Starting phenix.real_space_refine on Thu Nov 14 17:24:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8idb_35362/11_2024/8idb_35362.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8idb_35362/11_2024/8idb_35362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8idb_35362/11_2024/8idb_35362.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8idb_35362/11_2024/8idb_35362.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8idb_35362/11_2024/8idb_35362.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8idb_35362/11_2024/8idb_35362.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 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 27 5.16 5 C 4337 2.51 5 N 1208 2.21 5 O 1263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6835 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1421 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 8, 'TRANS': 196} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 119 Chain: "B" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1280 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 331 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 9, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 149 Chain: "C" Number of atoms: 2078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2078 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "D" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2056 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 6, 'TRANS': 288} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 4, 'ASP:plan': 6, 'PHE:plan': 6, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 145 Time building chain proxies: 10.17, per 1000 atoms: 1.49 Number of scatterers: 6835 At special positions: 0 Unit cell: (90.1, 99.64, 138.86, 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 27 16.00 O 1263 8.00 N 1208 7.00 C 4337 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 73 " - pdb=" SG CYS D 78 " 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: 2.03 Conformation dependent library (CDL) restraints added in 1.5 seconds 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1842 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 5 sheets defined 53.4% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 47 through 51 removed outlier: 4.281A pdb=" N LEU A 50 " --> pdb=" O MET A 47 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 51 " --> pdb=" O ARG A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 47 through 51' Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.563A pdb=" N LEU A 79 " --> pdb=" O HIS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 102 removed outlier: 3.610A pdb=" N VAL A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.973A pdb=" N ILE A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 142 through 154 removed outlier: 4.402A pdb=" N GLN A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG A 147 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 174 Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.911A pdb=" N MET A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 189 removed outlier: 3.583A pdb=" N GLY A 189 " --> pdb=" O ASN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 206 removed outlier: 4.198A pdb=" N MET A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 49 removed outlier: 3.730A pdb=" N THR B 45 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET B 47 " --> pdb=" O LYS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 84 removed outlier: 3.563A pdb=" N LEU B 79 " --> pdb=" O HIS B 75 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 81 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL B 82 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 108 removed outlier: 4.645A pdb=" N ALA B 105 " --> pdb=" O ASN B 101 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLU B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL B 108 " --> pdb=" O PHE B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.601A pdb=" N ASN B 117 " --> pdb=" O THR B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 126 removed outlier: 4.359A pdb=" N LEU B 124 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 146 through 154 removed outlier: 3.616A pdb=" N PHE B 154 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 186 removed outlier: 3.624A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'C' and resid 10 through 17 removed outlier: 3.806A pdb=" N PHE C 14 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 27 through 49 removed outlier: 3.917A pdb=" N SER C 31 " --> pdb=" O THR C 27 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 84 removed outlier: 3.856A pdb=" N ALA C 80 " --> pdb=" O THR C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 164 through 198 removed outlier: 3.893A pdb=" N GLN C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY C 183 " --> pdb=" O VAL C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 209 removed outlier: 3.851A pdb=" N ILE C 203 " --> pdb=" O ARG C 199 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET C 206 " --> pdb=" O GLU C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 245 removed outlier: 3.777A pdb=" N GLN C 217 " --> pdb=" O ARG C 213 " (cutoff:3.500A) Proline residue: C 219 - end of helix removed outlier: 3.570A pdb=" N ARG C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 257 removed outlier: 4.696A pdb=" N LEU C 251 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASN C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLN C 253 " --> pdb=" O ASN C 249 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE C 254 " --> pdb=" O ALA C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 292 removed outlier: 3.742A pdb=" N LEU C 269 " --> pdb=" O TYR C 265 " (cutoff:3.500A) Proline residue: C 273 - end of helix removed outlier: 4.014A pdb=" N THR C 290 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 17 removed outlier: 4.114A pdb=" N VAL D 10 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE D 14 " --> pdb=" O VAL D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 46 removed outlier: 4.067A pdb=" N ILE D 22 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 50 removed outlier: 3.998A pdb=" N ALA D 50 " --> pdb=" O SER D 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 47 through 50' Processing helix chain 'D' and resid 63 through 68 removed outlier: 3.926A pdb=" N SER D 67 " --> pdb=" O THR D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 88 removed outlier: 4.436A pdb=" N LYS D 79 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 114 removed outlier: 3.753A pdb=" N LYS D 114 " --> pdb=" O PRO D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 134 No H-bonds generated for 'chain 'D' and resid 132 through 134' Processing helix chain 'D' and resid 135 through 144 Processing helix chain 'D' and resid 159 through 169 removed outlier: 4.378A pdb=" N PHE D 163 " --> pdb=" O ILE D 159 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU D 169 " --> pdb=" O VAL D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 199 removed outlier: 3.660A pdb=" N PHE D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA D 175 " --> pdb=" O ASN D 171 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN D 180 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE D 182 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY D 183 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA D 189 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN D 190 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL D 192 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN D 193 " --> pdb=" O ALA D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 210 Processing helix chain 'D' and resid 217 through 247 removed outlier: 3.690A pdb=" N ALA D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 257 removed outlier: 5.386A pdb=" N GLN D 253 " --> pdb=" O ASN D 249 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE D 254 " --> pdb=" O ALA D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 295 removed outlier: 4.290A pdb=" N LEU D 277 " --> pdb=" O PRO D 273 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU D 278 " --> pdb=" O TRP D 274 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET D 282 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER D 283 " --> pdb=" O GLY D 279 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N THR D 286 " --> pdb=" O MET D 282 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA D 287 " --> pdb=" O SER D 283 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG D 292 " --> pdb=" O TYR D 288 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 removed outlier: 3.923A pdb=" N ILE A 3 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 25 " --> pdb=" O LEU A 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 86 removed outlier: 3.662A pdb=" N ASP A 164 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU A 161 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ALA A 195 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA A 163 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.691A pdb=" N VAL B 86 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU B 161 " --> pdb=" O LEU B 193 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 91 through 94 removed outlier: 7.520A pdb=" N LYS C 129 " --> pdb=" O LYS C 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 59 through 62 removed outlier: 6.454A pdb=" N GLN D 59 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL D 152 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE D 61 " --> pdb=" O LEU D 150 " (cutoff:3.500A) 276 hydrogen bonds defined for protein. 807 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: 1.56 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2314 1.34 - 1.46: 1317 1.46 - 1.58: 3240 1.58 - 1.70: 0 1.70 - 1.82: 50 Bond restraints: 6921 Sorted by residual: bond pdb=" CA GLU A 165 " pdb=" CB GLU A 165 " ideal model delta sigma weight residual 1.525 1.545 -0.020 8.30e-03 1.45e+04 5.81e+00 bond pdb=" CG1 ILE C 188 " pdb=" CD1 ILE C 188 " ideal model delta sigma weight residual 1.513 1.432 0.081 3.90e-02 6.57e+02 4.32e+00 bond pdb=" C VAL A 76 " pdb=" N PRO A 77 " ideal model delta sigma weight residual 1.336 1.358 -0.023 1.23e-02 6.61e+03 3.46e+00 bond pdb=" CB MET D 191 " pdb=" CG MET D 191 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.18e+00 bond pdb=" C VAL A 120 " pdb=" N PRO A 121 " ideal model delta sigma weight residual 1.335 1.351 -0.016 9.40e-03 1.13e+04 2.87e+00 ... (remaining 6916 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 9147 2.55 - 5.10: 234 5.10 - 7.66: 55 7.66 - 10.21: 16 10.21 - 12.76: 2 Bond angle restraints: 9454 Sorted by residual: angle pdb=" N PRO D 273 " pdb=" CA PRO D 273 " pdb=" C PRO D 273 " ideal model delta sigma weight residual 113.40 105.64 7.76 1.34e+00 5.57e-01 3.36e+01 angle pdb=" C ASP A 164 " pdb=" N GLU A 165 " pdb=" CA GLU A 165 " ideal model delta sigma weight residual 124.21 130.24 -6.03 1.21e+00 6.83e-01 2.48e+01 angle pdb=" C ASP A 89 " pdb=" N PHE A 90 " pdb=" CA PHE A 90 " ideal model delta sigma weight residual 121.54 130.95 -9.41 1.91e+00 2.74e-01 2.43e+01 angle pdb=" C HIS B 67 " pdb=" N VAL B 68 " pdb=" CA VAL B 68 " ideal model delta sigma weight residual 121.97 130.23 -8.26 1.80e+00 3.09e-01 2.11e+01 angle pdb=" C TYR D 103 " pdb=" N ASP D 104 " pdb=" CA ASP D 104 " ideal model delta sigma weight residual 121.54 129.71 -8.17 1.91e+00 2.74e-01 1.83e+01 ... (remaining 9449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 3873 17.60 - 35.19: 211 35.19 - 52.79: 32 52.79 - 70.39: 5 70.39 - 87.98: 4 Dihedral angle restraints: 4125 sinusoidal: 1294 harmonic: 2831 Sorted by residual: dihedral pdb=" CA VAL D 56 " pdb=" C VAL D 56 " pdb=" N GLU D 57 " pdb=" CA GLU D 57 " ideal model delta harmonic sigma weight residual 180.00 153.87 26.13 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA ASP D 54 " pdb=" C ASP D 54 " pdb=" N ARG D 55 " pdb=" CA ARG D 55 " ideal model delta harmonic sigma weight residual -180.00 -157.40 -22.60 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ASN C 17 " pdb=" C ASN C 17 " pdb=" N VAL C 18 " pdb=" CA VAL C 18 " ideal model delta harmonic sigma weight residual 180.00 158.23 21.77 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 4122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 937 0.060 - 0.120: 205 0.120 - 0.180: 47 0.180 - 0.240: 11 0.240 - 0.299: 3 Chirality restraints: 1203 Sorted by residual: chirality pdb=" CB VAL C 32 " pdb=" CA VAL C 32 " pdb=" CG1 VAL C 32 " pdb=" CG2 VAL C 32 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA MET C 20 " pdb=" N MET C 20 " pdb=" C MET C 20 " pdb=" CB MET C 20 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CB ILE C 185 " pdb=" CA ILE C 185 " pdb=" CG1 ILE C 185 " pdb=" CG2 ILE C 185 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 1200 not shown) Planarity restraints: 1222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 272 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C THR D 272 " -0.059 2.00e-02 2.50e+03 pdb=" O THR D 272 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO D 273 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 87 " 0.017 2.00e-02 2.50e+03 1.82e-02 5.79e+00 pdb=" CG PHE A 87 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 87 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 87 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 87 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 87 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 87 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 157 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.59e+00 pdb=" CD GLU C 157 " 0.041 2.00e-02 2.50e+03 pdb=" OE1 GLU C 157 " -0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU C 157 " -0.015 2.00e-02 2.50e+03 ... (remaining 1219 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1628 2.78 - 3.31: 6491 3.31 - 3.84: 10801 3.84 - 4.37: 11477 4.37 - 4.90: 19682 Nonbonded interactions: 50079 Sorted by model distance: nonbonded pdb=" OD1 ASP A 171 " pdb=" OG1 THR A 174 " model vdw 2.256 3.040 nonbonded pdb=" O GLY A 42 " pdb=" OG1 THR A 45 " model vdw 2.272 3.040 nonbonded pdb=" O ILE C 268 " pdb=" OG1 THR C 272 " model vdw 2.284 3.040 nonbonded pdb=" O GLU C 64 " pdb=" OG SER C 67 " model vdw 2.308 3.040 nonbonded pdb=" O ILE A 185 " pdb=" OG1 THR A 188 " model vdw 2.313 3.040 ... (remaining 50074 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 or (resid 9 through 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 26 or (resid 27 through 29 and (name \ N or name CA or name C or name O or name CB )) or resid 30 through 35 or (resid \ 36 and (name N or name CA or name C or name O or name CB )) or resid 37 through \ 42 or (resid 43 and (name N or name CA or name C or name O or name CB )) or res \ id 44 through 54 or resid 64 through 66 or (resid 67 and (name N or name CA or n \ ame C or name O or name CB )) or resid 68 through 70 or (resid 71 through 72 and \ (name N or name CA or name C or name O or name CB )) or resid 73 through 80 or \ (resid 81 and (name N or name CA or name C or name O or name CB )) or resid 82 t \ hrough 89 or (resid 90 through 92 and (name N or name CA or name C or name O or \ name CB )) or resid 93 through 95 or (resid 96 and (name N or name CA or name C \ or name O or name CB )) or resid 97 through 99 or (resid 100 and (name N or name \ CA or name C or name O or name CB )) or resid 101 through 108 or (resid 109 and \ (name N or name CA or name C or name O or name CB )) or (resid 110 through 115 \ and (name N or name CA or name C or name O or name CB )) or resid 116 or (resid \ 117 through 118 and (name N or name CA or name C or name O or name CB )) or resi \ d 119 through 121 or (resid 122 and (name N or name CA or name C or name O or na \ me CB )) or resid 123 through 124 or (resid 125 and (name N or name CA or name C \ or name O or name CB )) or resid 126 through 131 or (resid 132 through 140 and \ (name N or name CA or name C or name O or name CB )) or resid 141 through 143 or \ (resid 144 and (name N or name CA or name C or name O or name CB )) or resid 14 \ 5 through 153 or (resid 154 and (name N or name CA or name C or name O or name C \ B )) or resid 155 through 158 or (resid 159 through 160 and (name N or name CA o \ r name C or name O or name CB )) or resid 161 or (resid 162 through 167 and (nam \ e N or name CA or name C or name O or name CB )) or resid 168 or (resid 169 thro \ ugh 183 and (name N or name CA or name C or name O or name CB )) or resid 184 th \ rough 186 or (resid 187 and (name N or name CA or name C or name O or name CB )) \ or resid 188 through 191 or (resid 192 and (name N or name CA or name C or name \ O or name CB )) or resid 193 through 213)) selection = (chain 'B' and (resid 8 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 19 or (resid 20 through 23 and (nam \ e N or name CA or name C or name O or name CB )) or resid 24 through 65 or (resi \ d 66 through 67 and (name N or name CA or name C or name O or name CB )) or resi \ d 68 through 78 or (resid 79 through 81 and (name N or name CA or name C or name \ O or name CB )) or resid 82 through 88 or (resid 89 through 92 and (name N or n \ ame CA or name C or name O or name CB )) or resid 93 through 133 or (resid 134 t \ hrough 140 and (name N or name CA or name C or name O or name CB )) or resid 141 \ through 202 or (resid 203 and (name N or name CA or name C or name O or name CB \ )) or resid 204 through 205 or (resid 206 and (name N or name CA or name C or n \ ame O or name CB )) or resid 207 or (resid 208 and (name N or name CA or name C \ or name O or name CB )) or resid 209 through 213)) } ncs_group { reference = (chain 'C' and (resid 4 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 10 or (resid 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 14 or (resid 15 through 1 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 17 through 8 \ 5 or (resid 86 through 87 and (name N or name CA or name C or name O or name CB \ )) or resid 88 through 109 or (resid 110 through 117 and (name N or name CA or n \ ame C or name O or name CB )) or resid 118 through 136 or (resid 137 through 138 \ and (name N or name CA or name C or name O or name CB )) or resid 139 through 1 \ 40 or (resid 141 through 142 and (name N or name CA or name C or name O or name \ CB )) or resid 143 through 156 or (resid 157 through 158 and (name N or name CA \ or name C or name O or name CB )) or resid 159 through 166 or (resid 167 and (na \ me N or name CA or name C or name O or name CB )) or resid 168 through 177 or (r \ esid 178 and (name N or name CA or name C or name O or name CB )) or resid 179 t \ hrough 187 or (resid 188 through 189 and (name N or name CA or name C or name O \ or name CB )) or resid 190 through 191 or (resid 192 and (name N or name CA or n \ ame C or name O or name CB )) or resid 193 through 197 or (resid 198 and (name N \ or name CA or name C or name O or name CB )) or resid 199 or (resid 200 and (na \ me N or name CA or name C or name O or name CB )) or resid 201 or (resid 202 thr \ ough 203 and (name N or name CA or name C or name O or name CB )) or resid 204 o \ r (resid 205 through 208 and (name N or name CA or name C or name O or name CB ) \ ) or resid 209 through 214 or (resid 215 and (name N or name CA or name C or nam \ e O or name CB )) or resid 216 through 217 or (resid 218 and (name N or name CA \ or name C or name O or name CB )) or resid 219 or (resid 220 and (name N or name \ CA or name C or name O or name CB )) or resid 221 through 222 or (resid 223 thr \ ough 225 and (name N or name CA or name C or name O or name CB )) or resid 226 t \ hrough 229 or (resid 230 and (name N or name CA or name C or name O or name CB ) \ ) or resid 231 through 242 or (resid 243 through 246 and (name N or name CA or n \ ame C or name O or name CB )) or resid 247 through 255 or (resid 256 through 257 \ and (name N or name CA or name C or name O or name CB )) or resid 258 through 2 \ 69 or (resid 270 and (name N or name CA or name C or name O or name CB )) or res \ id 271 through 287 or (resid 288 and (name N or name CA or name C or name O or n \ ame CB )) or resid 289 through 294)) selection = (chain 'D' and (resid 4 through 58 or (resid 59 through 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 or (resid 62 and (name N or name \ CA or name C or name O or name CB )) or resid 63 or (resid 64 through 65 and (n \ ame N or name CA or name C or name O or name CB )) or resid 66 through 68 or (re \ sid 69 through 70 and (name N or name CA or name C or name O or name CB )) or re \ sid 71 through 72 or (resid 73 through 74 and (name N or name CA or name C or na \ me O or name CB )) or resid 75 through 77 or (resid 78 through 80 and (name N or \ name CA or name C or name O or name CB )) or resid 81 through 82 or (resid 83 a \ nd (name N or name CA or name C or name O or name CB )) or resid 84 through 143 \ or (resid 144 and (name N or name CA or name C or name O or name CB )) or resid \ 145 or (resid 152 and (name N or name CA or name C or name O or name CB )) or re \ sid 153 through 155 or (resid 156 through 158 and (name N or name CA or name C o \ r name O or name CB )) or resid 159 through 212 or (resid 213 and (name N or nam \ e CA or name C or name O or name CB )) or resid 214 through 245 or (resid 246 an \ d (name N or name CA or name C or name O or name CB )) or resid 247 through 294) \ ) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.770 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.460 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 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 : 0.005 0.081 6921 Z= 0.299 Angle : 1.036 12.762 9454 Z= 0.534 Chirality : 0.058 0.299 1203 Planarity : 0.006 0.055 1222 Dihedral : 11.652 87.982 2280 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.79 % Favored : 93.70 % Rotamer: Outliers : 0.32 % Allowed : 1.13 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.59 (0.22), residues: 968 helix: -2.26 (0.20), residues: 433 sheet: -2.07 (0.91), residues: 39 loop : -2.52 (0.23), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 274 HIS 0.002 0.001 HIS B 75 PHE 0.042 0.002 PHE A 87 TYR 0.025 0.002 TYR C 288 ARG 0.014 0.001 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 0.742 Fit side-chains REVERT: A 90 PHE cc_start: 0.8324 (m-80) cc_final: 0.8043 (m-80) REVERT: B 34 PHE cc_start: 0.8126 (p90) cc_final: 0.7885 (p90) REVERT: C 24 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7755 (tmm) REVERT: C 249 ASN cc_start: 0.8130 (p0) cc_final: 0.7776 (p0) REVERT: D 52 TYR cc_start: 0.8237 (m-80) cc_final: 0.8007 (m-80) outliers start: 2 outliers final: 0 residues processed: 141 average time/residue: 0.1484 time to fit residues: 29.1795 Evaluate side-chains 114 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.9990 chunk 72 optimal weight: 0.0270 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 29 optimal weight: 0.0670 chunk 45 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6921 Z= 0.186 Angle : 0.614 7.676 9454 Z= 0.317 Chirality : 0.041 0.154 1203 Planarity : 0.004 0.038 1222 Dihedral : 4.364 32.412 1032 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.86 % Favored : 94.83 % Rotamer: Outliers : 1.30 % Allowed : 13.29 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.43 (0.25), residues: 968 helix: -0.89 (0.23), residues: 455 sheet: -2.42 (0.87), residues: 41 loop : -2.26 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 274 HIS 0.002 0.001 HIS B 197 PHE 0.020 0.001 PHE B 104 TYR 0.004 0.001 TYR C 294 ARG 0.003 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.712 Fit side-chains REVERT: A 90 PHE cc_start: 0.8410 (m-80) cc_final: 0.7897 (m-80) REVERT: B 34 PHE cc_start: 0.8124 (p90) cc_final: 0.7830 (p90) REVERT: B 94 GLN cc_start: 0.9312 (mp-120) cc_final: 0.8988 (mm-40) REVERT: C 24 MET cc_start: 0.8201 (tmm) cc_final: 0.7905 (tmm) REVERT: C 129 LYS cc_start: 0.8679 (ptpp) cc_final: 0.8414 (ptpp) REVERT: C 180 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8214 (pp30) REVERT: D 52 TYR cc_start: 0.8371 (m-80) cc_final: 0.8141 (m-80) outliers start: 8 outliers final: 7 residues processed: 122 average time/residue: 0.1486 time to fit residues: 25.7181 Evaluate side-chains 115 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 209 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 4.9990 chunk 27 optimal weight: 0.0000 chunk 72 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 87 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 77 optimal weight: 0.0040 chunk 86 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 GLN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6921 Z= 0.176 Angle : 0.587 8.448 9454 Z= 0.302 Chirality : 0.041 0.137 1203 Planarity : 0.003 0.036 1222 Dihedral : 3.974 22.110 1029 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.06 % Favored : 94.63 % Rotamer: Outliers : 2.11 % Allowed : 17.50 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.86 (0.26), residues: 968 helix: -0.23 (0.25), residues: 447 sheet: -1.92 (0.88), residues: 44 loop : -2.18 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 274 HIS 0.002 0.001 HIS A 200 PHE 0.012 0.001 PHE B 104 TYR 0.005 0.001 TYR D 52 ARG 0.003 0.000 ARG C 243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.828 Fit side-chains REVERT: A 100 ASP cc_start: 0.8589 (m-30) cc_final: 0.8375 (m-30) REVERT: C 20 MET cc_start: 0.6845 (OUTLIER) cc_final: 0.6233 (mmp) REVERT: C 24 MET cc_start: 0.8100 (tmm) cc_final: 0.7795 (tmm) REVERT: C 129 LYS cc_start: 0.8769 (ptpp) cc_final: 0.8474 (ptpp) REVERT: C 180 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8105 (pp30) REVERT: D 52 TYR cc_start: 0.8396 (m-80) cc_final: 0.8169 (m-10) outliers start: 13 outliers final: 6 residues processed: 124 average time/residue: 0.1560 time to fit residues: 27.2394 Evaluate side-chains 121 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 209 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 5.9990 chunk 65 optimal weight: 0.0270 chunk 45 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 GLN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6921 Z= 0.242 Angle : 0.613 8.786 9454 Z= 0.318 Chirality : 0.042 0.161 1203 Planarity : 0.003 0.035 1222 Dihedral : 4.051 23.629 1029 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.51 % Favored : 93.18 % Rotamer: Outliers : 3.08 % Allowed : 19.45 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.63 (0.27), residues: 968 helix: 0.05 (0.25), residues: 447 sheet: -2.29 (0.86), residues: 46 loop : -2.12 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 274 HIS 0.002 0.001 HIS C 136 PHE 0.018 0.001 PHE A 90 TYR 0.007 0.001 TYR A 99 ARG 0.007 0.001 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.793 Fit side-chains REVERT: A 96 LYS cc_start: 0.9145 (tptm) cc_final: 0.8867 (tptm) REVERT: A 100 ASP cc_start: 0.8601 (m-30) cc_final: 0.8259 (m-30) REVERT: B 94 GLN cc_start: 0.9367 (mp-120) cc_final: 0.9052 (mm-40) REVERT: C 20 MET cc_start: 0.6997 (OUTLIER) cc_final: 0.6390 (mmp) REVERT: C 24 MET cc_start: 0.8197 (tmm) cc_final: 0.7916 (tmm) REVERT: C 276 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8513 (mm) REVERT: D 191 MET cc_start: 0.9116 (tpp) cc_final: 0.8916 (tpt) outliers start: 19 outliers final: 12 residues processed: 119 average time/residue: 0.1562 time to fit residues: 26.1688 Evaluate side-chains 118 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 209 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.5980 chunk 1 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 83 optimal weight: 0.0980 chunk 23 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 GLN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6921 Z= 0.195 Angle : 0.587 8.734 9454 Z= 0.302 Chirality : 0.041 0.150 1203 Planarity : 0.003 0.034 1222 Dihedral : 3.994 24.431 1029 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.58 % Favored : 94.11 % Rotamer: Outliers : 2.43 % Allowed : 22.37 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.45 (0.27), residues: 968 helix: 0.26 (0.25), residues: 450 sheet: -2.38 (0.85), residues: 46 loop : -2.08 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 274 HIS 0.002 0.001 HIS C 136 PHE 0.016 0.001 PHE A 90 TYR 0.007 0.001 TYR D 52 ARG 0.004 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.728 Fit side-chains REVERT: A 96 LYS cc_start: 0.9181 (tptm) cc_final: 0.8891 (tptm) REVERT: A 100 ASP cc_start: 0.8635 (m-30) cc_final: 0.8280 (m-30) REVERT: B 94 GLN cc_start: 0.9390 (mp-120) cc_final: 0.9098 (mm-40) REVERT: C 20 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6477 (mmp) REVERT: C 24 MET cc_start: 0.8191 (tmm) cc_final: 0.7966 (tmm) REVERT: C 180 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8497 (pp30) REVERT: D 191 MET cc_start: 0.9110 (tpp) cc_final: 0.8652 (tpt) outliers start: 15 outliers final: 10 residues processed: 119 average time/residue: 0.1525 time to fit residues: 25.6105 Evaluate side-chains 119 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 209 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.0170 chunk 18 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 92 optimal weight: 0.1980 chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.0470 chunk 89 optimal weight: 1.9990 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN C 180 GLN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6921 Z= 0.161 Angle : 0.582 8.581 9454 Z= 0.294 Chirality : 0.041 0.186 1203 Planarity : 0.003 0.033 1222 Dihedral : 3.872 24.370 1029 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.68 % Favored : 94.01 % Rotamer: Outliers : 3.08 % Allowed : 23.99 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.35 (0.27), residues: 968 helix: 0.35 (0.25), residues: 450 sheet: -2.21 (0.88), residues: 44 loop : -2.05 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 274 HIS 0.001 0.000 HIS B 199 PHE 0.012 0.001 PHE A 90 TYR 0.007 0.001 TYR D 52 ARG 0.003 0.000 ARG A 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 1.275 Fit side-chains REVERT: A 96 LYS cc_start: 0.9180 (tptm) cc_final: 0.8970 (tppt) REVERT: B 94 GLN cc_start: 0.9392 (mp-120) cc_final: 0.9105 (mm-40) REVERT: C 20 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6243 (mmp) REVERT: C 24 MET cc_start: 0.8147 (tmm) cc_final: 0.7947 (tmm) REVERT: C 180 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.7884 (pp30) REVERT: C 225 MET cc_start: 0.8068 (mmp) cc_final: 0.7756 (mmp) REVERT: D 191 MET cc_start: 0.8953 (tpp) cc_final: 0.8661 (tpt) outliers start: 19 outliers final: 12 residues processed: 126 average time/residue: 0.1572 time to fit residues: 28.1956 Evaluate side-chains 123 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 209 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 57 optimal weight: 0.0370 chunk 56 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN C 180 GLN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6921 Z= 0.177 Angle : 0.586 9.020 9454 Z= 0.297 Chirality : 0.041 0.173 1203 Planarity : 0.003 0.032 1222 Dihedral : 3.836 24.550 1029 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.68 % Favored : 94.01 % Rotamer: Outliers : 3.24 % Allowed : 24.31 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.30 (0.27), residues: 968 helix: 0.39 (0.25), residues: 450 sheet: -2.22 (0.88), residues: 44 loop : -2.02 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 274 HIS 0.003 0.001 HIS B 199 PHE 0.012 0.001 PHE A 90 TYR 0.004 0.001 TYR C 294 ARG 0.004 0.000 ARG C 88 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.842 Fit side-chains REVERT: A 96 LYS cc_start: 0.9225 (tptm) cc_final: 0.9016 (tppt) REVERT: B 94 GLN cc_start: 0.9386 (mp-120) cc_final: 0.9096 (mm-40) REVERT: C 20 MET cc_start: 0.7065 (OUTLIER) cc_final: 0.6390 (mmp) REVERT: C 24 MET cc_start: 0.8189 (tmm) cc_final: 0.7952 (tmm) REVERT: C 225 MET cc_start: 0.8104 (mmp) cc_final: 0.7772 (mmp) REVERT: D 191 MET cc_start: 0.8969 (tpp) cc_final: 0.8552 (tpt) outliers start: 20 outliers final: 14 residues processed: 124 average time/residue: 0.1553 time to fit residues: 27.1691 Evaluate side-chains 126 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 209 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 0.0040 chunk 8 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 GLN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6921 Z= 0.171 Angle : 0.597 8.972 9454 Z= 0.300 Chirality : 0.041 0.178 1203 Planarity : 0.003 0.030 1222 Dihedral : 3.832 24.469 1029 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.99 % Favored : 93.70 % Rotamer: Outliers : 2.76 % Allowed : 25.28 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.22 (0.27), residues: 968 helix: 0.50 (0.25), residues: 450 sheet: -2.18 (0.88), residues: 44 loop : -2.03 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 274 HIS 0.002 0.000 HIS B 199 PHE 0.012 0.001 PHE A 90 TYR 0.003 0.000 TYR D 294 ARG 0.004 0.000 ARG C 88 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.717 Fit side-chains REVERT: A 96 LYS cc_start: 0.9285 (tptm) cc_final: 0.8987 (tptm) REVERT: B 94 GLN cc_start: 0.9383 (mp-120) cc_final: 0.9097 (mm-40) REVERT: C 24 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.8001 (tmm) REVERT: C 180 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.7895 (pp30) REVERT: C 225 MET cc_start: 0.7984 (mmp) cc_final: 0.7632 (mmp) REVERT: D 191 MET cc_start: 0.8959 (tpp) cc_final: 0.8580 (tpt) REVERT: D 274 TRP cc_start: 0.7510 (t-100) cc_final: 0.7168 (t-100) outliers start: 17 outliers final: 13 residues processed: 123 average time/residue: 0.1482 time to fit residues: 26.1572 Evaluate side-chains 127 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 209 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 3.9990 chunk 88 optimal weight: 0.0970 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN C 180 GLN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6921 Z= 0.210 Angle : 0.624 8.985 9454 Z= 0.315 Chirality : 0.042 0.175 1203 Planarity : 0.003 0.031 1222 Dihedral : 3.883 24.904 1029 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.30 % Favored : 93.39 % Rotamer: Outliers : 2.59 % Allowed : 25.28 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.22 (0.27), residues: 968 helix: 0.49 (0.25), residues: 450 sheet: -2.21 (0.88), residues: 44 loop : -2.02 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 274 HIS 0.002 0.001 HIS B 199 PHE 0.014 0.001 PHE A 90 TYR 0.004 0.001 TYR C 255 ARG 0.003 0.000 ARG C 88 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: A 96 LYS cc_start: 0.9309 (tptm) cc_final: 0.8947 (tptm) REVERT: B 88 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: B 94 GLN cc_start: 0.9380 (mp-120) cc_final: 0.9091 (mm-40) REVERT: C 225 MET cc_start: 0.8026 (mmp) cc_final: 0.7676 (mmp) REVERT: D 191 MET cc_start: 0.9053 (tpp) cc_final: 0.8674 (tpt) REVERT: D 274 TRP cc_start: 0.7616 (t-100) cc_final: 0.7251 (t-100) outliers start: 16 outliers final: 13 residues processed: 121 average time/residue: 0.1518 time to fit residues: 25.8960 Evaluate side-chains 123 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 209 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.0670 chunk 63 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 88 optimal weight: 0.0370 chunk 76 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 GLN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6921 Z= 0.178 Angle : 0.625 9.218 9454 Z= 0.310 Chirality : 0.042 0.175 1203 Planarity : 0.003 0.030 1222 Dihedral : 3.870 24.580 1029 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.89 % Favored : 93.80 % Rotamer: Outliers : 2.43 % Allowed : 25.45 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.18 (0.27), residues: 968 helix: 0.56 (0.25), residues: 450 sheet: -2.22 (0.87), residues: 44 loop : -2.03 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 274 HIS 0.002 0.000 HIS B 199 PHE 0.013 0.001 PHE A 90 TYR 0.003 0.000 TYR C 255 ARG 0.003 0.000 ARG C 88 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1936 Ramachandran restraints generated. 968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 96 LYS cc_start: 0.9367 (tptm) cc_final: 0.9024 (tptm) REVERT: B 34 PHE cc_start: 0.8168 (p90) cc_final: 0.7865 (p90) REVERT: B 94 GLN cc_start: 0.9378 (mp-120) cc_final: 0.9098 (mm-40) REVERT: C 180 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.7739 (pp30) REVERT: C 225 MET cc_start: 0.8014 (mmp) cc_final: 0.7669 (mmp) REVERT: D 274 TRP cc_start: 0.7615 (t-100) cc_final: 0.7234 (t-100) outliers start: 15 outliers final: 13 residues processed: 121 average time/residue: 0.1512 time to fit residues: 25.8689 Evaluate side-chains 123 residues out of total 823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 154 PHE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 209 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 4 optimal weight: 0.0030 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN C 180 GLN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.096389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.083674 restraints weight = 29355.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.085228 restraints weight = 18227.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.086346 restraints weight = 12907.974| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6921 Z= 0.185 Angle : 0.632 9.434 9454 Z= 0.315 Chirality : 0.042 0.241 1203 Planarity : 0.003 0.030 1222 Dihedral : 3.857 24.780 1029 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.20 % Favored : 93.49 % Rotamer: Outliers : 2.76 % Allowed : 24.96 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.18 (0.27), residues: 968 helix: 0.57 (0.25), residues: 450 sheet: -2.23 (0.87), residues: 44 loop : -2.05 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 274 HIS 0.002 0.000 HIS B 199 PHE 0.013 0.001 PHE A 90 TYR 0.003 0.001 TYR C 255 ARG 0.003 0.000 ARG C 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1646.09 seconds wall clock time: 34 minutes 37.54 seconds (2077.54 seconds total)