Starting phenix.real_space_refine on Sat Dec 28 14:12:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jef_36186/12_2024/8jef_36186_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jef_36186/12_2024/8jef_36186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jef_36186/12_2024/8jef_36186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jef_36186/12_2024/8jef_36186.map" model { file = "/net/cci-nas-00/data/ceres_data/8jef_36186/12_2024/8jef_36186_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jef_36186/12_2024/8jef_36186_neut.cif" } resolution = 2.96 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= 0.020 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 63 5.16 5 C 5487 2.51 5 N 1477 2.21 5 O 1588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8615 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2123 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 9, 'TRANS': 274} Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 2, 'PHE:plan': 5, 'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 123 Chain: "C" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1701 Classifications: {'peptide': 215} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2577 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 431 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1772 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'3HO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.91, per 1000 atoms: 0.69 Number of scatterers: 8615 At special positions: 0 Unit cell: (89.25, 121.55, 131.75, 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 63 16.00 O 1588 8.00 N 1477 7.00 C 5487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=1.94 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.09 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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: 2.32 Conformation dependent library (CDL) restraints added in 1.1 seconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 12 sheets defined 33.5% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 30 through 54 removed outlier: 3.993A pdb=" N LEU A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 44 " --> pdb=" O PHE A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 80 removed outlier: 3.641A pdb=" N ILE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 96 through 131 removed outlier: 3.653A pdb=" N CYS A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 140 through 159 removed outlier: 4.117A pdb=" N THR A 159 " --> pdb=" O THR A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 188 through 215 removed outlier: 3.618A pdb=" N MET A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.756A pdb=" N CYS A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 244 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 262 Processing helix chain 'A' and resid 269 through 284 removed outlier: 3.606A pdb=" N LEU A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ALA A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.836A pdb=" N LEU A 289 " --> pdb=" O MET A 285 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'C' and resid 8 through 31 removed outlier: 3.767A pdb=" N ALA C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU C 14 " --> pdb=" O LYS C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.516A pdb=" N MET C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.622A pdb=" N ASP C 229 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR C 230 " --> pdb=" O LEU C 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 226 through 230' Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 272 through 281 removed outlier: 4.243A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.914A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 309 Processing helix chain 'C' and resid 329 through 352 removed outlier: 3.626A pdb=" N GLY C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.954A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 184 through 191 removed outlier: 4.343A pdb=" N VAL C 201 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLY C 40 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.861A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.789A 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: 6.893A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.152A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.887A 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: 6.821A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.064A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.626A 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: 6.645A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.776A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (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 58 through 60 removed outlier: 6.564A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.536A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 378 hydrogen bonds defined for protein. 1050 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: 2.46 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1571 1.33 - 1.45: 2314 1.45 - 1.57: 4813 1.57 - 1.69: 8 1.69 - 1.82: 89 Bond restraints: 8795 Sorted by residual: bond pdb=" N CYS A 266 " pdb=" CA CYS A 266 " ideal model delta sigma weight residual 1.457 1.618 -0.161 1.29e-02 6.01e+03 1.55e+02 bond pdb=" N ASN A 265 " pdb=" CA ASN A 265 " ideal model delta sigma weight residual 1.457 1.603 -0.146 1.29e-02 6.01e+03 1.28e+02 bond pdb=" C ASN A 265 " pdb=" N CYS A 266 " ideal model delta sigma weight residual 1.332 1.489 -0.157 1.40e-02 5.10e+03 1.25e+02 bond pdb=" CA ASN A 265 " pdb=" C ASN A 265 " ideal model delta sigma weight residual 1.523 1.662 -0.139 1.34e-02 5.57e+03 1.08e+02 bond pdb=" CB SER A 181 " pdb=" OG SER A 181 " ideal model delta sigma weight residual 1.417 1.618 -0.201 2.00e-02 2.50e+03 1.01e+02 ... (remaining 8790 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.25: 11870 10.25 - 20.50: 36 20.50 - 30.75: 11 30.75 - 41.01: 4 41.01 - 51.26: 1 Bond angle restraints: 11922 Sorted by residual: angle pdb=" O GLN A 264 " pdb=" C GLN A 264 " pdb=" N ASN A 265 " ideal model delta sigma weight residual 122.68 81.78 40.90 1.27e+00 6.20e-01 1.04e+03 angle pdb=" N ASP A 85 " pdb=" CA ASP A 85 " pdb=" C ASP A 85 " ideal model delta sigma weight residual 113.18 146.27 -33.09 1.21e+00 6.83e-01 7.48e+02 angle pdb=" N PRO S 224 " pdb=" CA PRO S 224 " pdb=" C PRO S 224 " ideal model delta sigma weight residual 112.47 61.21 51.26 2.06e+00 2.36e-01 6.19e+02 angle pdb=" N LEU A 167 " pdb=" CA LEU A 167 " pdb=" CB LEU A 167 " ideal model delta sigma weight residual 111.43 76.45 34.98 1.48e+00 4.57e-01 5.59e+02 angle pdb=" N ARG A 22 " pdb=" CA ARG A 22 " pdb=" C ARG A 22 " ideal model delta sigma weight residual 113.18 89.54 23.64 1.21e+00 6.83e-01 3.82e+02 ... (remaining 11917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 4609 16.03 - 32.07: 450 32.07 - 48.10: 112 48.10 - 64.13: 25 64.13 - 80.16: 7 Dihedral angle restraints: 5203 sinusoidal: 1947 harmonic: 3256 Sorted by residual: dihedral pdb=" C ILE A 169 " pdb=" N ILE A 169 " pdb=" CA ILE A 169 " pdb=" CB ILE A 169 " ideal model delta harmonic sigma weight residual -122.00 -79.06 -42.94 0 2.50e+00 1.60e-01 2.95e+02 dihedral pdb=" N ILE A 169 " pdb=" C ILE A 169 " pdb=" CA ILE A 169 " pdb=" CB ILE A 169 " ideal model delta harmonic sigma weight residual 123.40 80.70 42.70 0 2.50e+00 1.60e-01 2.92e+02 dihedral pdb=" N PRO S 224 " pdb=" C PRO S 224 " pdb=" CA PRO S 224 " pdb=" CB PRO S 224 " ideal model delta harmonic sigma weight residual 115.10 73.40 41.70 0 2.50e+00 1.60e-01 2.78e+02 ... (remaining 5200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.203: 1333 0.203 - 0.406: 15 0.406 - 0.609: 8 0.609 - 0.812: 1 0.812 - 1.015: 4 Chirality restraints: 1361 Sorted by residual: chirality pdb=" CA CYS A 183 " pdb=" N CYS A 183 " pdb=" C CYS A 183 " pdb=" CB CYS A 183 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.57e+01 chirality pdb=" CA VAL A 272 " pdb=" N VAL A 272 " pdb=" C VAL A 272 " pdb=" CB VAL A 272 " both_signs ideal model delta sigma weight residual False 2.44 1.53 0.91 2.00e-01 2.50e+01 2.06e+01 chirality pdb=" CA PRO S 224 " pdb=" N PRO S 224 " pdb=" C PRO S 224 " pdb=" CB PRO S 224 " both_signs ideal model delta sigma weight residual False 2.72 1.82 0.89 2.00e-01 2.50e+01 2.00e+01 ... (remaining 1358 not shown) Planarity restraints: 1513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 264 " -0.144 2.00e-02 2.50e+03 2.20e-01 4.82e+02 pdb=" C GLN A 264 " 0.380 2.00e-02 2.50e+03 pdb=" O GLN A 264 " -0.128 2.00e-02 2.50e+03 pdb=" N ASN A 265 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 167 " -0.047 2.00e-02 2.50e+03 9.52e-02 9.07e+01 pdb=" C LEU A 167 " 0.165 2.00e-02 2.50e+03 pdb=" O LEU A 167 " -0.065 2.00e-02 2.50e+03 pdb=" N LEU A 168 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 165 " -0.042 2.00e-02 2.50e+03 8.88e-02 7.88e+01 pdb=" C LYS A 165 " 0.153 2.00e-02 2.50e+03 pdb=" O LYS A 165 " -0.061 2.00e-02 2.50e+03 pdb=" N LYS A 166 " -0.050 2.00e-02 2.50e+03 ... (remaining 1510 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 7 2.13 - 2.82: 2731 2.82 - 3.51: 11152 3.51 - 4.21: 19116 4.21 - 4.90: 34991 Nonbonded interactions: 67997 Sorted by model distance: nonbonded pdb=" N PRO S 224 " pdb=" O PRO S 224 " model vdw 1.435 2.496 nonbonded pdb=" C TYR S 223 " pdb=" O PRO S 224 " model vdw 1.768 3.270 nonbonded pdb=" O ILE A 169 " pdb=" CD1 ILE A 169 " model vdw 1.955 3.460 nonbonded pdb=" N ILE A 26 " pdb=" O ILE A 26 " model vdw 1.960 2.496 nonbonded pdb=" O ILE A 169 " pdb=" CA ALA A 174 " model vdw 1.960 3.470 ... (remaining 67992 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.200 Find NCS groups from input model: 0.090 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:14.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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 : 0.007 0.201 8795 Z= 0.461 Angle : 1.629 51.258 11922 Z= 1.018 Chirality : 0.087 1.015 1361 Planarity : 0.008 0.220 1513 Dihedral : 13.879 80.164 3084 Min Nonbonded Distance : 1.435 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.60 % Favored : 93.95 % Rotamer: Outliers : 1.89 % Allowed : 1.78 % Favored : 96.33 % Cbeta Deviations : 2.19 % 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: -0.30 (0.26), residues: 1108 helix: 0.98 (0.31), residues: 345 sheet: 0.33 (0.30), residues: 292 loop : -1.43 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 142 HIS 0.003 0.000 HIS S 35 PHE 0.090 0.002 PHE A 107 TYR 0.014 0.001 TYR S 223 ARG 0.004 0.000 ARG A 251 *********************** 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 161 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 23 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7897 (p0) REVERT: A 78 ILE cc_start: 0.7176 (pt) cc_final: 0.6956 (pp) REVERT: A 101 ARG cc_start: 0.7023 (mtt180) cc_final: 0.6752 (mtt90) REVERT: A 189 HIS cc_start: 0.4807 (OUTLIER) cc_final: 0.4355 (t-170) REVERT: A 285 MET cc_start: 0.7491 (ptm) cc_final: 0.6447 (tpt) REVERT: A 288 MET cc_start: 0.7662 (mtp) cc_final: 0.6991 (mtm) REVERT: C 242 ARG cc_start: 0.8396 (mtt-85) cc_final: 0.7134 (mmt180) REVERT: C 305 CYS cc_start: 0.8346 (m) cc_final: 0.8126 (p) REVERT: B 42 ARG cc_start: 0.8119 (mmm160) cc_final: 0.7891 (mtp85) REVERT: B 163 ASP cc_start: 0.6850 (t0) cc_final: 0.6581 (t0) REVERT: B 268 ASN cc_start: 0.8700 (m-40) cc_final: 0.8391 (m110) outliers start: 17 outliers final: 4 residues processed: 159 average time/residue: 1.2896 time to fit residues: 218.1430 Evaluate side-chains 126 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 194 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN S 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8795 Z= 0.292 Angle : 0.620 9.514 11922 Z= 0.330 Chirality : 0.045 0.171 1361 Planarity : 0.005 0.083 1513 Dihedral : 6.602 56.396 1227 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.32 % Favored : 93.50 % Rotamer: Outliers : 2.33 % Allowed : 12.44 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.09 % 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: 0.04 (0.26), residues: 1108 helix: 1.50 (0.30), residues: 346 sheet: 0.23 (0.30), residues: 300 loop : -1.25 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.014 0.002 PHE A 232 TYR 0.017 0.001 TYR S 178 ARG 0.004 0.000 ARG A 228 *********************** 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 152 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 23 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.7811 (t0) REVERT: A 76 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.6987 (mm) REVERT: A 101 ARG cc_start: 0.7031 (mtt180) cc_final: 0.6648 (mtt90) REVERT: A 182 ILE cc_start: 0.6940 (OUTLIER) cc_final: 0.6575 (tp) REVERT: A 189 HIS cc_start: 0.4824 (OUTLIER) cc_final: 0.4424 (t-170) REVERT: A 228 ARG cc_start: 0.7419 (tmt-80) cc_final: 0.6138 (ptp-170) REVERT: A 285 MET cc_start: 0.7360 (ptm) cc_final: 0.6496 (tpt) REVERT: A 288 MET cc_start: 0.7711 (mtp) cc_final: 0.7219 (mtm) REVERT: C 25 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7235 (tm-30) REVERT: C 242 ARG cc_start: 0.8562 (mtt-85) cc_final: 0.7243 (mmt180) REVERT: C 305 CYS cc_start: 0.8452 (m) cc_final: 0.8141 (p) REVERT: B 42 ARG cc_start: 0.8148 (mmm160) cc_final: 0.7947 (mtp85) REVERT: B 118 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7992 (p0) REVERT: B 163 ASP cc_start: 0.7090 (t0) cc_final: 0.6818 (t0) REVERT: B 262 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8071 (ttp) REVERT: B 268 ASN cc_start: 0.8712 (m-40) cc_final: 0.8378 (m110) REVERT: G 58 GLU cc_start: 0.7836 (pm20) cc_final: 0.7601 (pm20) outliers start: 21 outliers final: 7 residues processed: 145 average time/residue: 1.3206 time to fit residues: 202.9820 Evaluate side-chains 133 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN B 88 ASN B 237 ASN S 157 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8795 Z= 0.218 Angle : 0.553 7.547 11922 Z= 0.293 Chirality : 0.044 0.162 1361 Planarity : 0.004 0.080 1513 Dihedral : 5.797 56.209 1222 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.96 % Favored : 93.95 % Rotamer: Outliers : 2.22 % Allowed : 15.67 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.09 % 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: 0.18 (0.26), residues: 1108 helix: 1.72 (0.30), residues: 345 sheet: 0.28 (0.30), residues: 300 loop : -1.24 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE C 189 TYR 0.015 0.001 TYR S 178 ARG 0.005 0.000 ARG B 46 *********************** 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 149 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 76 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6866 (mm) REVERT: A 97 ASP cc_start: 0.5934 (t0) cc_final: 0.5510 (t0) REVERT: A 101 ARG cc_start: 0.6971 (mtt180) cc_final: 0.6608 (mtt90) REVERT: A 158 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8175 (mt) REVERT: A 182 ILE cc_start: 0.6983 (OUTLIER) cc_final: 0.6688 (tp) REVERT: A 189 HIS cc_start: 0.5039 (OUTLIER) cc_final: 0.4574 (t-170) REVERT: A 228 ARG cc_start: 0.7511 (tmt-80) cc_final: 0.6075 (ptp-170) REVERT: A 285 MET cc_start: 0.7327 (ptm) cc_final: 0.6442 (tpt) REVERT: A 288 MET cc_start: 0.7640 (mtp) cc_final: 0.7300 (mtm) REVERT: C 242 ARG cc_start: 0.8530 (mtt-85) cc_final: 0.7155 (mmt180) REVERT: C 305 CYS cc_start: 0.8437 (m) cc_final: 0.8149 (p) REVERT: B 17 GLN cc_start: 0.8489 (tm-30) cc_final: 0.8282 (tm-30) REVERT: B 118 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7983 (p0) REVERT: B 163 ASP cc_start: 0.7105 (t0) cc_final: 0.6836 (t0) REVERT: B 237 ASN cc_start: 0.8502 (t0) cc_final: 0.8271 (t0) REVERT: B 254 ASP cc_start: 0.8029 (t0) cc_final: 0.7718 (OUTLIER) REVERT: B 268 ASN cc_start: 0.8680 (m-40) cc_final: 0.8349 (m110) REVERT: G 58 GLU cc_start: 0.7871 (pm20) cc_final: 0.7633 (pm20) outliers start: 20 outliers final: 7 residues processed: 144 average time/residue: 1.3148 time to fit residues: 201.1178 Evaluate side-chains 136 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 275 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 ASN S 39 GLN S 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8795 Z= 0.311 Angle : 0.579 7.200 11922 Z= 0.308 Chirality : 0.045 0.158 1361 Planarity : 0.005 0.088 1513 Dihedral : 5.753 56.992 1220 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.50 % Favored : 93.41 % Rotamer: Outliers : 2.56 % Allowed : 16.67 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.09 % 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: 0.14 (0.26), residues: 1108 helix: 1.73 (0.30), residues: 341 sheet: 0.24 (0.30), residues: 300 loop : -1.25 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.015 0.001 PHE C 196 TYR 0.016 0.001 TYR S 178 ARG 0.009 0.000 ARG B 46 *********************** 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 158 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 76 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6804 (mm) REVERT: A 97 ASP cc_start: 0.6048 (t0) cc_final: 0.5750 (t0) REVERT: A 101 ARG cc_start: 0.6938 (mtt180) cc_final: 0.6541 (mtt90) REVERT: A 158 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8130 (mt) REVERT: A 182 ILE cc_start: 0.6861 (OUTLIER) cc_final: 0.6590 (tp) REVERT: A 189 HIS cc_start: 0.4857 (OUTLIER) cc_final: 0.4615 (t-170) REVERT: A 228 ARG cc_start: 0.7561 (tmt-80) cc_final: 0.6071 (ptt180) REVERT: A 285 MET cc_start: 0.7434 (ptm) cc_final: 0.6498 (tpt) REVERT: A 288 MET cc_start: 0.7720 (mtp) cc_final: 0.7200 (mtm) REVERT: C 242 ARG cc_start: 0.8562 (mtt-85) cc_final: 0.7180 (mmt180) REVERT: C 305 CYS cc_start: 0.8444 (m) cc_final: 0.8162 (p) REVERT: B 17 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8228 (tm-30) REVERT: B 118 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.8011 (p0) REVERT: B 163 ASP cc_start: 0.7272 (t0) cc_final: 0.6904 (t0) REVERT: B 254 ASP cc_start: 0.8062 (t0) cc_final: 0.7685 (t0) REVERT: B 268 ASN cc_start: 0.8700 (m-40) cc_final: 0.8362 (m110) REVERT: G 58 GLU cc_start: 0.7967 (pm20) cc_final: 0.7683 (pm20) REVERT: S 76 LYS cc_start: 0.8553 (mtmm) cc_final: 0.8270 (pmtt) REVERT: S 222 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7634 (mt-10) REVERT: S 223 TYR cc_start: 0.8451 (OUTLIER) cc_final: 0.7663 (t80) outliers start: 23 outliers final: 9 residues processed: 151 average time/residue: 1.2931 time to fit residues: 207.5028 Evaluate side-chains 141 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 ASN B 237 ASN S 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8795 Z= 0.375 Angle : 0.616 9.281 11922 Z= 0.325 Chirality : 0.046 0.181 1361 Planarity : 0.005 0.095 1513 Dihedral : 5.809 55.356 1220 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.05 % Favored : 93.86 % Rotamer: Outliers : 2.33 % Allowed : 18.22 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -0.00 (0.26), residues: 1108 helix: 1.57 (0.30), residues: 339 sheet: 0.16 (0.30), residues: 300 loop : -1.29 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.016 0.002 PHE C 196 TYR 0.016 0.002 TYR S 178 ARG 0.012 0.000 ARG B 46 *********************** 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 149 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 1.004 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 76 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6635 (mt) REVERT: A 101 ARG cc_start: 0.6959 (mtt180) cc_final: 0.6675 (mtt90) REVERT: A 158 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8171 (mt) REVERT: A 182 ILE cc_start: 0.6858 (OUTLIER) cc_final: 0.6627 (tp) REVERT: A 189 HIS cc_start: 0.4937 (OUTLIER) cc_final: 0.4634 (t-170) REVERT: A 228 ARG cc_start: 0.7495 (tmt-80) cc_final: 0.6052 (ptp-170) REVERT: A 285 MET cc_start: 0.7559 (ptm) cc_final: 0.6685 (tpt) REVERT: A 288 MET cc_start: 0.7781 (mtp) cc_final: 0.7358 (mtm) REVERT: C 242 ARG cc_start: 0.8646 (mtt-85) cc_final: 0.7269 (mmt180) REVERT: C 305 CYS cc_start: 0.8476 (m) cc_final: 0.8165 (p) REVERT: C 349 LYS cc_start: 0.7671 (mmpt) cc_final: 0.7355 (mmtm) REVERT: B 17 GLN cc_start: 0.8532 (tm-30) cc_final: 0.8277 (tm-30) REVERT: B 118 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.8127 (p0) REVERT: B 163 ASP cc_start: 0.7364 (t0) cc_final: 0.7121 (t0) REVERT: B 254 ASP cc_start: 0.8103 (t0) cc_final: 0.7728 (t0) REVERT: B 268 ASN cc_start: 0.8704 (m-40) cc_final: 0.8369 (m110) REVERT: G 58 GLU cc_start: 0.8028 (pm20) cc_final: 0.7741 (pm20) REVERT: S 222 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7583 (mt-10) REVERT: S 223 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.7717 (t80) outliers start: 21 outliers final: 9 residues processed: 145 average time/residue: 1.3253 time to fit residues: 204.1031 Evaluate side-chains 137 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 ASN B 237 ASN S 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8795 Z= 0.189 Angle : 0.559 9.001 11922 Z= 0.295 Chirality : 0.043 0.194 1361 Planarity : 0.005 0.083 1513 Dihedral : 5.573 56.005 1220 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.05 % Favored : 93.86 % Rotamer: Outliers : 2.56 % Allowed : 19.00 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: 0.09 (0.26), residues: 1108 helix: 1.65 (0.30), residues: 339 sheet: 0.24 (0.30), residues: 298 loop : -1.26 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.003 0.000 HIS S 35 PHE 0.011 0.001 PHE C 189 TYR 0.016 0.001 TYR S 178 ARG 0.012 0.000 ARG B 46 *********************** 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 158 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.164 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 76 LEU cc_start: 0.7157 (tm) cc_final: 0.6568 (mt) REVERT: A 97 ASP cc_start: 0.6042 (t0) cc_final: 0.5704 (t0) REVERT: A 101 ARG cc_start: 0.6923 (mtt180) cc_final: 0.6659 (mtt90) REVERT: A 158 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8191 (mt) REVERT: A 182 ILE cc_start: 0.6869 (OUTLIER) cc_final: 0.6635 (tp) REVERT: A 189 HIS cc_start: 0.5105 (OUTLIER) cc_final: 0.4844 (t-170) REVERT: A 228 ARG cc_start: 0.7444 (tmt-80) cc_final: 0.6040 (ptp-170) REVERT: A 285 MET cc_start: 0.7531 (ptm) cc_final: 0.6636 (tpt) REVERT: A 288 MET cc_start: 0.7774 (mtp) cc_final: 0.7371 (mtm) REVERT: C 242 ARG cc_start: 0.8581 (mtt-85) cc_final: 0.7224 (mmt180) REVERT: C 305 CYS cc_start: 0.8428 (m) cc_final: 0.8134 (p) REVERT: B 17 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8298 (tm-30) REVERT: B 118 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.8010 (p0) REVERT: B 146 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8406 (mp) REVERT: B 163 ASP cc_start: 0.7203 (t0) cc_final: 0.6845 (t0) REVERT: B 254 ASP cc_start: 0.8060 (t0) cc_final: 0.7664 (t0) REVERT: B 268 ASN cc_start: 0.8667 (m-40) cc_final: 0.8333 (m110) REVERT: G 58 GLU cc_start: 0.8042 (pm20) cc_final: 0.7731 (pm20) REVERT: S 76 LYS cc_start: 0.8561 (mtmm) cc_final: 0.8357 (pmtt) REVERT: S 222 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7578 (mt-10) outliers start: 23 outliers final: 12 residues processed: 154 average time/residue: 1.2904 time to fit residues: 212.5082 Evaluate side-chains 143 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 ASN B 237 ASN S 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8795 Z= 0.185 Angle : 0.559 9.346 11922 Z= 0.295 Chirality : 0.043 0.214 1361 Planarity : 0.005 0.088 1513 Dihedral : 5.407 55.378 1220 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.56 % Allowed : 19.67 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: 0.09 (0.26), residues: 1108 helix: 1.65 (0.30), residues: 341 sheet: 0.16 (0.30), residues: 307 loop : -1.24 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.000 HIS S 35 PHE 0.011 0.001 PHE C 189 TYR 0.018 0.001 TYR C 296 ARG 0.012 0.000 ARG B 46 *********************** 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 154 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 76 LEU cc_start: 0.6938 (tm) cc_final: 0.6511 (mt) REVERT: A 158 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8192 (mt) REVERT: A 182 ILE cc_start: 0.6846 (OUTLIER) cc_final: 0.6627 (tp) REVERT: A 285 MET cc_start: 0.7495 (ptm) cc_final: 0.6453 (tpt) REVERT: A 288 MET cc_start: 0.7835 (mtp) cc_final: 0.7251 (mtm) REVERT: C 242 ARG cc_start: 0.8548 (mtt-85) cc_final: 0.7175 (mmt180) REVERT: C 305 CYS cc_start: 0.8425 (m) cc_final: 0.8131 (p) REVERT: C 349 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7271 (mptt) REVERT: B 118 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7995 (p0) REVERT: B 146 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8371 (mp) REVERT: B 163 ASP cc_start: 0.7108 (t0) cc_final: 0.6763 (t0) REVERT: B 237 ASN cc_start: 0.8528 (t0) cc_final: 0.8326 (t0) REVERT: B 254 ASP cc_start: 0.8066 (t0) cc_final: 0.7663 (t0) REVERT: B 268 ASN cc_start: 0.8657 (m-40) cc_final: 0.8314 (m110) REVERT: G 58 GLU cc_start: 0.8013 (pm20) cc_final: 0.7673 (pm20) REVERT: S 76 LYS cc_start: 0.8557 (mtmm) cc_final: 0.8350 (pmtt) REVERT: S 222 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7621 (mt-10) outliers start: 23 outliers final: 10 residues processed: 150 average time/residue: 1.2280 time to fit residues: 196.1966 Evaluate side-chains 138 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 52 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.0570 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 96 optimal weight: 0.2980 chunk 101 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 ASN S 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8795 Z= 0.197 Angle : 0.577 9.556 11922 Z= 0.303 Chirality : 0.044 0.241 1361 Planarity : 0.004 0.078 1513 Dihedral : 5.174 54.359 1218 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.89 % Allowed : 20.00 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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 (0.26), residues: 1108 helix: 1.53 (0.30), residues: 343 sheet: 0.24 (0.30), residues: 303 loop : -1.23 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.011 0.001 PHE C 189 TYR 0.026 0.001 TYR A 269 ARG 0.013 0.000 ARG B 46 *********************** 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 155 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 109 MET cc_start: 0.6811 (tpp) cc_final: 0.6582 (tpp) REVERT: A 158 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8189 (mt) REVERT: A 285 MET cc_start: 0.7504 (ptm) cc_final: 0.6459 (tpt) REVERT: A 288 MET cc_start: 0.7840 (mtp) cc_final: 0.7240 (mtm) REVERT: C 242 ARG cc_start: 0.8553 (mtt-85) cc_final: 0.7183 (mmt180) REVERT: C 305 CYS cc_start: 0.8425 (m) cc_final: 0.8130 (p) REVERT: C 349 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7304 (mptt) REVERT: B 118 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8001 (p0) REVERT: B 146 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8386 (mp) REVERT: B 163 ASP cc_start: 0.7154 (t0) cc_final: 0.6804 (t0) REVERT: B 254 ASP cc_start: 0.8056 (t0) cc_final: 0.7669 (t0) REVERT: B 268 ASN cc_start: 0.8651 (m-40) cc_final: 0.8303 (m110) REVERT: G 58 GLU cc_start: 0.8015 (pm20) cc_final: 0.7685 (pm20) REVERT: S 43 LYS cc_start: 0.8976 (mptp) cc_final: 0.8769 (mmtt) REVERT: S 222 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7590 (mt-10) REVERT: S 223 TYR cc_start: 0.8300 (OUTLIER) cc_final: 0.7754 (t80) outliers start: 26 outliers final: 14 residues processed: 151 average time/residue: 1.2340 time to fit residues: 198.7448 Evaluate side-chains 144 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 ASN B 237 ASN S 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8795 Z= 0.201 Angle : 0.582 9.416 11922 Z= 0.304 Chirality : 0.044 0.250 1361 Planarity : 0.005 0.083 1513 Dihedral : 5.150 54.035 1218 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.33 % Allowed : 20.44 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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 (0.26), residues: 1108 helix: 1.62 (0.30), residues: 337 sheet: 0.26 (0.30), residues: 303 loop : -1.29 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.003 0.000 HIS S 35 PHE 0.011 0.001 PHE C 189 TYR 0.025 0.001 TYR A 269 ARG 0.014 0.000 ARG B 46 *********************** 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 152 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 158 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8188 (mt) REVERT: A 285 MET cc_start: 0.7478 (ptm) cc_final: 0.6618 (tmt) REVERT: A 288 MET cc_start: 0.7872 (mtp) cc_final: 0.7651 (mtm) REVERT: C 242 ARG cc_start: 0.8549 (mtt-85) cc_final: 0.7187 (mmt180) REVERT: C 305 CYS cc_start: 0.8420 (m) cc_final: 0.8098 (p) REVERT: C 349 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7311 (mptt) REVERT: B 118 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7992 (p0) REVERT: B 146 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8388 (mp) REVERT: B 163 ASP cc_start: 0.7165 (t0) cc_final: 0.6793 (t0) REVERT: B 254 ASP cc_start: 0.8063 (t0) cc_final: 0.7686 (t0) REVERT: B 268 ASN cc_start: 0.8654 (m-40) cc_final: 0.8305 (m110) REVERT: G 58 GLU cc_start: 0.8017 (pm20) cc_final: 0.7685 (pm20) REVERT: S 43 LYS cc_start: 0.8976 (mptp) cc_final: 0.8769 (mmtt) REVERT: S 222 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7563 (mt-10) REVERT: S 223 TYR cc_start: 0.8319 (OUTLIER) cc_final: 0.7733 (t80) outliers start: 21 outliers final: 13 residues processed: 148 average time/residue: 1.2338 time to fit residues: 194.8031 Evaluate side-chains 141 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 ASN S 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8795 Z= 0.195 Angle : 0.593 9.563 11922 Z= 0.310 Chirality : 0.044 0.258 1361 Planarity : 0.005 0.077 1513 Dihedral : 5.117 52.964 1218 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.00 % Allowed : 21.44 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: 0.01 (0.26), residues: 1108 helix: 1.50 (0.29), residues: 344 sheet: 0.20 (0.29), residues: 306 loop : -1.29 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.003 0.000 HIS S 35 PHE 0.011 0.001 PHE C 189 TYR 0.024 0.001 TYR A 269 ARG 0.015 0.000 ARG B 46 ********************** 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 147 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 127 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7222 (t80) REVERT: A 158 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8218 (mt) REVERT: A 285 MET cc_start: 0.7465 (ptm) cc_final: 0.6602 (tmt) REVERT: A 288 MET cc_start: 0.7880 (mtp) cc_final: 0.7647 (mtm) REVERT: C 242 ARG cc_start: 0.8539 (mtt-85) cc_final: 0.7221 (mmt180) REVERT: C 305 CYS cc_start: 0.8427 (m) cc_final: 0.8122 (p) REVERT: C 349 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7311 (mptt) REVERT: B 118 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7982 (p0) REVERT: B 146 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8381 (mp) REVERT: B 163 ASP cc_start: 0.7130 (t0) cc_final: 0.6766 (t0) REVERT: B 254 ASP cc_start: 0.8053 (t0) cc_final: 0.7683 (t0) REVERT: B 268 ASN cc_start: 0.8650 (m-40) cc_final: 0.8302 (m110) REVERT: G 58 GLU cc_start: 0.8019 (pm20) cc_final: 0.7683 (pm20) REVERT: S 43 LYS cc_start: 0.8979 (mptp) cc_final: 0.8767 (mmtt) REVERT: S 222 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7597 (mt-10) REVERT: S 223 TYR cc_start: 0.8303 (OUTLIER) cc_final: 0.7783 (t80) outliers start: 18 outliers final: 11 residues processed: 144 average time/residue: 1.3132 time to fit residues: 201.4507 Evaluate side-chains 140 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 24 optimal weight: 40.0000 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 76 optimal weight: 0.0050 chunk 4 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 ASN S 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.139747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.086439 restraints weight = 11828.209| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.79 r_work: 0.2930 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8795 Z= 0.188 Angle : 0.582 9.556 11922 Z= 0.305 Chirality : 0.044 0.250 1361 Planarity : 0.005 0.081 1513 Dihedral : 5.041 51.843 1218 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.00 % Allowed : 21.56 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -0.02 (0.26), residues: 1108 helix: 1.40 (0.29), residues: 351 sheet: 0.24 (0.29), residues: 306 loop : -1.33 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.003 0.000 HIS S 35 PHE 0.010 0.001 PHE C 189 TYR 0.028 0.001 TYR A 269 ARG 0.015 0.000 ARG B 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3807.60 seconds wall clock time: 68 minutes 51.24 seconds (4131.24 seconds total)