Starting phenix.real_space_refine on Thu Mar 13 16:40:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vv5_32138/03_2025/7vv5_32138.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vv5_32138/03_2025/7vv5_32138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vv5_32138/03_2025/7vv5_32138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vv5_32138/03_2025/7vv5_32138.map" model { file = "/net/cci-nas-00/data/ceres_data/7vv5_32138/03_2025/7vv5_32138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vv5_32138/03_2025/7vv5_32138.cif" } resolution = 2.76 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= 0.001 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 66 5.16 5 C 5660 2.51 5 N 1474 2.21 5 O 1629 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8829 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1813 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2598 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 427 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1786 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2139 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 8, 'TRANS': 259} Chain: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'6IB': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.32, per 1000 atoms: 0.60 Number of scatterers: 8829 At special positions: 0 Unit cell: (116.772, 108.356, 104.148, 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 66 16.00 O 1629 8.00 N 1474 7.00 C 5660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.06 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.05 Simple disulfide: pdb=" SG CYS R 26 " - pdb=" SG CYS R 258 " distance=2.04 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " 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: 2.22 Conformation dependent library (CDL) restraints added in 1.0 seconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 37.5% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.671A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.505A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.492A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.819A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 4.123A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 43 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.338A 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 removed outlier: 3.640A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.730A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 57 removed outlier: 3.529A pdb=" N VAL R 34 " --> pdb=" O THR R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 94 removed outlier: 3.831A pdb=" N VAL R 66 " --> pdb=" O ASN R 62 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR R 67 " --> pdb=" O ALA R 63 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 133 removed outlier: 3.602A pdb=" N VAL R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 139 Processing helix chain 'R' and resid 144 through 168 Processing helix chain 'R' and resid 176 through 212 removed outlier: 3.926A pdb=" N THR R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 236 Processing helix chain 'R' and resid 236 through 245 removed outlier: 4.339A pdb=" N GLY R 240 " --> pdb=" O GLY R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 250 Processing helix chain 'R' and resid 256 through 280 Proline residue: R 262 - end of helix Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 280 through 285 Processing helix chain 'R' and resid 286 through 288 No H-bonds generated for 'chain 'R' and resid 286 through 288' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.303A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.442A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.853A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.892A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.788A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.444A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.520A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.594A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.698A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.137A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.464A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1257 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: 2.64 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 2811 1.35 - 1.48: 2505 1.48 - 1.61: 3616 1.61 - 1.75: 2 1.75 - 1.88: 90 Bond restraints: 9024 Sorted by residual: bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.669 -0.134 2.00e-02 2.50e+03 4.52e+01 bond pdb=" C ALA S 40 " pdb=" N PRO S 41 " ideal model delta sigma weight residual 1.333 1.415 -0.082 1.44e-02 4.82e+03 3.26e+01 bond pdb=" CG LEU B 79 " pdb=" CD2 LEU B 79 " ideal model delta sigma weight residual 1.521 1.419 0.102 3.30e-02 9.18e+02 9.62e+00 bond pdb=" CG1 ILE B 123 " pdb=" CD1 ILE B 123 " ideal model delta sigma weight residual 1.513 1.406 0.107 3.90e-02 6.57e+02 7.51e+00 bond pdb=" C LEU R 237 " pdb=" N PRO R 238 " ideal model delta sigma weight residual 1.335 1.368 -0.034 1.28e-02 6.10e+03 6.99e+00 ... (remaining 9019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 11938 3.21 - 6.43: 258 6.43 - 9.64: 26 9.64 - 12.86: 3 12.86 - 16.07: 5 Bond angle restraints: 12230 Sorted by residual: angle pdb=" N PRO S 41 " pdb=" CA PRO S 41 " pdb=" C PRO S 41 " ideal model delta sigma weight residual 113.81 121.95 -8.14 1.45e+00 4.76e-01 3.15e+01 angle pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 122.74 130.63 -7.89 1.44e+00 4.82e-01 3.01e+01 angle pdb=" N LEU R 237 " pdb=" CA LEU R 237 " pdb=" C LEU R 237 " ideal model delta sigma weight residual 113.45 120.88 -7.43 1.39e+00 5.18e-01 2.85e+01 angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 121.54 131.52 -9.98 1.91e+00 2.74e-01 2.73e+01 angle pdb=" C TRP R 250 " pdb=" N LYS R 251 " pdb=" CA LYS R 251 " ideal model delta sigma weight residual 122.08 129.29 -7.21 1.47e+00 4.63e-01 2.41e+01 ... (remaining 12225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 4521 17.14 - 34.27: 579 34.27 - 51.41: 199 51.41 - 68.55: 56 68.55 - 85.69: 12 Dihedral angle restraints: 5367 sinusoidal: 2131 harmonic: 3236 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 159.43 -66.43 1 1.00e+01 1.00e-02 5.76e+01 dihedral pdb=" CA THR R 30 " pdb=" C THR R 30 " pdb=" N LEU R 31 " pdb=" CA LEU R 31 " ideal model delta harmonic sigma weight residual -180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ASP R 254 " pdb=" C ASP R 254 " pdb=" N VAL R 255 " pdb=" CA VAL R 255 " ideal model delta harmonic sigma weight residual -180.00 -154.78 -25.22 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 5364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1130 0.082 - 0.164: 227 0.164 - 0.246: 20 0.246 - 0.329: 7 0.329 - 0.411: 1 Chirality restraints: 1385 Sorted by residual: chirality pdb=" CB VAL A 218 " pdb=" CA VAL A 218 " pdb=" CG1 VAL A 218 " pdb=" CG2 VAL A 218 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.62 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CG LEU S 162 " pdb=" CB LEU S 162 " pdb=" CD1 LEU S 162 " pdb=" CD2 LEU S 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 1382 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER S 172 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.72e+00 pdb=" N PRO S 173 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO S 173 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO S 173 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.046 5.00e-02 4.00e+02 6.78e-02 7.35e+00 pdb=" N PRO S 75 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 149 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.78e+00 pdb=" C VAL R 149 " -0.042 2.00e-02 2.50e+03 pdb=" O VAL R 149 " 0.016 2.00e-02 2.50e+03 pdb=" N CYS R 150 " 0.014 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1853 2.77 - 3.30: 7280 3.30 - 3.83: 15787 3.83 - 4.37: 18448 4.37 - 4.90: 32102 Nonbonded interactions: 75470 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.236 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.286 3.040 nonbonded pdb=" O GLY R 27 " pdb=" OH TYR R 89 " model vdw 2.291 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.297 3.040 nonbonded pdb=" O SER R 264 " pdb=" OG SER R 268 " model vdw 2.306 3.040 ... (remaining 75465 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: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.630 Find NCS groups from input model: 0.090 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:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 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 : 0.012 0.134 9024 Z= 0.753 Angle : 1.174 16.073 12230 Z= 0.632 Chirality : 0.067 0.411 1385 Planarity : 0.008 0.069 1530 Dihedral : 18.052 85.686 3269 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 10.86 % Allowed : 18.27 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.21), residues: 1108 helix: -2.79 (0.16), residues: 387 sheet: -0.57 (0.29), residues: 279 loop : -1.65 (0.25), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP S 47 HIS 0.011 0.003 HIS S 35 PHE 0.028 0.004 PHE B 151 TYR 0.023 0.004 TYR S 50 ARG 0.005 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 216 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8256 (m-30) cc_final: 0.8052 (m-30) REVERT: A 29 LYS cc_start: 0.7879 (tppt) cc_final: 0.7514 (tppt) REVERT: A 32 ARG cc_start: 0.8335 (ptp90) cc_final: 0.7888 (ptp-170) REVERT: A 205 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6655 (mtm180) REVERT: A 248 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8127 (mttp) REVERT: A 273 LEU cc_start: 0.8539 (tp) cc_final: 0.8186 (tp) REVERT: A 305 CYS cc_start: 0.8128 (t) cc_final: 0.7844 (p) REVERT: B 10 GLU cc_start: 0.8181 (tp30) cc_final: 0.7699 (tp30) REVERT: B 15 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8502 (mtmt) REVERT: B 127 LYS cc_start: 0.9073 (mptm) cc_final: 0.8839 (mmtp) REVERT: B 146 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8856 (tp) REVERT: B 172 GLU cc_start: 0.7580 (pp20) cc_final: 0.7307 (tm-30) REVERT: B 188 MET cc_start: 0.8860 (mmm) cc_final: 0.8497 (mmm) REVERT: S 23 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8647 (p) REVERT: R 22 LEU cc_start: 0.6317 (OUTLIER) cc_final: 0.5832 (tm) REVERT: R 24 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6586 (mm) REVERT: R 28 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7115 (mmpt) REVERT: R 32 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7658 (tp) REVERT: R 52 LEU cc_start: 0.9279 (mt) cc_final: 0.9052 (mt) REVERT: R 58 ARG cc_start: 0.7892 (mmt-90) cc_final: 0.7662 (mmp80) REVERT: R 152 LEU cc_start: 0.8596 (mt) cc_final: 0.8371 (mt) REVERT: R 278 ILE cc_start: 0.9025 (mt) cc_final: 0.8749 (mt) REVERT: R 289 TRP cc_start: 0.5361 (p-90) cc_final: 0.4344 (m-10) outliers start: 104 outliers final: 34 residues processed: 303 average time/residue: 1.0979 time to fit residues: 355.6609 Evaluate side-chains 223 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 28 LYS Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 248 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS A 204 GLN A 213 HIS A 255 ASN B 175 GLN B 259 GLN B 311 HIS S 3 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.134126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.092675 restraints weight = 11431.039| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.32 r_work: 0.2925 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9024 Z= 0.195 Angle : 0.606 9.758 12230 Z= 0.311 Chirality : 0.043 0.213 1385 Planarity : 0.005 0.040 1530 Dihedral : 10.054 82.043 1368 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 5.11 % Allowed : 24.01 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.52 (0.24), residues: 1108 helix: 0.27 (0.25), residues: 381 sheet: 0.05 (0.31), residues: 262 loop : -1.01 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.020 0.001 PHE R 257 TYR 0.017 0.001 TYR R 222 ARG 0.007 0.001 ARG S 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 207 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8671 (tt0) REVERT: A 20 ASP cc_start: 0.8813 (m-30) cc_final: 0.8505 (m-30) REVERT: A 21 ARG cc_start: 0.8327 (mtm110) cc_final: 0.8044 (ttm-80) REVERT: A 29 LYS cc_start: 0.7989 (tppt) cc_final: 0.7686 (tppt) REVERT: B 8 ARG cc_start: 0.7635 (mpt-90) cc_final: 0.7368 (mpt-90) REVERT: B 9 GLN cc_start: 0.8400 (mm110) cc_final: 0.8018 (tm-30) REVERT: B 10 GLU cc_start: 0.8431 (tp30) cc_final: 0.7955 (tp30) REVERT: B 23 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8733 (tmmm) REVERT: B 101 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8948 (mtm) REVERT: B 127 LYS cc_start: 0.9234 (mptm) cc_final: 0.8848 (mmtp) REVERT: B 146 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8966 (tp) REVERT: B 188 MET cc_start: 0.9150 (mmm) cc_final: 0.8933 (mmm) REVERT: B 266 HIS cc_start: 0.8843 (t-90) cc_final: 0.8477 (t70) REVERT: G 20 LYS cc_start: 0.8915 (ttmt) cc_final: 0.8698 (ttmm) REVERT: G 32 LYS cc_start: 0.8854 (tttt) cc_final: 0.8574 (tmtp) REVERT: G 37 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8646 (mp) REVERT: S 43 LYS cc_start: 0.8759 (mppt) cc_final: 0.8514 (mppt) REVERT: S 62 ASP cc_start: 0.8710 (OUTLIER) cc_final: 0.8453 (p0) REVERT: S 87 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7230 (mtp85) REVERT: R 22 LEU cc_start: 0.5728 (OUTLIER) cc_final: 0.5253 (tm) REVERT: R 52 LEU cc_start: 0.9238 (mt) cc_final: 0.9008 (mt) REVERT: R 58 ARG cc_start: 0.8076 (mmt-90) cc_final: 0.7679 (mmp80) REVERT: R 221 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8056 (mp) REVERT: R 249 ILE cc_start: 0.8319 (mt) cc_final: 0.8046 (mm) REVERT: R 278 ILE cc_start: 0.8929 (mt) cc_final: 0.8651 (mt) outliers start: 49 outliers final: 16 residues processed: 232 average time/residue: 1.4192 time to fit residues: 348.0225 Evaluate side-chains 209 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 128 CYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 50 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS A 255 ASN B 36 ASN G 24 ASN S 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.130731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.088885 restraints weight = 11624.140| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.34 r_work: 0.2866 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 9024 Z= 0.348 Angle : 0.643 10.988 12230 Z= 0.327 Chirality : 0.045 0.192 1385 Planarity : 0.004 0.034 1530 Dihedral : 9.028 81.620 1320 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.43 % Allowed : 25.68 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.06 (0.25), residues: 1108 helix: 1.10 (0.26), residues: 393 sheet: 0.00 (0.30), residues: 271 loop : -0.81 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.006 0.001 HIS B 91 PHE 0.018 0.002 PHE R 257 TYR 0.018 0.002 TYR R 222 ARG 0.008 0.001 ARG S 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 192 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7867 (tppt) cc_final: 0.7309 (tppt) REVERT: A 32 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8242 (ptp-170) REVERT: A 243 MET cc_start: 0.8683 (tpp) cc_final: 0.8453 (ttm) REVERT: A 312 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8195 (mmpt) REVERT: B 9 GLN cc_start: 0.8423 (mm110) cc_final: 0.8033 (tm-30) REVERT: B 10 GLU cc_start: 0.8438 (tp30) cc_final: 0.7990 (tp30) REVERT: B 15 LYS cc_start: 0.8892 (ttmt) cc_final: 0.8591 (mtmt) REVERT: B 23 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8744 (tmmm) REVERT: B 101 MET cc_start: 0.9340 (OUTLIER) cc_final: 0.8986 (mtm) REVERT: B 127 LYS cc_start: 0.9259 (mptm) cc_final: 0.8875 (mmtp) REVERT: B 172 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8519 (mm-30) REVERT: B 188 MET cc_start: 0.9263 (mmm) cc_final: 0.8982 (mmm) REVERT: B 197 ARG cc_start: 0.8401 (mmp-170) cc_final: 0.8029 (mmp-170) REVERT: B 266 HIS cc_start: 0.8903 (t-90) cc_final: 0.8684 (t-90) REVERT: G 17 GLU cc_start: 0.8210 (tp30) cc_final: 0.7943 (tp30) REVERT: G 20 LYS cc_start: 0.8959 (ttmt) cc_final: 0.8716 (ttmm) REVERT: G 37 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8703 (mp) REVERT: S 43 LYS cc_start: 0.8821 (mppt) cc_final: 0.8584 (mppt) REVERT: S 87 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7432 (mtp85) REVERT: S 89 GLU cc_start: 0.8552 (mp0) cc_final: 0.8305 (pp20) REVERT: R 22 LEU cc_start: 0.5765 (OUTLIER) cc_final: 0.5307 (tm) REVERT: R 52 LEU cc_start: 0.9233 (mt) cc_final: 0.9010 (mt) REVERT: R 58 ARG cc_start: 0.8084 (mmt-90) cc_final: 0.7727 (mmp80) REVERT: R 249 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.8064 (mm) REVERT: R 278 ILE cc_start: 0.8989 (mt) cc_final: 0.8684 (mt) outliers start: 52 outliers final: 28 residues processed: 225 average time/residue: 1.3640 time to fit residues: 324.6913 Evaluate side-chains 217 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 128 CYS Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Chi-restraints excluded: chain R residue 249 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 59 optimal weight: 0.0570 chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 overall best weight: 1.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS B 36 ASN G 24 ASN S 3 GLN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.129101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.088762 restraints weight = 11880.105| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.32 r_work: 0.2879 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9024 Z= 0.223 Angle : 0.592 10.400 12230 Z= 0.301 Chirality : 0.043 0.158 1385 Planarity : 0.004 0.046 1530 Dihedral : 8.567 80.784 1318 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.64 % Allowed : 25.26 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.48 (0.25), residues: 1108 helix: 1.65 (0.27), residues: 382 sheet: -0.01 (0.30), residues: 280 loop : -0.56 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS B 91 PHE 0.020 0.001 PHE R 183 TYR 0.019 0.001 TYR R 222 ARG 0.011 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 190 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8232 (ptp90) REVERT: A 243 MET cc_start: 0.8526 (tpp) cc_final: 0.8325 (ttm) REVERT: A 304 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8120 (tm-30) REVERT: A 308 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8077 (mt-10) REVERT: B 8 ARG cc_start: 0.7710 (mpt180) cc_final: 0.7498 (mpt180) REVERT: B 9 GLN cc_start: 0.8405 (mm110) cc_final: 0.8110 (tm-30) REVERT: B 10 GLU cc_start: 0.8432 (tp30) cc_final: 0.7989 (tp30) REVERT: B 15 LYS cc_start: 0.8865 (ttmt) cc_final: 0.8475 (mtmt) REVERT: B 23 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8684 (tmmm) REVERT: B 101 MET cc_start: 0.9332 (OUTLIER) cc_final: 0.8916 (mtm) REVERT: B 127 LYS cc_start: 0.9233 (mptm) cc_final: 0.8821 (mmtm) REVERT: B 135 VAL cc_start: 0.9266 (t) cc_final: 0.9053 (p) REVERT: B 188 MET cc_start: 0.9247 (mmm) cc_final: 0.8954 (mmm) REVERT: B 197 ARG cc_start: 0.8355 (mmp-170) cc_final: 0.7886 (mmp-170) REVERT: B 226 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: B 266 HIS cc_start: 0.8922 (t-90) cc_final: 0.8693 (t-90) REVERT: G 17 GLU cc_start: 0.8152 (tp30) cc_final: 0.7600 (tp30) REVERT: G 20 LYS cc_start: 0.8922 (ttmt) cc_final: 0.8672 (ttmm) REVERT: G 37 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8614 (mp) REVERT: S 43 LYS cc_start: 0.8823 (mppt) cc_final: 0.8538 (mppt) REVERT: S 87 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7444 (mtp85) REVERT: S 168 ARG cc_start: 0.9006 (mtt90) cc_final: 0.8707 (mtt90) REVERT: R 22 LEU cc_start: 0.5791 (OUTLIER) cc_final: 0.5370 (tm) REVERT: R 58 ARG cc_start: 0.8067 (mmt-90) cc_final: 0.7624 (mmp80) REVERT: R 181 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.6864 (tt0) REVERT: R 208 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7486 (mmm160) REVERT: R 249 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.8045 (mm) REVERT: R 270 LEU cc_start: 0.8770 (tp) cc_final: 0.8467 (tm) REVERT: R 278 ILE cc_start: 0.8912 (mt) cc_final: 0.8581 (mt) outliers start: 54 outliers final: 26 residues processed: 222 average time/residue: 1.3027 time to fit residues: 306.7199 Evaluate side-chains 219 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 128 CYS Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Chi-restraints excluded: chain R residue 249 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 20 optimal weight: 6.9990 chunk 90 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 70 optimal weight: 0.0010 chunk 105 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS B 36 ASN G 24 ASN S 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.131486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.091743 restraints weight = 11884.882| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.30 r_work: 0.2930 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9024 Z= 0.153 Angle : 0.544 9.909 12230 Z= 0.276 Chirality : 0.041 0.158 1385 Planarity : 0.004 0.038 1530 Dihedral : 8.070 80.097 1318 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.91 % Allowed : 26.72 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.25), residues: 1108 helix: 1.95 (0.27), residues: 383 sheet: 0.20 (0.31), residues: 256 loop : -0.58 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.015 0.001 PHE R 257 TYR 0.020 0.001 TYR R 222 ARG 0.009 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 203 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8043 (tppt) cc_final: 0.7780 (tppt) REVERT: A 238 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7230 (tp30) REVERT: A 244 HIS cc_start: 0.8429 (m90) cc_final: 0.7890 (m90) REVERT: A 273 LEU cc_start: 0.8523 (tp) cc_final: 0.8144 (tp) REVERT: A 304 GLN cc_start: 0.8367 (tm-30) cc_final: 0.7976 (tm-30) REVERT: A 308 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8040 (mt-10) REVERT: A 312 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8054 (mmpt) REVERT: B 8 ARG cc_start: 0.7759 (mpt180) cc_final: 0.7457 (mpt-90) REVERT: B 9 GLN cc_start: 0.8421 (mm110) cc_final: 0.8130 (tm-30) REVERT: B 10 GLU cc_start: 0.8413 (tp30) cc_final: 0.7982 (tp30) REVERT: B 15 LYS cc_start: 0.8810 (ttmt) cc_final: 0.8440 (mtmt) REVERT: B 23 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8663 (tmmm) REVERT: B 101 MET cc_start: 0.9227 (OUTLIER) cc_final: 0.8790 (mtm) REVERT: B 127 LYS cc_start: 0.9161 (mptm) cc_final: 0.8738 (mmtm) REVERT: B 135 VAL cc_start: 0.9166 (t) cc_final: 0.8919 (p) REVERT: B 146 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8872 (tm) REVERT: B 170 ASP cc_start: 0.8770 (t70) cc_final: 0.8551 (t0) REVERT: B 188 MET cc_start: 0.9235 (mmm) cc_final: 0.8931 (mmm) REVERT: B 197 ARG cc_start: 0.8302 (mmp-170) cc_final: 0.7866 (mmp-170) REVERT: B 217 MET cc_start: 0.9029 (pmm) cc_final: 0.8671 (ppp) REVERT: B 226 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: B 266 HIS cc_start: 0.8920 (t-90) cc_final: 0.8703 (t-90) REVERT: G 20 LYS cc_start: 0.8888 (ttmt) cc_final: 0.8665 (ttmm) REVERT: G 29 LYS cc_start: 0.8593 (mmmt) cc_final: 0.8337 (mptm) REVERT: G 37 LEU cc_start: 0.8882 (tp) cc_final: 0.8565 (mp) REVERT: S 43 LYS cc_start: 0.8826 (mppt) cc_final: 0.8549 (mppt) REVERT: S 62 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8440 (p0) REVERT: S 87 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7604 (mtp85) REVERT: R 22 LEU cc_start: 0.5651 (OUTLIER) cc_final: 0.5293 (tm) REVERT: R 58 ARG cc_start: 0.8070 (mmt-90) cc_final: 0.7570 (mmp80) REVERT: R 60 ARG cc_start: 0.7973 (ttm170) cc_final: 0.7720 (ttp-170) REVERT: R 249 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8097 (mm) REVERT: R 270 LEU cc_start: 0.8735 (tp) cc_final: 0.8446 (tm) REVERT: R 278 ILE cc_start: 0.8852 (mt) cc_final: 0.8512 (mt) outliers start: 47 outliers final: 20 residues processed: 233 average time/residue: 1.3139 time to fit residues: 325.0340 Evaluate side-chains 218 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 128 CYS Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Chi-restraints excluded: chain R residue 249 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 72 optimal weight: 0.0770 chunk 53 optimal weight: 1.9990 overall best weight: 2.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS B 36 ASN G 24 ASN S 3 GLN S 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.130901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.089203 restraints weight = 11480.452| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.31 r_work: 0.2874 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 9024 Z= 0.345 Angle : 0.622 11.186 12230 Z= 0.316 Chirality : 0.045 0.164 1385 Planarity : 0.004 0.045 1530 Dihedral : 8.076 79.853 1312 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.01 % Allowed : 27.45 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.82 (0.26), residues: 1108 helix: 2.13 (0.27), residues: 377 sheet: 0.06 (0.30), residues: 277 loop : -0.45 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP S 47 HIS 0.005 0.001 HIS B 91 PHE 0.017 0.002 PHE R 183 TYR 0.015 0.002 TYR R 222 ARG 0.009 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 183 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 HIS cc_start: 0.8463 (m90) cc_final: 0.7973 (m90) REVERT: A 308 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8113 (mt-10) REVERT: A 312 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8196 (mmpt) REVERT: B 8 ARG cc_start: 0.7815 (mpt180) cc_final: 0.7563 (mpt-90) REVERT: B 9 GLN cc_start: 0.8469 (mm110) cc_final: 0.8136 (tm-30) REVERT: B 10 GLU cc_start: 0.8439 (tp30) cc_final: 0.8003 (tp30) REVERT: B 15 LYS cc_start: 0.8846 (ttmt) cc_final: 0.8489 (mtmt) REVERT: B 101 MET cc_start: 0.9363 (OUTLIER) cc_final: 0.8950 (mtm) REVERT: B 127 LYS cc_start: 0.9250 (mptm) cc_final: 0.8902 (mmtp) REVERT: B 135 VAL cc_start: 0.9328 (t) cc_final: 0.9121 (p) REVERT: B 188 MET cc_start: 0.9263 (mmm) cc_final: 0.8948 (mmm) REVERT: B 197 ARG cc_start: 0.8429 (mmp-170) cc_final: 0.8036 (mmp-170) REVERT: B 217 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8689 (ppp) REVERT: B 226 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7817 (mp0) REVERT: B 266 HIS cc_start: 0.8939 (t-90) cc_final: 0.8729 (t-90) REVERT: G 17 GLU cc_start: 0.8030 (tp30) cc_final: 0.7670 (tp30) REVERT: G 20 LYS cc_start: 0.8939 (ttmt) cc_final: 0.8683 (ttmm) REVERT: R 22 LEU cc_start: 0.5779 (OUTLIER) cc_final: 0.5383 (tm) REVERT: R 58 ARG cc_start: 0.8100 (mmt-90) cc_final: 0.7586 (mmp80) REVERT: R 181 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.6967 (tt0) REVERT: R 208 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7461 (mmm160) REVERT: R 249 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8123 (mm) REVERT: R 270 LEU cc_start: 0.8809 (tp) cc_final: 0.8514 (tm) REVERT: R 278 ILE cc_start: 0.8959 (mt) cc_final: 0.8628 (mt) outliers start: 48 outliers final: 25 residues processed: 212 average time/residue: 1.2906 time to fit residues: 289.8575 Evaluate side-chains 212 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 128 CYS Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Chi-restraints excluded: chain R residue 249 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 24 optimal weight: 0.3980 chunk 99 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS B 36 ASN G 24 ASN S 3 GLN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.131840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.092874 restraints weight = 11797.397| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.19 r_work: 0.2949 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9024 Z= 0.212 Angle : 0.582 10.386 12230 Z= 0.294 Chirality : 0.042 0.164 1385 Planarity : 0.004 0.042 1530 Dihedral : 7.835 79.345 1312 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.70 % Allowed : 27.77 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1108 helix: 2.27 (0.27), residues: 379 sheet: 0.16 (0.31), residues: 268 loop : -0.37 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.011 0.001 PHE A 189 TYR 0.018 0.001 TYR R 222 ARG 0.010 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 189 time to evaluate : 2.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7193 (tp30) REVERT: A 244 HIS cc_start: 0.8480 (m90) cc_final: 0.8062 (m90) REVERT: A 273 LEU cc_start: 0.8548 (tp) cc_final: 0.8238 (tp) REVERT: A 306 GLN cc_start: 0.8510 (tp40) cc_final: 0.8257 (mp10) REVERT: A 308 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8094 (mt-10) REVERT: A 312 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8174 (mmpt) REVERT: B 8 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7585 (mpt-90) REVERT: B 9 GLN cc_start: 0.8465 (mm110) cc_final: 0.8150 (tm-30) REVERT: B 10 GLU cc_start: 0.8443 (tp30) cc_final: 0.7997 (tp30) REVERT: B 15 LYS cc_start: 0.8891 (ttmt) cc_final: 0.8538 (mtmt) REVERT: B 101 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.8738 (mtm) REVERT: B 127 LYS cc_start: 0.9265 (mptm) cc_final: 0.8895 (mmtm) REVERT: B 170 ASP cc_start: 0.8818 (t70) cc_final: 0.8611 (t0) REVERT: B 188 MET cc_start: 0.9201 (mmm) cc_final: 0.8886 (mmm) REVERT: B 197 ARG cc_start: 0.8398 (mmp-170) cc_final: 0.8015 (mmp-170) REVERT: B 217 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8649 (ppp) REVERT: B 226 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7889 (mp0) REVERT: B 266 HIS cc_start: 0.8959 (t-90) cc_final: 0.8751 (t-90) REVERT: G 17 GLU cc_start: 0.8095 (tp30) cc_final: 0.7719 (tp30) REVERT: G 20 LYS cc_start: 0.9024 (ttmt) cc_final: 0.8779 (ttmm) REVERT: G 37 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8631 (mp) REVERT: S 43 LYS cc_start: 0.8817 (mppt) cc_final: 0.8543 (mppt) REVERT: S 62 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8492 (p0) REVERT: S 93 MET cc_start: 0.8906 (tpp) cc_final: 0.8698 (tpp) REVERT: S 148 ARG cc_start: 0.8037 (mmm-85) cc_final: 0.7462 (mmm-85) REVERT: S 168 ARG cc_start: 0.8915 (mtt180) cc_final: 0.8663 (mtt180) REVERT: R 22 LEU cc_start: 0.5803 (OUTLIER) cc_final: 0.5458 (tm) REVERT: R 58 ARG cc_start: 0.8100 (mmt-90) cc_final: 0.7498 (mmp80) REVERT: R 181 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.6852 (tt0) REVERT: R 208 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7540 (mmm160) REVERT: R 249 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8211 (mm) REVERT: R 270 LEU cc_start: 0.8792 (tp) cc_final: 0.8517 (tm) REVERT: R 278 ILE cc_start: 0.8905 (mt) cc_final: 0.8561 (mt) outliers start: 45 outliers final: 25 residues processed: 214 average time/residue: 1.4744 time to fit residues: 335.0699 Evaluate side-chains 219 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 128 CYS Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Chi-restraints excluded: chain R residue 249 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 107 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS B 36 ASN G 24 ASN S 3 GLN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.131021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.091972 restraints weight = 11905.168| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.19 r_work: 0.2933 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9024 Z= 0.266 Angle : 0.607 10.362 12230 Z= 0.307 Chirality : 0.043 0.167 1385 Planarity : 0.004 0.048 1530 Dihedral : 7.783 79.133 1311 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 5.22 % Allowed : 28.18 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.01 (0.26), residues: 1108 helix: 2.29 (0.27), residues: 379 sheet: 0.13 (0.31), residues: 270 loop : -0.32 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.005 0.001 HIS B 91 PHE 0.015 0.001 PHE R 183 TYR 0.023 0.002 TYR R 222 ARG 0.012 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 179 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8242 (m-30) REVERT: A 238 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7188 (tp30) REVERT: A 244 HIS cc_start: 0.8515 (m90) cc_final: 0.8103 (m90) REVERT: A 273 LEU cc_start: 0.8530 (tp) cc_final: 0.8174 (tp) REVERT: A 306 GLN cc_start: 0.8523 (tp40) cc_final: 0.8208 (mm110) REVERT: A 312 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8146 (mmpt) REVERT: B 8 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7576 (mpt-90) REVERT: B 9 GLN cc_start: 0.8460 (mm110) cc_final: 0.8158 (tm-30) REVERT: B 10 GLU cc_start: 0.8489 (tp30) cc_final: 0.8063 (tp30) REVERT: B 15 LYS cc_start: 0.8921 (ttmt) cc_final: 0.8563 (mtmt) REVERT: B 101 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.8808 (mtm) REVERT: B 127 LYS cc_start: 0.9276 (mptm) cc_final: 0.8954 (mmtp) REVERT: B 188 MET cc_start: 0.9215 (mmm) cc_final: 0.8893 (mmm) REVERT: B 197 ARG cc_start: 0.8428 (mmp-170) cc_final: 0.8048 (mmp-170) REVERT: B 217 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8622 (ppp) REVERT: B 226 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7884 (mp0) REVERT: G 17 GLU cc_start: 0.8150 (tp30) cc_final: 0.7931 (tp30) REVERT: G 20 LYS cc_start: 0.9014 (ttmt) cc_final: 0.8781 (ttmm) REVERT: S 43 LYS cc_start: 0.8838 (mppt) cc_final: 0.8561 (mppt) REVERT: S 62 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8486 (p0) REVERT: S 87 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7973 (mtp85) REVERT: S 93 MET cc_start: 0.8911 (tpp) cc_final: 0.8681 (tpp) REVERT: R 22 LEU cc_start: 0.5849 (OUTLIER) cc_final: 0.5515 (tm) REVERT: R 58 ARG cc_start: 0.8101 (mmt-90) cc_final: 0.7520 (mmp80) REVERT: R 181 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.6866 (tt0) REVERT: R 208 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7542 (mmm160) REVERT: R 249 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8264 (mm) REVERT: R 270 LEU cc_start: 0.8806 (tp) cc_final: 0.8545 (tm) REVERT: R 278 ILE cc_start: 0.8931 (mt) cc_final: 0.8591 (mt) outliers start: 50 outliers final: 30 residues processed: 208 average time/residue: 1.2864 time to fit residues: 284.0532 Evaluate side-chains 220 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 128 CYS Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Chi-restraints excluded: chain R residue 249 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 91 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS B 36 ASN G 24 ASN S 3 GLN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.089632 restraints weight = 11519.339| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.32 r_work: 0.2875 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9024 Z= 0.312 Angle : 0.634 10.841 12230 Z= 0.322 Chirality : 0.044 0.168 1385 Planarity : 0.004 0.051 1530 Dihedral : 7.818 78.628 1311 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 5.43 % Allowed : 28.50 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.03 (0.26), residues: 1108 helix: 2.27 (0.27), residues: 378 sheet: 0.18 (0.31), residues: 276 loop : -0.30 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.005 0.001 HIS B 91 PHE 0.013 0.001 PHE A 196 TYR 0.023 0.002 TYR R 222 ARG 0.012 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 180 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8212 (m-30) REVERT: A 238 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7200 (tp30) REVERT: A 244 HIS cc_start: 0.8441 (m90) cc_final: 0.7971 (m90) REVERT: A 273 LEU cc_start: 0.8535 (tp) cc_final: 0.8166 (tp) REVERT: A 306 GLN cc_start: 0.8550 (tp40) cc_final: 0.8302 (mm110) REVERT: A 312 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8164 (mmpt) REVERT: B 8 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7565 (mpt-90) REVERT: B 9 GLN cc_start: 0.8471 (mm110) cc_final: 0.8134 (tm-30) REVERT: B 10 GLU cc_start: 0.8485 (tp30) cc_final: 0.8040 (tp30) REVERT: B 15 LYS cc_start: 0.8850 (ttmt) cc_final: 0.8505 (mtmt) REVERT: B 101 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.8887 (mtm) REVERT: B 127 LYS cc_start: 0.9251 (mptm) cc_final: 0.8912 (mmtp) REVERT: B 130 GLU cc_start: 0.8767 (mp0) cc_final: 0.8480 (mp0) REVERT: B 188 MET cc_start: 0.9277 (mmm) cc_final: 0.8980 (mmm) REVERT: B 197 ARG cc_start: 0.8415 (mmp-170) cc_final: 0.8001 (mmp-170) REVERT: B 226 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7849 (mp0) REVERT: G 17 GLU cc_start: 0.8129 (tp30) cc_final: 0.7890 (tp30) REVERT: G 20 LYS cc_start: 0.8966 (ttmt) cc_final: 0.8704 (ttmm) REVERT: S 62 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8453 (p0) REVERT: S 148 ARG cc_start: 0.8060 (mmm-85) cc_final: 0.7482 (mmm-85) REVERT: R 22 LEU cc_start: 0.5759 (OUTLIER) cc_final: 0.5461 (tm) REVERT: R 58 ARG cc_start: 0.8110 (mmt-90) cc_final: 0.7505 (mmp80) REVERT: R 181 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.6902 (tt0) REVERT: R 208 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7459 (mmm160) REVERT: R 249 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8404 (mm) REVERT: R 270 LEU cc_start: 0.8779 (tp) cc_final: 0.8511 (tm) REVERT: R 278 ILE cc_start: 0.8928 (mt) cc_final: 0.8590 (mt) outliers start: 52 outliers final: 30 residues processed: 209 average time/residue: 1.2790 time to fit residues: 283.4956 Evaluate side-chains 218 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 128 CYS Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Chi-restraints excluded: chain R residue 249 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 69 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS B 36 ASN G 24 ASN S 3 GLN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.131393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.092241 restraints weight = 11692.568| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.20 r_work: 0.2938 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9024 Z= 0.231 Angle : 0.621 10.310 12230 Z= 0.315 Chirality : 0.043 0.167 1385 Planarity : 0.004 0.055 1530 Dihedral : 7.690 78.352 1311 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.97 % Allowed : 29.75 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1108 helix: 2.31 (0.27), residues: 379 sheet: 0.20 (0.31), residues: 274 loop : -0.26 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS B 91 PHE 0.012 0.001 PHE B 292 TYR 0.013 0.001 TYR A 302 ARG 0.013 0.001 ARG B 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8261 (m-30) REVERT: A 238 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7187 (tp30) REVERT: A 244 HIS cc_start: 0.8513 (m90) cc_final: 0.8061 (m90) REVERT: A 273 LEU cc_start: 0.8555 (tp) cc_final: 0.8189 (tp) REVERT: A 312 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8169 (mmpt) REVERT: B 8 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7590 (mpt-90) REVERT: B 9 GLN cc_start: 0.8465 (mm110) cc_final: 0.8155 (tm-30) REVERT: B 10 GLU cc_start: 0.8487 (tp30) cc_final: 0.8063 (tp30) REVERT: B 15 LYS cc_start: 0.8913 (ttmt) cc_final: 0.8564 (mtmt) REVERT: B 101 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.8749 (mtm) REVERT: B 127 LYS cc_start: 0.9276 (mptm) cc_final: 0.8925 (mmtm) REVERT: B 130 GLU cc_start: 0.8758 (mp0) cc_final: 0.8476 (mp0) REVERT: B 170 ASP cc_start: 0.8813 (t70) cc_final: 0.8608 (t0) REVERT: B 188 MET cc_start: 0.9227 (mmm) cc_final: 0.8922 (mmm) REVERT: B 197 ARG cc_start: 0.8397 (mmp-170) cc_final: 0.7990 (mmp-170) REVERT: B 226 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7886 (mp0) REVERT: B 266 HIS cc_start: 0.8895 (t-90) cc_final: 0.8613 (t70) REVERT: G 17 GLU cc_start: 0.8172 (tp30) cc_final: 0.7939 (tp30) REVERT: G 20 LYS cc_start: 0.9022 (ttmt) cc_final: 0.8803 (ttmm) REVERT: S 43 LYS cc_start: 0.8736 (mppt) cc_final: 0.8368 (mtmm) REVERT: S 62 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8501 (p0) REVERT: S 148 ARG cc_start: 0.8005 (mmm-85) cc_final: 0.7457 (mmm-85) REVERT: R 22 LEU cc_start: 0.5777 (OUTLIER) cc_final: 0.5514 (tm) REVERT: R 58 ARG cc_start: 0.8071 (mmt-90) cc_final: 0.7484 (mmp80) REVERT: R 181 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.6939 (tt0) REVERT: R 208 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7558 (mmm160) REVERT: R 249 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8463 (mm) REVERT: R 270 LEU cc_start: 0.8791 (tp) cc_final: 0.8535 (tm) REVERT: R 278 ILE cc_start: 0.8901 (mt) cc_final: 0.8561 (mt) outliers start: 38 outliers final: 25 residues processed: 207 average time/residue: 1.4304 time to fit residues: 314.4315 Evaluate side-chains 216 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 128 CYS Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Chi-restraints excluded: chain R residue 249 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 54 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 102 optimal weight: 0.0010 chunk 34 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.0870 overall best weight: 0.5966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS B 36 ASN G 24 ASN S 3 GLN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.133806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.095375 restraints weight = 11834.840| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.19 r_work: 0.2991 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9024 Z= 0.163 Angle : 0.594 9.436 12230 Z= 0.300 Chirality : 0.042 0.168 1385 Planarity : 0.004 0.060 1530 Dihedral : 7.510 78.353 1310 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.92 % Allowed : 31.11 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.16 (0.26), residues: 1108 helix: 2.37 (0.26), residues: 380 sheet: 0.23 (0.31), residues: 268 loop : -0.19 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.029 0.001 PHE R 257 TYR 0.018 0.001 TYR R 222 ARG 0.014 0.001 ARG A 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8864.00 seconds wall clock time: 154 minutes 6.24 seconds (9246.24 seconds total)