.02 (0.25), residues: 1139 helix: 1.68 (0.26), residues: 403 sheet: 0.58 (0.30), residues: 263 loop : -0.06 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.002 HIS G 44 PHE 0.028 0.002 PHE R 110 TYR 0.022 0.002 TYR R 93 ARG 0.005 0.001 ARG S 148 Details of bonding type rmsd hydrogen bonds : bond 0.04391 ( 457) hydrogen bonds : angle 4.94403 ( 1272) SS BOND : bond 0.00242 ( 5) SS BOND : angle 2.24379 ( 10) covalent geometry : bond 0.00520 ( 9307) covalent geometry : angle 0.63067 (12613) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 137 time to evaluate : 1.159 Fit side-chains revert: symmetry clash REVERT: R 162 MET cc_start: 0.7517 (ptt) cc_final: 0.7175 (ptt) REVERT: R 272 MET cc_start: 0.6865 (mtm) cc_final: 0.6081 (ptt) REVERT: R 293 TYR cc_start: 0.6862 (m-80) cc_final: 0.6374 (m-80) REVERT: A 46 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6692 (mtpm) REVERT: A 184 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7867 (tp) REVERT: A 208 ARG cc_start: 0.8228 (mtm110) cc_final: 0.7954 (ttp80) REVERT: A 253 ILE cc_start: 0.8427 (OUTLIER) cc_final: 0.8207 (mm) REVERT: A 270 LYS cc_start: 0.7547 (mttt) cc_final: 0.7067 (mmpt) REVERT: A 274 PHE cc_start: 0.7228 (t80) cc_final: 0.6887 (t80) REVERT: B 19 ARG cc_start: 0.7778 (ttp-110) cc_final: 0.6830 (tpp-160) REVERT: B 57 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8618 (mttt) REVERT: B 217 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8378 (pmt) REVERT: B 219 ARG cc_start: 0.7748 (mtt-85) cc_final: 0.7390 (mtm110) REVERT: B 254 ASP cc_start: 0.7367 (t70) cc_final: 0.7106 (t0) REVERT: S 87 ARG cc_start: 0.7578 (mtt180) cc_final: 0.7323 (mtt90) REVERT: S 159 ASN cc_start: 0.8703 (m-40) cc_final: 0.8458 (m110) outliers start: 42 outliers final: 17 residues processed: 160 average time/residue: 1.2399 time to fit residues: 211.3967 Evaluate side-chains 149 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 75 optimal weight: 0.0470 chunk 17 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN B 75 GLN B 176 GLN B 293 ASN B 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.119453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.094054 restraints weight = 14433.957| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.78 r_work: 0.3190 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9312 Z= 0.172 Angle : 0.579 8.264 12623 Z= 0.306 Chirality : 0.043 0.143 1424 Planarity : 0.004 0.051 1588 Dihedral : 5.204 56.827 1266 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.02 % Favored : 97.89 % Rotamer: Outliers : 3.93 % Allowed : 12.90 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.00 (0.25), residues: 1139 helix: 1.65 (0.27), residues: 411 sheet: 0.53 (0.30), residues: 264 loop : -0.06 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS G 44 PHE 0.027 0.002 PHE R 110 TYR 0.027 0.002 TYR R 93 ARG 0.003 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 457) hydrogen bonds : angle 4.80132 ( 1272) SS BOND : bond 0.00584 ( 5) SS BOND : angle 1.68841 ( 10) covalent geometry : bond 0.00396 ( 9307) covalent geometry : angle 0.57764 (12613) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.954 Fit side-chains REVERT: R 36 MET cc_start: 0.6656 (tpp) cc_final: 0.3408 (tmm) REVERT: R 162 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.7084 (ptt) REVERT: R 182 TYR cc_start: 0.7150 (p90) cc_final: 0.6772 (p90) REVERT: R 272 MET cc_start: 0.6526 (mtm) cc_final: 0.5946 (ptt) REVERT: R 293 TYR cc_start: 0.6832 (m-80) cc_final: 0.6377 (m-80) REVERT: A 46 LYS cc_start: 0.6672 (mtmm) cc_final: 0.6431 (mtpm) REVERT: A 184 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7872 (tp) REVERT: A 270 LYS cc_start: 0.7602 (mttt) cc_final: 0.7132 (mmpt) REVERT: A 274 PHE cc_start: 0.7216 (t80) cc_final: 0.6897 (t80) REVERT: B 57 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8570 (mttt) REVERT: B 217 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8343 (pmt) REVERT: B 219 ARG cc_start: 0.7753 (mtt-85) cc_final: 0.7333 (mtm110) REVERT: B 254 ASP cc_start: 0.7368 (t70) cc_final: 0.7067 (t0) REVERT: S 87 ARG cc_start: 0.7610 (mtt180) cc_final: 0.7273 (mtt90) REVERT: S 159 ASN cc_start: 0.8687 (m-40) cc_final: 0.8456 (m110) REVERT: L 8 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6769 (pttm) outliers start: 39 outliers final: 18 residues processed: 152 average time/residue: 1.2430 time to fit residues: 201.3551 Evaluate side-chains 145 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain L residue 8 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 33 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN B 293 ASN G 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.119615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.095103 restraints weight = 14404.472| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.75 r_work: 0.3186 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9312 Z= 0.150 Angle : 0.551 8.809 12623 Z= 0.291 Chirality : 0.042 0.143 1424 Planarity : 0.004 0.053 1588 Dihedral : 4.550 27.920 1262 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.37 % Favored : 97.54 % Rotamer: Outliers : 2.92 % Allowed : 14.92 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.00 (0.26), residues: 1139 helix: 1.73 (0.27), residues: 407 sheet: 0.52 (0.31), residues: 264 loop : -0.10 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 PHE 0.025 0.002 PHE R 110 TYR 0.021 0.002 TYR R 93 ARG 0.003 0.000 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.03686 ( 457) hydrogen bonds : angle 4.67911 ( 1272) SS BOND : bond 0.00383 ( 5) SS BOND : angle 1.55647 ( 10) covalent geometry : bond 0.00342 ( 9307) covalent geometry : angle 0.54927 (12613) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.969 Fit side-chains REVERT: R 54 PHE cc_start: 0.6467 (m-10) cc_final: 0.6233 (m-10) REVERT: R 139 ARG cc_start: 0.7779 (mtm-85) cc_final: 0.6708 (pmt-80) REVERT: R 148 VAL cc_start: 0.7278 (t) cc_final: 0.7072 (p) REVERT: R 162 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.7093 (ptt) REVERT: R 182 TYR cc_start: 0.7173 (p90) cc_final: 0.6920 (p90) REVERT: R 272 MET cc_start: 0.6703 (mtm) cc_final: 0.6065 (ttp) REVERT: R 293 TYR cc_start: 0.6878 (m-80) cc_final: 0.6500 (m-80) REVERT: A 184 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7875 (tp) REVERT: A 270 LYS cc_start: 0.7608 (mttt) cc_final: 0.7269 (mmtm) REVERT: A 274 PHE cc_start: 0.7290 (t80) cc_final: 0.6955 (t80) REVERT: A 311 ASN cc_start: 0.7802 (t0) cc_final: 0.7590 (t0) REVERT: B 57 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8524 (mttt) REVERT: B 217 MET cc_start: 0.8580 (pmm) cc_final: 0.8333 (pmt) REVERT: B 219 ARG cc_start: 0.7808 (mtt-85) cc_final: 0.7366 (mtm110) REVERT: S 87 ARG cc_start: 0.7590 (mtt180) cc_final: 0.7288 (mtt90) REVERT: S 142 SER cc_start: 0.7000 (p) cc_final: 0.6494 (t) REVERT: S 159 ASN cc_start: 0.8659 (m-40) cc_final: 0.8439 (m110) REVERT: L 8 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.6656 (pttm) outliers start: 29 outliers final: 16 residues processed: 147 average time/residue: 1.2244 time to fit residues: 191.8962 Evaluate side-chains 144 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain L residue 8 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 26 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 92 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 75 GLN B 176 GLN B 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.118123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.093509 restraints weight = 14256.357| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.70 r_work: 0.3155 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9312 Z= 0.210 Angle : 0.608 8.855 12623 Z= 0.318 Chirality : 0.044 0.146 1424 Planarity : 0.004 0.052 1588 Dihedral : 4.712 28.226 1260 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.72 % Favored : 97.19 % Rotamer: Outliers : 3.23 % Allowed : 15.32 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.83 (0.25), residues: 1139 helix: 1.58 (0.27), residues: 407 sheet: 0.37 (0.31), residues: 264 loop : -0.17 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS G 44 PHE 0.025 0.002 PHE R 110 TYR 0.022 0.002 TYR R 93 ARG 0.004 0.000 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 457) hydrogen bonds : angle 4.85237 ( 1272) SS BOND : bond 0.00417 ( 5) SS BOND : angle 1.57904 ( 10) covalent geometry : bond 0.00491 ( 9307) covalent geometry : angle 0.60655 (12613) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 1.091 Fit side-chains REVERT: R 36 MET cc_start: 0.6415 (tpp) cc_final: 0.3745 (tmm) REVERT: R 139 ARG cc_start: 0.7795 (mtm-85) cc_final: 0.6747 (pmt-80) REVERT: R 148 VAL cc_start: 0.7238 (t) cc_final: 0.7025 (p) REVERT: R 162 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.7045 (ptt) REVERT: R 272 MET cc_start: 0.6594 (mtm) cc_final: 0.6063 (ttp) REVERT: R 293 TYR cc_start: 0.6903 (m-80) cc_final: 0.6511 (m-80) REVERT: A 5 LEU cc_start: 0.8347 (mt) cc_final: 0.8056 (mp) REVERT: A 184 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.7928 (tp) REVERT: A 270 LYS cc_start: 0.7578 (mttt) cc_final: 0.7125 (mmpt) REVERT: A 274 PHE cc_start: 0.7356 (t80) cc_final: 0.7025 (t80) REVERT: B 57 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8591 (mttt) REVERT: B 177 THR cc_start: 0.8507 (OUTLIER) cc_final: 0.8264 (m) REVERT: B 217 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8291 (pmt) REVERT: B 219 ARG cc_start: 0.7762 (mtt-85) cc_final: 0.7325 (mtm110) REVERT: S 142 SER cc_start: 0.7072 (p) cc_final: 0.6869 (m) REVERT: S 159 ASN cc_start: 0.8718 (m-40) cc_final: 0.8478 (m110) REVERT: L 8 LYS cc_start: 0.7252 (OUTLIER) cc_final: 0.6524 (pttm) outliers start: 32 outliers final: 17 residues processed: 148 average time/residue: 1.2504 time to fit residues: 198.5919 Evaluate side-chains 141 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 248 SER Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain L residue 8 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 1 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 3 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN B 293 ASN G 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.120928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.096703 restraints weight = 14426.884| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.73 r_work: 0.3209 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9312 Z= 0.121 Angle : 0.534 10.750 12623 Z= 0.280 Chirality : 0.041 0.145 1424 Planarity : 0.004 0.052 1588 Dihedral : 4.349 27.816 1260 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.11 % Favored : 97.81 % Rotamer: Outliers : 2.52 % Allowed : 16.03 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.04 (0.26), residues: 1139 helix: 1.79 (0.27), residues: 413 sheet: 0.44 (0.30), residues: 267 loop : -0.08 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 297 HIS 0.003 0.001 HIS R 231 PHE 0.025 0.001 PHE R 110 TYR 0.024 0.002 TYR R 93 ARG 0.005 0.000 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.03476 ( 457) hydrogen bonds : angle 4.55596 ( 1272) SS BOND : bond 0.00284 ( 5) SS BOND : angle 1.52268 ( 10) covalent geometry : bond 0.00265 ( 9307) covalent geometry : angle 0.53246 (12613) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 1.052 Fit side-chains REVERT: R 36 MET cc_start: 0.6384 (tpp) cc_final: 0.3703 (tmm) REVERT: R 139 ARG cc_start: 0.7767 (mtm-85) cc_final: 0.6748 (pmt-80) REVERT: R 162 MET cc_start: 0.7325 (OUTLIER) cc_final: 0.6894 (ptt) REVERT: R 182 TYR cc_start: 0.7071 (p90) cc_final: 0.6301 (p90) REVERT: R 272 MET cc_start: 0.6621 (mtm) cc_final: 0.6111 (ttp) REVERT: R 293 TYR cc_start: 0.6787 (m-80) cc_final: 0.6476 (m-80) REVERT: A 184 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7909 (tp) REVERT: A 270 LYS cc_start: 0.7583 (mttt) cc_final: 0.7102 (mmpt) REVERT: A 274 PHE cc_start: 0.7264 (t80) cc_final: 0.6922 (t80) REVERT: B 177 THR cc_start: 0.8437 (p) cc_final: 0.8158 (m) REVERT: B 217 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8248 (pmt) REVERT: B 219 ARG cc_start: 0.7797 (mtt-85) cc_final: 0.7337 (mtm110) REVERT: S 142 SER cc_start: 0.7011 (p) cc_final: 0.6648 (m) REVERT: S 159 ASN cc_start: 0.8661 (m-40) cc_final: 0.8458 (m110) REVERT: S 174 GLN cc_start: 0.8492 (tt0) cc_final: 0.8269 (pt0) REVERT: S 201 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.8093 (t) REVERT: L 8 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6574 (pttm) outliers start: 25 outliers final: 10 residues processed: 145 average time/residue: 1.2051 time to fit residues: 186.8356 Evaluate side-chains 136 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain L residue 8 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 53 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 48 optimal weight: 0.0070 chunk 45 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN B 176 GLN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.121111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.096931 restraints weight = 14660.148| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.71 r_work: 0.3221 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9312 Z= 0.121 Angle : 0.536 10.935 12623 Z= 0.277 Chirality : 0.041 0.146 1424 Planarity : 0.004 0.052 1588 Dihedral : 4.235 27.761 1260 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.37 % Favored : 97.54 % Rotamer: Outliers : 2.32 % Allowed : 16.43 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.26), residues: 1139 helix: 1.88 (0.26), residues: 414 sheet: 0.39 (0.30), residues: 268 loop : -0.07 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS G 44 PHE 0.028 0.001 PHE R 286 TYR 0.020 0.001 TYR R 93 ARG 0.004 0.000 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 457) hydrogen bonds : angle 4.45003 ( 1272) SS BOND : bond 0.00299 ( 5) SS BOND : angle 1.45267 ( 10) covalent geometry : bond 0.00267 ( 9307) covalent geometry : angle 0.53508 (12613) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 1.272 Fit side-chains REVERT: R 36 MET cc_start: 0.6388 (tpp) cc_final: 0.3675 (tmm) REVERT: R 139 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.6731 (pmt-80) REVERT: R 162 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.6926 (ptt) REVERT: R 182 TYR cc_start: 0.7011 (p90) cc_final: 0.6334 (p90) REVERT: R 272 MET cc_start: 0.6602 (mtm) cc_final: 0.6098 (ttp) REVERT: R 293 TYR cc_start: 0.6796 (m-80) cc_final: 0.6503 (m-80) REVERT: A 184 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7874 (tp) REVERT: A 270 LYS cc_start: 0.7552 (mttt) cc_final: 0.7138 (mmpt) REVERT: A 274 PHE cc_start: 0.7303 (t80) cc_final: 0.6967 (t80) REVERT: B 177 THR cc_start: 0.8472 (p) cc_final: 0.8246 (m) REVERT: B 219 ARG cc_start: 0.7825 (mtt-85) cc_final: 0.7366 (mtm110) REVERT: G 21 MET cc_start: 0.6750 (mmp) cc_final: 0.6487 (tpp) REVERT: S 142 SER cc_start: 0.6976 (p) cc_final: 0.6671 (m) REVERT: S 201 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.8102 (t) REVERT: L 8 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.6560 (ptpt) outliers start: 23 outliers final: 10 residues processed: 140 average time/residue: 1.2276 time to fit residues: 184.0492 Evaluate side-chains 135 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 248 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain L residue 8 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 111 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN B 176 GLN B 293 ASN S 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.119274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.094713 restraints weight = 14398.983| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.71 r_work: 0.3166 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9312 Z= 0.175 Angle : 0.574 10.944 12623 Z= 0.299 Chirality : 0.043 0.148 1424 Planarity : 0.004 0.053 1588 Dihedral : 4.495 28.152 1260 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.28 % Favored : 97.63 % Rotamer: Outliers : 2.32 % Allowed : 16.94 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.26), residues: 1139 helix: 1.82 (0.27), residues: 407 sheet: 0.29 (0.30), residues: 274 loop : -0.10 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.004 0.001 HIS G 44 PHE 0.027 0.002 PHE R 110 TYR 0.043 0.002 TYR R 93 ARG 0.003 0.000 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 457) hydrogen bonds : angle 4.66834 ( 1272) SS BOND : bond 0.00321 ( 5) SS BOND : angle 1.51142 ( 10) covalent geometry : bond 0.00406 ( 9307) covalent geometry : angle 0.57232 (12613) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 1.043 Fit side-chains REVERT: R 36 MET cc_start: 0.6521 (tpp) cc_final: 0.3750 (tmm) REVERT: R 139 ARG cc_start: 0.7716 (mtm-85) cc_final: 0.6672 (pmt-80) REVERT: R 162 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.7040 (ptt) REVERT: R 182 TYR cc_start: 0.7050 (p90) cc_final: 0.6342 (p90) REVERT: R 272 MET cc_start: 0.6622 (mtm) cc_final: 0.6111 (ttp) REVERT: R 293 TYR cc_start: 0.6855 (m-80) cc_final: 0.6573 (m-80) REVERT: A 184 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7913 (tp) REVERT: A 270 LYS cc_start: 0.7589 (mttt) cc_final: 0.7274 (mmtm) REVERT: A 274 PHE cc_start: 0.7327 (t80) cc_final: 0.6985 (t80) REVERT: B 177 THR cc_start: 0.8505 (p) cc_final: 0.8305 (m) REVERT: B 219 ARG cc_start: 0.7826 (mtt-85) cc_final: 0.7378 (mtm110) REVERT: G 21 MET cc_start: 0.6762 (mmp) cc_final: 0.6478 (tpp) REVERT: S 142 SER cc_start: 0.6959 (p) cc_final: 0.6658 (m) REVERT: L 8 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6679 (pttm) outliers start: 23 outliers final: 11 residues processed: 140 average time/residue: 1.2305 time to fit residues: 184.1209 Evaluate side-chains 137 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 248 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain L residue 8 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 9 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN B 293 ASN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.120895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.096559 restraints weight = 14572.877| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.73 r_work: 0.3216 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9312 Z= 0.124 Angle : 0.536 12.065 12623 Z= 0.278 Chirality : 0.041 0.147 1424 Planarity : 0.004 0.054 1588 Dihedral : 4.296 27.710 1260 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.11 % Favored : 97.81 % Rotamer: Outliers : 1.92 % Allowed : 18.04 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.11 (0.26), residues: 1139 helix: 1.91 (0.26), residues: 414 sheet: 0.40 (0.30), residues: 272 loop : -0.07 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.002 0.001 HIS R 231 PHE 0.032 0.001 PHE R 286 TYR 0.037 0.002 TYR R 93 ARG 0.004 0.000 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.03375 ( 457) hydrogen bonds : angle 4.47893 ( 1272) SS BOND : bond 0.00269 ( 5) SS BOND : angle 1.38063 ( 10) covalent geometry : bond 0.00277 ( 9307) covalent geometry : angle 0.53439 (12613) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.042 Fit side-chains REVERT: R 36 MET cc_start: 0.6416 (tpp) cc_final: 0.3700 (tmm) REVERT: R 139 ARG cc_start: 0.7704 (mtm-85) cc_final: 0.6647 (pmt-80) REVERT: R 162 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6921 (ptt) REVERT: R 182 TYR cc_start: 0.7012 (p90) cc_final: 0.6327 (p90) REVERT: R 272 MET cc_start: 0.6891 (mtm) cc_final: 0.6123 (ttp) REVERT: R 293 TYR cc_start: 0.6798 (m-80) cc_final: 0.6502 (m-80) REVERT: A 184 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7896 (tt) REVERT: A 270 LYS cc_start: 0.7572 (mttt) cc_final: 0.7144 (mmpt) REVERT: A 274 PHE cc_start: 0.7254 (t80) cc_final: 0.6913 (t80) REVERT: B 177 THR cc_start: 0.8507 (p) cc_final: 0.8305 (m) REVERT: B 219 ARG cc_start: 0.7815 (mtt-85) cc_final: 0.7355 (mtm110) REVERT: G 21 MET cc_start: 0.6774 (mmp) cc_final: 0.6474 (tpp) REVERT: S 142 SER cc_start: 0.7002 (p) cc_final: 0.6704 (m) REVERT: S 201 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.8067 (t) REVERT: L 8 LYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6766 (pttm) outliers start: 19 outliers final: 13 residues processed: 137 average time/residue: 1.2279 time to fit residues: 179.6041 Evaluate side-chains 137 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 93 TYR Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain L residue 8 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 47 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 96 optimal weight: 0.1980 chunk 45 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN B 176 GLN B 293 ASN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.120355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.096021 restraints weight = 14426.073| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.71 r_work: 0.3208 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9312 Z= 0.140 Angle : 0.548 11.418 12623 Z= 0.284 Chirality : 0.042 0.147 1424 Planarity : 0.004 0.054 1588 Dihedral : 4.331 27.834 1260 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.11 % Favored : 97.81 % Rotamer: Outliers : 2.22 % Allowed : 18.15 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.10 (0.26), residues: 1139 helix: 1.92 (0.26), residues: 414 sheet: 0.40 (0.30), residues: 271 loop : -0.09 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 PHE 0.029 0.001 PHE R 110 TYR 0.031 0.002 TYR R 93 ARG 0.004 0.000 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 457) hydrogen bonds : angle 4.54753 ( 1272) SS BOND : bond 0.00267 ( 5) SS BOND : angle 1.40105 ( 10) covalent geometry : bond 0.00320 ( 9307) covalent geometry : angle 0.54655 (12613) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7004.59 seconds wall clock time: 121 minutes 28.71 seconds (7288.71 seconds total)