Starting phenix.real_space_refine on Sun Jul 27 03:33:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vv5_32138/07_2025/7vv5_32138.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vv5_32138/07_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_32138/07_2025/7vv5_32138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vv5_32138/07_2025/7vv5_32138.map" model { file = "/net/cci-nas-00/data/ceres_data/7vv5_32138/07_2025/7vv5_32138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vv5_32138/07_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-5711/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: 5.63, per 1000 atoms: 0.64 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: 2.25 Conformation dependent library (CDL) restraints added in 999.1 milliseconds 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: 1.09 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: 2.78 Time building geometry restraints manager: 2.67 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: 0.310 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 24.030 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.440 ------------------------------------------------------------------------------- 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 9028 Z= 0.506 Angle : 1.177 16.073 12238 Z= 0.634 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 Details of bonding type rmsd hydrogen bonds : bond 0.16487 ( 437) hydrogen bonds : angle 7.57451 ( 1257) SS BOND : bond 0.01765 ( 4) SS BOND : angle 3.32485 ( 8) covalent geometry : bond 0.01165 ( 9024) covalent geometry : angle 1.17381 (12230) *********************** 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 : 1.029 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: 1.0660 time to fit residues: 345.4609 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 : 0.961 ------------------------------------------------------------------------------- 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: 5.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.133690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.092141 restraints weight = 11434.080| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.33 r_work: 0.2917 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9028 Z= 0.145 Angle : 0.610 9.783 12238 Z= 0.313 Chirality : 0.043 0.208 1385 Planarity : 0.005 0.040 1530 Dihedral : 10.070 82.139 1368 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 5.01 % Allowed : 24.32 % Favored : 70.67 % 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: -0.50 (0.24), residues: 1108 helix: 0.30 (0.25), residues: 381 sheet: 0.05 (0.31), residues: 262 loop : -1.00 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 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 Details of bonding type rmsd hydrogen bonds : bond 0.04159 ( 437) hydrogen bonds : angle 4.94651 ( 1257) SS BOND : bond 0.01246 ( 4) SS BOND : angle 1.99750 ( 8) covalent geometry : bond 0.00315 ( 9024) covalent geometry : angle 0.60782 (12230) *********************** 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 254 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 206 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8693 (tt0) REVERT: A 21 ARG cc_start: 0.8339 (mtm110) cc_final: 0.8045 (ttm-80) REVERT: A 29 LYS cc_start: 0.8015 (tppt) cc_final: 0.7709 (tppt) REVERT: A 305 CYS cc_start: 0.8746 (t) cc_final: 0.8168 (t) REVERT: B 8 ARG cc_start: 0.7648 (mpt-90) cc_final: 0.7384 (mpt-90) REVERT: B 9 GLN cc_start: 0.8400 (mm110) cc_final: 0.8034 (tm-30) REVERT: B 10 GLU cc_start: 0.8433 (tp30) cc_final: 0.7955 (tp30) REVERT: B 23 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8745 (tmmm) REVERT: B 101 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8949 (mtm) REVERT: B 127 LYS cc_start: 0.9235 (mptm) cc_final: 0.8846 (mmtp) REVERT: B 146 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8973 (tp) REVERT: B 188 MET cc_start: 0.9167 (mmm) cc_final: 0.8944 (mmm) REVERT: B 266 HIS cc_start: 0.8844 (t-90) cc_final: 0.8477 (t70) REVERT: G 20 LYS cc_start: 0.8925 (ttmt) cc_final: 0.8707 (ttmm) REVERT: G 32 LYS cc_start: 0.8846 (tttt) cc_final: 0.8586 (tmtp) REVERT: G 37 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8633 (mp) REVERT: S 43 LYS cc_start: 0.8762 (mppt) cc_final: 0.8522 (mppt) REVERT: S 62 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8446 (p0) REVERT: S 87 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7245 (mtp85) REVERT: S 168 ARG cc_start: 0.9070 (mtt90) cc_final: 0.8644 (mtt90) REVERT: S 222 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8312 (mt-10) REVERT: R 22 LEU cc_start: 0.5736 (OUTLIER) cc_final: 0.5268 (tm) REVERT: R 52 LEU cc_start: 0.9239 (mt) cc_final: 0.9012 (mt) REVERT: R 58 ARG cc_start: 0.8072 (mmt-90) cc_final: 0.7684 (mmp80) REVERT: R 221 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8098 (mp) REVERT: R 249 ILE cc_start: 0.8311 (mt) cc_final: 0.8036 (mm) REVERT: R 278 ILE cc_start: 0.8928 (mt) cc_final: 0.8650 (mt) outliers start: 48 outliers final: 17 residues processed: 231 average time/residue: 1.5710 time to fit residues: 385.1139 Evaluate side-chains 208 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 2.432 ------------------------------------------------------------------------------- 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 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 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: 0.0670 chunk 79 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 overall best weight: 2.7924 ------------------------------------------------------------------------------- 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 S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.130861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.088980 restraints weight = 11611.137| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.34 r_work: 0.2869 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9028 Z= 0.225 Angle : 0.635 10.957 12238 Z= 0.325 Chirality : 0.045 0.189 1385 Planarity : 0.004 0.035 1530 Dihedral : 8.918 81.609 1320 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.95 % Allowed : 24.74 % Favored : 69.31 % 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: 0.07 (0.25), residues: 1108 helix: 1.14 (0.26), residues: 391 sheet: -0.00 (0.31), residues: 271 loop : -0.83 (0.28), residues: 446 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 0.015 0.002 PHE A 196 TYR 0.018 0.002 TYR R 222 ARG 0.008 0.001 ARG S 190 Details of bonding type rmsd hydrogen bonds : bond 0.04386 ( 437) hydrogen bonds : angle 4.73462 ( 1257) SS BOND : bond 0.01634 ( 4) SS BOND : angle 2.67000 ( 8) covalent geometry : bond 0.00513 ( 9024) covalent geometry : angle 0.63138 (12230) *********************** 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 245 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 188 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8682 (tt0) REVERT: A 29 LYS cc_start: 0.7860 (tppt) cc_final: 0.7303 (tppt) REVERT: A 32 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8239 (ptp-170) REVERT: A 243 MET cc_start: 0.8692 (tpp) cc_final: 0.8475 (ttm) REVERT: A 312 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8261 (mmpt) REVERT: B 9 GLN cc_start: 0.8424 (mm110) cc_final: 0.8106 (tm-30) REVERT: B 10 GLU cc_start: 0.8446 (tp30) cc_final: 0.7979 (tp30) REVERT: B 15 LYS cc_start: 0.8902 (ttmt) cc_final: 0.8604 (mtmt) REVERT: B 23 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8759 (tmmm) REVERT: B 101 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.8967 (mtm) REVERT: B 127 LYS cc_start: 0.9261 (mptm) cc_final: 0.8878 (mmtp) REVERT: B 172 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8524 (mm-30) REVERT: B 188 MET cc_start: 0.9268 (mmm) cc_final: 0.8986 (mmm) REVERT: B 197 ARG cc_start: 0.8443 (mmp-170) cc_final: 0.8051 (mmp-170) REVERT: B 226 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7990 (mp0) REVERT: B 266 HIS cc_start: 0.8894 (t-90) cc_final: 0.8668 (t-90) REVERT: G 17 GLU cc_start: 0.8211 (tp30) cc_final: 0.7944 (tp30) REVERT: G 20 LYS cc_start: 0.8966 (ttmt) cc_final: 0.8723 (ttmm) REVERT: G 37 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8697 (mp) REVERT: S 43 LYS cc_start: 0.8822 (mppt) cc_final: 0.8568 (mppt) REVERT: S 87 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7453 (mtp85) REVERT: S 89 GLU cc_start: 0.8551 (mp0) cc_final: 0.8306 (pp20) REVERT: S 168 ARG cc_start: 0.9058 (mtt90) cc_final: 0.8849 (mtt90) REVERT: R 22 LEU cc_start: 0.5794 (OUTLIER) cc_final: 0.5352 (tm) REVERT: R 52 LEU cc_start: 0.9231 (mt) cc_final: 0.9007 (mt) REVERT: R 58 ARG cc_start: 0.8090 (mmt-90) cc_final: 0.7744 (mmp80) REVERT: R 249 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.8079 (mm) REVERT: R 278 ILE cc_start: 0.8997 (mt) cc_final: 0.8688 (mt) outliers start: 57 outliers final: 28 residues processed: 224 average time/residue: 1.3306 time to fit residues: 315.4929 Evaluate side-chains 215 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU 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 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 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: 0.8980 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 chunk 46 optimal weight: 0.3980 chunk 98 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3678 r_free = 0.3678 target = 0.134916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.096010 restraints weight = 11638.060| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.21 r_work: 0.2996 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9028 Z= 0.111 Angle : 0.562 10.297 12238 Z= 0.284 Chirality : 0.042 0.156 1385 Planarity : 0.004 0.054 1530 Dihedral : 8.318 80.833 1318 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 5.01 % Allowed : 25.47 % Favored : 69.52 % 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: 0.58 (0.25), residues: 1108 helix: 1.73 (0.27), residues: 383 sheet: 0.14 (0.31), residues: 269 loop : -0.57 (0.29), residues: 456 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 0.012 0.001 PHE R 257 TYR 0.018 0.001 TYR R 222 ARG 0.011 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 437) hydrogen bonds : angle 4.46194 ( 1257) SS BOND : bond 0.00931 ( 4) SS BOND : angle 1.74502 ( 8) covalent geometry : bond 0.00237 ( 9024) covalent geometry : angle 0.55993 (12230) *********************** 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 247 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 199 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 ARG cc_start: 0.7713 (mpt180) cc_final: 0.7480 (mpt180) REVERT: B 9 GLN cc_start: 0.8419 (mm110) cc_final: 0.8147 (tm-30) REVERT: B 10 GLU cc_start: 0.8403 (tp30) cc_final: 0.8023 (tp30) REVERT: B 15 LYS cc_start: 0.8951 (ttmt) cc_final: 0.8547 (mtmt) REVERT: B 101 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8735 (mtm) REVERT: B 127 LYS cc_start: 0.9215 (mptm) cc_final: 0.8822 (mmtm) REVERT: B 135 VAL cc_start: 0.9133 (t) cc_final: 0.8896 (p) REVERT: B 188 MET cc_start: 0.9184 (mmm) cc_final: 0.8870 (mmm) REVERT: B 197 ARG cc_start: 0.8344 (mmp-170) cc_final: 0.8004 (mmp-170) REVERT: B 226 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: G 17 GLU cc_start: 0.8211 (tp30) cc_final: 0.7592 (tp30) REVERT: G 20 LYS cc_start: 0.8983 (ttmt) cc_final: 0.8744 (ttmm) REVERT: G 37 LEU cc_start: 0.8928 (tp) cc_final: 0.8621 (mp) REVERT: S 43 LYS cc_start: 0.8796 (mppt) cc_final: 0.8576 (mppt) REVERT: S 87 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7395 (mtp85) REVERT: R 22 LEU cc_start: 0.5790 (OUTLIER) cc_final: 0.5410 (tm) REVERT: R 58 ARG cc_start: 0.8122 (mmt-90) cc_final: 0.7607 (mmp80) REVERT: R 208 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7632 (mmm160) REVERT: R 249 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8060 (mm) REVERT: R 278 ILE cc_start: 0.8935 (mt) cc_final: 0.8604 (mt) outliers start: 48 outliers final: 22 residues processed: 225 average time/residue: 1.2559 time to fit residues: 299.8434 Evaluate side-chains 211 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 218 VAL Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR 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 153 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 323 ASP 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 R residue 22 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 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: 7.9990 chunk 90 optimal weight: 0.0980 chunk 44 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 34 optimal weight: 0.2980 chunk 83 optimal weight: 7.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.130526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.090363 restraints weight = 11849.205| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.32 r_work: 0.2912 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9028 Z= 0.135 Angle : 0.575 10.132 12238 Z= 0.288 Chirality : 0.042 0.158 1385 Planarity : 0.004 0.044 1530 Dihedral : 7.990 80.616 1314 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.01 % Allowed : 26.30 % Favored : 68.68 % 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: 0.75 (0.26), residues: 1108 helix: 2.02 (0.27), residues: 378 sheet: 0.11 (0.31), residues: 272 loop : -0.50 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.024 0.001 PHE R 257 TYR 0.018 0.001 TYR R 222 ARG 0.009 0.001 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 437) hydrogen bonds : angle 4.33512 ( 1257) SS BOND : bond 0.01249 ( 4) SS BOND : angle 2.09245 ( 8) covalent geometry : bond 0.00303 ( 9024) covalent geometry : angle 0.57276 (12230) *********************** 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 240 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 192 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8071 (tppt) cc_final: 0.7803 (tppt) REVERT: A 32 ARG cc_start: 0.8462 (ptp-110) cc_final: 0.8191 (ptp-170) REVERT: A 273 LEU cc_start: 0.8518 (tp) cc_final: 0.8189 (tp) REVERT: A 312 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8059 (mmpt) REVERT: B 8 ARG cc_start: 0.7774 (mpt180) cc_final: 0.7464 (mpt-90) REVERT: B 9 GLN cc_start: 0.8432 (mm110) cc_final: 0.8133 (tm-30) REVERT: B 10 GLU cc_start: 0.8451 (tp30) cc_final: 0.7992 (tp30) REVERT: B 15 LYS cc_start: 0.8819 (ttmt) cc_final: 0.8423 (mtmt) REVERT: B 101 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.8847 (mtm) REVERT: B 127 LYS cc_start: 0.9199 (mptm) cc_final: 0.8762 (mmtm) REVERT: B 135 VAL cc_start: 0.9216 (t) cc_final: 0.9008 (p) REVERT: B 188 MET cc_start: 0.9246 (mmm) cc_final: 0.8941 (mmm) REVERT: B 217 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8797 (pmt) REVERT: B 226 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: B 266 HIS cc_start: 0.8835 (t-90) cc_final: 0.8549 (t70) REVERT: G 20 LYS cc_start: 0.8899 (ttmt) cc_final: 0.8678 (ttmm) REVERT: G 37 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8606 (mp) REVERT: S 43 LYS cc_start: 0.8819 (mppt) cc_final: 0.8531 (mppt) REVERT: S 62 ASP cc_start: 0.8715 (OUTLIER) cc_final: 0.8456 (p0) REVERT: S 87 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8119 (ptp-170) REVERT: S 206 ARG cc_start: 0.8318 (mtm110) cc_final: 0.7825 (tmm-80) REVERT: R 22 LEU cc_start: 0.5603 (OUTLIER) cc_final: 0.5215 (tm) REVERT: R 58 ARG cc_start: 0.8078 (mmt-90) cc_final: 0.7563 (mmp80) REVERT: R 181 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.6800 (tt0) REVERT: R 208 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7515 (mmm160) REVERT: R 249 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8101 (mm) REVERT: R 270 LEU cc_start: 0.8743 (tp) cc_final: 0.8445 (tm) REVERT: R 278 ILE cc_start: 0.8852 (mt) cc_final: 0.8526 (mt) outliers start: 48 outliers final: 27 residues processed: 219 average time/residue: 1.3320 time to fit residues: 309.2057 Evaluate side-chains 221 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 306 GLN Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 31 SER 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 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 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 31 LEU Chi-restraints excluded: chain R residue 42 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 13 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 52 optimal weight: 0.1980 chunk 63 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.131122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.089481 restraints weight = 11461.562| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.31 r_work: 0.2878 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9028 Z= 0.213 Angle : 0.624 10.961 12238 Z= 0.318 Chirality : 0.044 0.163 1385 Planarity : 0.004 0.043 1530 Dihedral : 8.124 80.167 1313 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 5.85 % Allowed : 25.78 % 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: 0.80 (0.26), residues: 1108 helix: 2.11 (0.27), residues: 379 sheet: 0.08 (0.31), residues: 271 loop : -0.48 (0.29), residues: 458 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 257 TYR 0.020 0.002 TYR R 222 ARG 0.010 0.001 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 437) hydrogen bonds : angle 4.45604 ( 1257) SS BOND : bond 0.01765 ( 4) SS BOND : angle 2.78749 ( 8) covalent geometry : bond 0.00487 ( 9024) covalent geometry : angle 0.62042 (12230) *********************** 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 241 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 185 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8517 (ptp-110) cc_final: 0.8213 (ptp-170) REVERT: A 242 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7420 (mtm-85) REVERT: A 244 HIS cc_start: 0.8471 (m90) cc_final: 0.7959 (m90) REVERT: A 312 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8199 (mmpt) REVERT: B 8 ARG cc_start: 0.7799 (mpt180) cc_final: 0.7555 (mpt-90) REVERT: B 9 GLN cc_start: 0.8457 (mm110) cc_final: 0.8137 (tm-30) REVERT: B 10 GLU cc_start: 0.8440 (tp30) cc_final: 0.8004 (tp30) REVERT: B 15 LYS cc_start: 0.8853 (ttmt) cc_final: 0.8498 (mtmt) REVERT: B 101 MET cc_start: 0.9360 (OUTLIER) cc_final: 0.8956 (mtm) REVERT: B 127 LYS cc_start: 0.9249 (mptm) cc_final: 0.8891 (mmtp) REVERT: B 135 VAL cc_start: 0.9330 (t) cc_final: 0.9127 (p) REVERT: B 188 MET cc_start: 0.9263 (mmm) cc_final: 0.8951 (mmm) REVERT: B 197 ARG cc_start: 0.8400 (mmp-170) cc_final: 0.8102 (mmp-170) REVERT: B 226 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: G 17 GLU cc_start: 0.8018 (tp30) cc_final: 0.7613 (tp30) REVERT: G 20 LYS cc_start: 0.8973 (ttmt) cc_final: 0.8702 (ttmm) REVERT: S 43 LYS cc_start: 0.8859 (mppt) cc_final: 0.8573 (mppt) REVERT: S 62 ASP cc_start: 0.8764 (OUTLIER) cc_final: 0.8474 (p0) REVERT: S 206 ARG cc_start: 0.8307 (mtm110) cc_final: 0.7854 (tmm-80) REVERT: R 22 LEU cc_start: 0.5774 (OUTLIER) cc_final: 0.5379 (tm) REVERT: R 58 ARG cc_start: 0.8102 (mmt-90) cc_final: 0.7586 (mmp80) REVERT: R 181 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.6975 (tt0) REVERT: R 208 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7533 (mmm160) REVERT: R 249 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8114 (mm) REVERT: R 270 LEU cc_start: 0.8800 (tp) cc_final: 0.8519 (tm) REVERT: R 278 ILE cc_start: 0.8957 (mt) cc_final: 0.8622 (mt) outliers start: 56 outliers final: 31 residues processed: 220 average time/residue: 1.2821 time to fit residues: 299.7512 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 : 1.002 ------------------------------------------------------------------------------- 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 242 ARG Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 306 GLN 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 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 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 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 31 LEU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 86 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 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: 10.0000 chunk 74 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 99 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 9 optimal weight: 0.1980 chunk 31 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 306 GLN B 36 ASN G 24 ASN S 3 GLN S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.132305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.090567 restraints weight = 11533.306| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.34 r_work: 0.2898 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9028 Z= 0.166 Angle : 0.597 10.486 12238 Z= 0.303 Chirality : 0.043 0.163 1385 Planarity : 0.004 0.044 1530 Dihedral : 7.966 79.712 1313 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.53 % Allowed : 26.62 % Favored : 67.85 % 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: 0.93 (0.26), residues: 1108 helix: 2.21 (0.27), residues: 378 sheet: 0.17 (0.31), residues: 268 loop : -0.41 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS B 91 PHE 0.018 0.001 PHE R 183 TYR 0.019 0.002 TYR A 302 ARG 0.010 0.001 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 437) hydrogen bonds : angle 4.41104 ( 1257) SS BOND : bond 0.01398 ( 4) SS BOND : angle 2.31634 ( 8) covalent geometry : bond 0.00376 ( 9024) covalent geometry : angle 0.59431 (12230) *********************** 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 239 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 186 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8209 (m-30) REVERT: A 32 ARG cc_start: 0.8487 (ptp-110) cc_final: 0.8192 (ptp-170) REVERT: A 242 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7504 (mtm-85) REVERT: A 244 HIS cc_start: 0.8441 (m90) cc_final: 0.8023 (m90) REVERT: A 273 LEU cc_start: 0.8500 (tp) cc_final: 0.8175 (tp) REVERT: A 304 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8126 (tm-30) REVERT: A 312 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8146 (mmpt) REVERT: B 8 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7521 (mpt-90) REVERT: B 9 GLN cc_start: 0.8454 (mm110) cc_final: 0.8134 (tm-30) REVERT: B 10 GLU cc_start: 0.8424 (tp30) cc_final: 0.7994 (tp30) REVERT: B 15 LYS cc_start: 0.8843 (ttmt) cc_final: 0.8495 (mtmt) REVERT: B 101 MET cc_start: 0.9336 (OUTLIER) cc_final: 0.8874 (mtm) REVERT: B 127 LYS cc_start: 0.9283 (mptm) cc_final: 0.8949 (mmtp) REVERT: B 135 VAL cc_start: 0.9288 (t) cc_final: 0.9085 (p) REVERT: B 188 MET cc_start: 0.9246 (mmm) cc_final: 0.8942 (mmm) REVERT: B 217 MET cc_start: 0.9068 (pmm) cc_final: 0.8848 (ppp) REVERT: B 226 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: G 20 LYS cc_start: 0.8915 (ttmt) cc_final: 0.8650 (ttmm) REVERT: G 37 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8640 (mp) REVERT: S 62 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8455 (p0) REVERT: S 87 ARG cc_start: 0.8492 (ptp-170) cc_final: 0.8213 (ptp-170) REVERT: S 118 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.8101 (p) REVERT: S 206 ARG cc_start: 0.8291 (mtm110) cc_final: 0.7862 (tmm-80) REVERT: R 22 LEU cc_start: 0.5797 (OUTLIER) cc_final: 0.5420 (tm) REVERT: R 58 ARG cc_start: 0.8095 (mmt-90) cc_final: 0.7590 (mmp80) REVERT: R 181 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.6958 (tt0) REVERT: R 208 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7536 (mmm160) REVERT: R 249 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8173 (mm) REVERT: R 270 LEU cc_start: 0.8794 (tp) cc_final: 0.8506 (tm) REVERT: R 278 ILE cc_start: 0.8917 (mt) cc_final: 0.8573 (mt) outliers start: 53 outliers final: 27 residues processed: 219 average time/residue: 1.5953 time to fit residues: 370.7368 Evaluate side-chains 220 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 242 ARG Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 8 ARG 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 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 118 THR Chi-restraints excluded: chain S residue 138 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 31 LEU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 86 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 107 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 306 GLN 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 = 0.3637 r_free = 0.3637 target = 0.131765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.092739 restraints weight = 11918.058| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.21 r_work: 0.2948 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9028 Z= 0.150 Angle : 0.601 10.212 12238 Z= 0.305 Chirality : 0.042 0.165 1385 Planarity : 0.004 0.049 1530 Dihedral : 7.818 79.436 1312 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.80 % Allowed : 28.08 % Favored : 67.12 % 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: 0.96 (0.26), residues: 1108 helix: 2.26 (0.27), residues: 378 sheet: 0.16 (0.31), residues: 268 loop : -0.39 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.016 0.001 PHE R 257 TYR 0.020 0.001 TYR A 302 ARG 0.011 0.001 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 437) hydrogen bonds : angle 4.36279 ( 1257) SS BOND : bond 0.01296 ( 4) SS BOND : angle 2.12879 ( 8) covalent geometry : bond 0.00342 ( 9024) covalent geometry : angle 0.59825 (12230) *********************** 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 233 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 187 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8239 (m-30) REVERT: A 242 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7516 (mtm-85) REVERT: A 244 HIS cc_start: 0.8504 (m90) cc_final: 0.8070 (m90) REVERT: A 273 LEU cc_start: 0.8564 (tp) cc_final: 0.8218 (tp) REVERT: A 312 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8096 (mmpt) REVERT: B 8 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7595 (mpt-90) REVERT: B 9 GLN cc_start: 0.8461 (mm110) cc_final: 0.8154 (tm-30) REVERT: B 10 GLU cc_start: 0.8445 (tp30) cc_final: 0.7996 (tp30) REVERT: B 15 LYS cc_start: 0.8886 (ttmt) cc_final: 0.8533 (mtmt) REVERT: B 101 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.8773 (mtm) REVERT: B 127 LYS cc_start: 0.9280 (mptm) cc_final: 0.8911 (mmtm) REVERT: B 188 MET cc_start: 0.9207 (mmm) cc_final: 0.8889 (mmm) REVERT: B 226 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: G 17 GLU cc_start: 0.7992 (tp30) cc_final: 0.7648 (tp30) REVERT: G 20 LYS cc_start: 0.8997 (ttmt) cc_final: 0.8754 (ttmm) REVERT: G 29 LYS cc_start: 0.8704 (mmmt) cc_final: 0.8427 (mptp) REVERT: S 43 LYS cc_start: 0.8795 (mppt) cc_final: 0.8518 (mppt) REVERT: S 62 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.8494 (p0) REVERT: S 148 ARG cc_start: 0.7998 (mmm-85) cc_final: 0.7437 (mmm-85) REVERT: S 206 ARG cc_start: 0.8361 (mtm110) cc_final: 0.7909 (tmm-80) REVERT: R 22 LEU cc_start: 0.5806 (OUTLIER) cc_final: 0.5471 (tm) REVERT: R 58 ARG cc_start: 0.8112 (mmt-90) cc_final: 0.7533 (mmp80) REVERT: R 181 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.6851 (tt0) REVERT: R 208 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7628 (mmm160) REVERT: R 249 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8256 (mm) REVERT: R 270 LEU cc_start: 0.8793 (tp) cc_final: 0.8519 (tm) REVERT: R 278 ILE cc_start: 0.8918 (mt) cc_final: 0.8577 (mt) outliers start: 46 outliers final: 30 residues processed: 214 average time/residue: 1.3019 time to fit residues: 295.5134 Evaluate side-chains 226 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 242 ARG Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 306 GLN 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 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 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 S residue 62 ASP Chi-restraints excluded: chain S residue 138 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 91 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 0.0060 chunk 59 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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 306 GLN 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 = 0.3662 r_free = 0.3662 target = 0.133666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.095123 restraints weight = 11838.845| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.20 r_work: 0.2986 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9028 Z= 0.119 Angle : 0.590 9.983 12238 Z= 0.299 Chirality : 0.042 0.171 1385 Planarity : 0.004 0.052 1530 Dihedral : 7.562 79.201 1311 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.28 % Allowed : 28.71 % Favored : 67.01 % 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: 1.06 (0.26), residues: 1108 helix: 2.31 (0.27), residues: 380 sheet: 0.16 (0.31), residues: 268 loop : -0.28 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.018 0.001 PHE R 257 TYR 0.023 0.001 TYR R 222 ARG 0.012 0.001 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03488 ( 437) hydrogen bonds : angle 4.26364 ( 1257) SS BOND : bond 0.01019 ( 4) SS BOND : angle 2.06057 ( 8) covalent geometry : bond 0.00265 ( 9024) covalent geometry : angle 0.58780 (12230) *********************** 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 234 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7542 (mtm-85) REVERT: A 273 LEU cc_start: 0.8560 (tp) cc_final: 0.8202 (tp) REVERT: A 304 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8103 (tm-30) REVERT: A 312 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8112 (mmpt) REVERT: B 8 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7580 (mpt-90) REVERT: B 9 GLN cc_start: 0.8449 (mm110) cc_final: 0.8158 (tm-30) REVERT: B 10 GLU cc_start: 0.8467 (tp30) cc_final: 0.8055 (tp30) REVERT: B 15 LYS cc_start: 0.8894 (ttmt) cc_final: 0.8543 (mtmt) REVERT: B 46 ARG cc_start: 0.8515 (mtm-85) cc_final: 0.8265 (ttp80) REVERT: B 101 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8671 (mtm) REVERT: B 127 LYS cc_start: 0.9207 (mptm) cc_final: 0.8828 (mmtm) REVERT: B 146 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8900 (tm) REVERT: B 188 MET cc_start: 0.9194 (mmm) cc_final: 0.8855 (mmm) REVERT: B 197 ARG cc_start: 0.8341 (mmp-170) cc_final: 0.8079 (mmp-170) REVERT: B 226 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: B 266 HIS cc_start: 0.8843 (t-90) cc_final: 0.8605 (t70) REVERT: G 17 GLU cc_start: 0.8047 (tp30) cc_final: 0.7683 (tp30) REVERT: G 20 LYS cc_start: 0.9009 (ttmt) cc_final: 0.8780 (ttmm) REVERT: G 29 LYS cc_start: 0.8676 (mmmt) cc_final: 0.8444 (mptp) REVERT: S 43 LYS cc_start: 0.8788 (mppt) cc_final: 0.8504 (mppt) REVERT: S 62 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8480 (p0) REVERT: S 148 ARG cc_start: 0.8018 (mmm-85) cc_final: 0.7539 (mmm-85) REVERT: S 206 ARG cc_start: 0.8343 (mtm110) cc_final: 0.7865 (tmm-80) REVERT: R 22 LEU cc_start: 0.5806 (OUTLIER) cc_final: 0.5494 (tm) REVERT: R 58 ARG cc_start: 0.8078 (mmt-90) cc_final: 0.7622 (mmp80) REVERT: R 60 ARG cc_start: 0.7854 (ttm170) cc_final: 0.7614 (ttp-170) REVERT: R 181 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.6840 (tt0) REVERT: R 208 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7598 (mmm160) REVERT: R 245 LEU cc_start: 0.8648 (tm) cc_final: 0.8319 (tm) REVERT: R 249 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8473 (mm) REVERT: R 270 LEU cc_start: 0.8779 (tp) cc_final: 0.8518 (tm) REVERT: R 278 ILE cc_start: 0.8843 (mt) cc_final: 0.8501 (mt) outliers start: 41 outliers final: 21 residues processed: 216 average time/residue: 1.5635 time to fit residues: 358.4748 Evaluate side-chains 221 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 242 ARG 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 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 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 138 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 94 optimal weight: 0.0870 chunk 84 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 36 ASN G 24 ASN S 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.133400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.094922 restraints weight = 11804.058| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.19 r_work: 0.2984 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9028 Z= 0.134 Angle : 0.611 8.672 12238 Z= 0.310 Chirality : 0.042 0.169 1385 Planarity : 0.004 0.055 1530 Dihedral : 7.448 79.152 1310 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.65 % Allowed : 29.75 % 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: 1.00 (0.26), residues: 1108 helix: 2.20 (0.27), residues: 386 sheet: 0.11 (0.31), residues: 268 loop : -0.28 (0.30), residues: 454 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 0.016 0.001 PHE R 257 TYR 0.023 0.001 TYR R 222 ARG 0.013 0.001 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03591 ( 437) hydrogen bonds : angle 4.23865 ( 1257) SS BOND : bond 0.01196 ( 4) SS BOND : angle 2.18070 ( 8) covalent geometry : bond 0.00307 ( 9024) covalent geometry : angle 0.60867 (12230) ********************** 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 219 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8743 (tmtt) cc_final: 0.8535 (pttp) REVERT: A 242 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7539 (mtm-85) REVERT: A 304 GLN cc_start: 0.8470 (tm-30) cc_final: 0.7991 (tm-30) REVERT: A 312 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8098 (mmpt) REVERT: B 8 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7595 (mpt-90) REVERT: B 9 GLN cc_start: 0.8461 (mm110) cc_final: 0.8158 (tm-30) REVERT: B 10 GLU cc_start: 0.8497 (tp30) cc_final: 0.8060 (tp30) REVERT: B 15 LYS cc_start: 0.8906 (ttmt) cc_final: 0.8563 (mtmt) REVERT: B 101 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8686 (mtm) REVERT: B 127 LYS cc_start: 0.9192 (mptm) cc_final: 0.8816 (mmtm) REVERT: B 130 GLU cc_start: 0.8742 (mp0) cc_final: 0.8516 (mp0) REVERT: B 146 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8966 (tm) REVERT: B 188 MET cc_start: 0.9206 (mmm) cc_final: 0.8862 (mmm) REVERT: B 226 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7835 (mp0) REVERT: G 17 GLU cc_start: 0.8035 (tp30) cc_final: 0.7634 (tp30) REVERT: G 20 LYS cc_start: 0.8948 (ttmt) cc_final: 0.8703 (ttmm) REVERT: G 29 LYS cc_start: 0.8666 (mmmt) cc_final: 0.8396 (mptp) REVERT: S 43 LYS cc_start: 0.8808 (mppt) cc_final: 0.8497 (mppt) REVERT: S 148 ARG cc_start: 0.8065 (mmm-85) cc_final: 0.7533 (mmm-85) REVERT: S 206 ARG cc_start: 0.8331 (mtm110) cc_final: 0.7842 (tmm-80) REVERT: S 234 GLU cc_start: 0.7285 (mp0) cc_final: 0.7040 (mp0) REVERT: R 22 LEU cc_start: 0.5809 (OUTLIER) cc_final: 0.5469 (tm) REVERT: R 58 ARG cc_start: 0.8083 (mmt-90) cc_final: 0.7636 (mmp80) REVERT: R 60 ARG cc_start: 0.7829 (ttm170) cc_final: 0.7490 (mtm-85) REVERT: R 158 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8296 (tp) REVERT: R 181 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.6899 (tt0) REVERT: R 208 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7585 (mmm160) REVERT: R 245 LEU cc_start: 0.8599 (tm) cc_final: 0.8259 (tm) REVERT: R 270 LEU cc_start: 0.8752 (tp) cc_final: 0.8502 (tm) REVERT: R 278 ILE cc_start: 0.8794 (mt) cc_final: 0.8469 (mt) outliers start: 35 outliers final: 19 residues processed: 202 average time/residue: 1.7310 time to fit residues: 370.6189 Evaluate side-chains 207 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 242 ARG 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 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 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 138 THR 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 54 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 306 GLN 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 = 0.3647 r_free = 0.3647 target = 0.132494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.093441 restraints weight = 11884.917| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.24 r_work: 0.2956 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9028 Z= 0.157 Angle : 0.624 9.371 12238 Z= 0.317 Chirality : 0.043 0.171 1385 Planarity : 0.004 0.057 1530 Dihedral : 7.416 78.944 1310 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.55 % Allowed : 30.27 % Favored : 66.18 % 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: 1.06 (0.26), residues: 1108 helix: 2.21 (0.27), residues: 382 sheet: 0.13 (0.31), residues: 268 loop : -0.16 (0.30), residues: 458 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 0.016 0.001 PHE R 183 TYR 0.020 0.002 TYR A 302 ARG 0.014 0.001 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 437) hydrogen bonds : angle 4.32799 ( 1257) SS BOND : bond 0.01363 ( 4) SS BOND : angle 2.42466 ( 8) covalent geometry : bond 0.00361 ( 9024) covalent geometry : angle 0.62068 (12230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9498.41 seconds wall clock time: 167 minutes 11.50 seconds (10031.50 seconds total)