Starting phenix.real_space_refine on Wed Feb 4 04:07:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jkx_61573/02_2026/9jkx_61573_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jkx_61573/02_2026/9jkx_61573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jkx_61573/02_2026/9jkx_61573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jkx_61573/02_2026/9jkx_61573.map" model { file = "/net/cci-nas-00/data/ceres_data/9jkx_61573/02_2026/9jkx_61573_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jkx_61573/02_2026/9jkx_61573_neut.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.016 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 5457 2.51 5 N 1471 2.21 5 O 1583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8574 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2121 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 9, 'TRANS': 275} Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 4, 'PHE:plan': 7, 'TRP:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 118 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: {'ASP:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2574 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 390 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'P9X': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.74, per 1000 atoms: 0.20 Number of scatterers: 8574 At special positions: 0 Unit cell: (88.4, 120.7, 134.3, 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 1583 8.00 N 1471 7.00 C 5457 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=2.04 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " 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: 0.53 Conformation dependent library (CDL) restraints added in 204.6 milliseconds 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 35.6% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 25 through 55 Proline residue: A 31 - end of helix removed outlier: 3.742A pdb=" N ILE A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE A 54 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS A 55 " --> pdb=" O ILE A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 80 removed outlier: 3.612A pdb=" N LEU A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 97 through 130 removed outlier: 3.612A pdb=" N ALA A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 119 " --> pdb=" O ILE A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 140 through 160 Processing helix chain 'A' and resid 165 through 170 removed outlier: 4.700A pdb=" N ILE A 169 " --> pdb=" O LYS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 removed outlier: 4.010A pdb=" N ALA A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE A 193 " --> pdb=" O HIS A 189 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU A 194 " --> pdb=" O GLU A 190 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 218 Processing helix chain 'A' and resid 223 through 261 removed outlier: 3.628A pdb=" N MET A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) Proline residue: A 246 - end of helix removed outlier: 3.544A pdb=" N SER A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 282 removed outlier: 3.565A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 294 removed outlier: 4.071A pdb=" N ASN A 286 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'C' and resid 6 through 31 Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.727A pdb=" N MET C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 216 removed outlier: 3.524A pdb=" N GLU C 216 " --> pdb=" O HIS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 270 through 279 Processing helix chain 'C' and resid 303 through 310 removed outlier: 3.516A pdb=" N LEU C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 352 Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.588A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.509A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.562A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.576A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.514A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.162A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.977A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 185 through 190 removed outlier: 3.568A pdb=" N PHE C 189 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU C 39 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N ALA C 226 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 268 " --> pdb=" O HIS C 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.542A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.887A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.647A 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: 6.806A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.960A 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: 6.832A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.182A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.544A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.374A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.591A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.782A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL S 37 " --> pdb=" O TYR S 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.782A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141 removed outlier: 3.627A pdb=" N ARG S 160 " --> pdb=" O THR S 141 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 194 through 195 removed outlier: 6.674A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1104 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: 1.50 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1486 1.32 - 1.45: 2402 1.45 - 1.57: 4783 1.57 - 1.70: 0 1.70 - 1.83: 89 Bond restraints: 8760 Sorted by residual: bond pdb=" C4 P9X A 401 " pdb=" O1 P9X A 401 " ideal model delta sigma weight residual 1.342 1.521 -0.179 2.00e-02 2.50e+03 7.98e+01 bond pdb=" C3 P9X A 401 " pdb=" C4 P9X A 401 " ideal model delta sigma weight residual 1.357 1.507 -0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" C1 P9X A 401 " pdb=" C2 P9X A 401 " ideal model delta sigma weight residual 1.550 1.403 0.147 2.00e-02 2.50e+03 5.44e+01 bond pdb=" C1 P9X A 401 " pdb=" O1 P9X A 401 " ideal model delta sigma weight residual 1.455 1.566 -0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" C8 P9X A 401 " pdb=" C9 P9X A 401 " ideal model delta sigma weight residual 1.391 1.313 0.078 2.00e-02 2.50e+03 1.54e+01 ... (remaining 8755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.75: 11865 7.75 - 15.50: 22 15.50 - 23.25: 4 23.25 - 30.99: 0 30.99 - 38.74: 1 Bond angle restraints: 11892 Sorted by residual: angle pdb=" N ALA S 221 " pdb=" CA ALA S 221 " pdb=" C ALA S 221 " ideal model delta sigma weight residual 111.07 149.81 -38.74 1.07e+00 8.73e-01 1.31e+03 angle pdb=" N TYR A 284 " pdb=" CA TYR A 284 " pdb=" C TYR A 284 " ideal model delta sigma weight residual 112.54 131.56 -19.02 1.22e+00 6.72e-01 2.43e+02 angle pdb=" C THR A 283 " pdb=" CA THR A 283 " pdb=" CB THR A 283 " ideal model delta sigma weight residual 110.74 131.90 -21.16 1.66e+00 3.63e-01 1.62e+02 angle pdb=" C ALA S 221 " pdb=" CA ALA S 221 " pdb=" CB ALA S 221 " ideal model delta sigma weight residual 110.88 92.47 18.41 1.57e+00 4.06e-01 1.37e+02 angle pdb=" C PHE A 107 " pdb=" CA PHE A 107 " pdb=" CB PHE A 107 " ideal model delta sigma weight residual 110.96 93.50 17.46 1.54e+00 4.22e-01 1.29e+02 ... (remaining 11887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 4531 17.83 - 35.66: 482 35.66 - 53.49: 130 53.49 - 71.32: 25 71.32 - 89.15: 5 Dihedral angle restraints: 5173 sinusoidal: 1913 harmonic: 3260 Sorted by residual: dihedral pdb=" C THR A 283 " pdb=" N THR A 283 " pdb=" CA THR A 283 " pdb=" CB THR A 283 " ideal model delta harmonic sigma weight residual -122.00 -151.30 29.30 0 2.50e+00 1.60e-01 1.37e+02 dihedral pdb=" N THR A 283 " pdb=" C THR A 283 " pdb=" CA THR A 283 " pdb=" CB THR A 283 " ideal model delta harmonic sigma weight residual 123.40 143.04 -19.64 0 2.50e+00 1.60e-01 6.17e+01 dihedral pdb=" CD ARG A 89 " pdb=" NE ARG A 89 " pdb=" CZ ARG A 89 " pdb=" NH1 ARG A 89 " ideal model delta sinusoidal sigma weight residual 0.00 65.63 -65.63 1 1.00e+01 1.00e-02 5.64e+01 ... (remaining 5170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.279: 1343 0.279 - 0.557: 9 0.557 - 0.836: 1 0.836 - 1.114: 1 1.114 - 1.393: 1 Chirality restraints: 1355 Sorted by residual: chirality pdb=" CA ALA S 221 " pdb=" N ALA S 221 " pdb=" C ALA S 221 " pdb=" CB ALA S 221 " both_signs ideal model delta sigma weight residual False 2.48 1.09 1.39 2.00e-01 2.50e+01 4.85e+01 chirality pdb=" CA THR A 283 " pdb=" N THR A 283 " pdb=" C THR A 283 " pdb=" CB THR A 283 " both_signs ideal model delta sigma weight residual False 2.53 1.49 1.04 2.00e-01 2.50e+01 2.69e+01 chirality pdb=" CA PHE A 180 " pdb=" N PHE A 180 " pdb=" C PHE A 180 " pdb=" CB PHE A 180 " both_signs ideal model delta sigma weight residual False 2.51 3.15 -0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 1352 not shown) Planarity restraints: 1512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 89 " 0.994 9.50e-02 1.11e+02 4.46e-01 1.20e+02 pdb=" NE ARG A 89 " -0.060 2.00e-02 2.50e+03 pdb=" CZ ARG A 89 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 89 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 89 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 111 " 0.818 9.50e-02 1.11e+02 3.67e-01 8.18e+01 pdb=" NE ARG A 111 " -0.050 2.00e-02 2.50e+03 pdb=" CZ ARG A 111 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 111 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 111 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 284 " 0.041 2.00e-02 2.50e+03 2.41e-02 1.16e+01 pdb=" CG TYR A 284 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A 284 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 284 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 284 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 284 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 284 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 284 " 0.015 2.00e-02 2.50e+03 ... (remaining 1509 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 2 1.99 - 2.71: 363 2.71 - 3.44: 12111 3.44 - 4.17: 19084 4.17 - 4.90: 35061 Nonbonded interactions: 66621 Sorted by model distance: nonbonded pdb=" O THR A 283 " pdb=" ND2 ASN A 286 " model vdw 1.257 3.120 nonbonded pdb=" O ARG A 89 " pdb=" OD1 ASP A 92 " model vdw 1.984 3.040 nonbonded pdb=" O ARG A 89 " pdb=" OD2 ASP A 92 " model vdw 2.052 3.040 nonbonded pdb=" O ARG A 89 " pdb=" CG ASP A 92 " model vdw 2.100 3.270 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.148 3.040 ... (remaining 66616 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: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.320 Find NCS groups from input model: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 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 0.179 8765 Z= 0.333 Angle : 1.040 38.744 11902 Z= 0.720 Chirality : 0.078 1.393 1355 Planarity : 0.016 0.446 1512 Dihedral : 16.009 89.147 3052 Min Nonbonded Distance : 1.257 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.86 % Favored : 94.05 % Rotamer: Outliers : 3.39 % Allowed : 16.16 % Favored : 80.45 % Cbeta Deviations : 0.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.26), residues: 1109 helix: 1.27 (0.30), residues: 348 sheet: -0.04 (0.31), residues: 292 loop : -1.09 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 218 TYR 0.052 0.002 TYR A 284 PHE 0.034 0.001 PHE A 198 TRP 0.010 0.001 TRP A 93 HIS 0.005 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00544 ( 8760) covalent geometry : angle 1.03962 (11892) SS BOND : bond 0.00376 ( 5) SS BOND : angle 1.48719 ( 10) hydrogen bonds : bond 0.21166 ( 387) hydrogen bonds : angle 7.22590 ( 1104) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.279 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: 0.6996 (OUTLIER) cc_final: 0.6796 (ttp) REVERT: A 193 PHE cc_start: 0.5919 (OUTLIER) cc_final: 0.5203 (m-10) REVERT: A 269 TYR cc_start: 0.7328 (m-80) cc_final: 0.7035 (m-80) REVERT: A 274 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7624 (pp) REVERT: A 277 PHE cc_start: 0.8136 (m-10) cc_final: 0.7728 (m-80) outliers start: 30 outliers final: 13 residues processed: 145 average time/residue: 0.0975 time to fit residues: 18.5845 Evaluate side-chains 133 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 93 TRP Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain G residue 63 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 0.0170 chunk 106 optimal weight: 5.9990 overall best weight: 1.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.117286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.077293 restraints weight = 14802.040| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.21 r_work: 0.2820 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8765 Z= 0.173 Angle : 0.598 7.458 11902 Z= 0.319 Chirality : 0.045 0.217 1355 Planarity : 0.004 0.053 1512 Dihedral : 8.213 56.981 1269 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.05 % Allowed : 17.18 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.26), residues: 1109 helix: 1.68 (0.28), residues: 363 sheet: 0.09 (0.30), residues: 304 loop : -1.15 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 313 TYR 0.022 0.002 TYR S 235 PHE 0.018 0.001 PHE A 38 TRP 0.013 0.001 TRP S 47 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 8760) covalent geometry : angle 0.59664 (11892) SS BOND : bond 0.00434 ( 5) SS BOND : angle 1.26178 ( 10) hydrogen bonds : bond 0.04961 ( 387) hydrogen bonds : angle 5.02326 ( 1104) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.261 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 49 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8344 (mm) REVERT: A 193 PHE cc_start: 0.5628 (OUTLIER) cc_final: 0.4617 (m-10) REVERT: A 269 TYR cc_start: 0.7417 (m-80) cc_final: 0.7038 (m-80) REVERT: A 277 PHE cc_start: 0.8567 (m-10) cc_final: 0.7971 (m-80) REVERT: A 296 PHE cc_start: 0.5396 (OUTLIER) cc_final: 0.4707 (p90) REVERT: G 58 GLU cc_start: 0.8098 (pm20) cc_final: 0.7856 (pm20) outliers start: 27 outliers final: 20 residues processed: 143 average time/residue: 0.0973 time to fit residues: 18.4604 Evaluate side-chains 138 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 PHE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain C residue 256 ASN Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 94 optimal weight: 0.9990 chunk 31 optimal weight: 0.0040 chunk 11 optimal weight: 0.5980 chunk 15 optimal weight: 0.0980 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 58 optimal weight: 0.0370 chunk 69 optimal weight: 0.9980 overall best weight: 0.3470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.121192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.080959 restraints weight = 14826.020| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.32 r_work: 0.2863 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8765 Z= 0.106 Angle : 0.517 7.054 11902 Z= 0.276 Chirality : 0.042 0.182 1355 Planarity : 0.004 0.054 1512 Dihedral : 6.895 57.894 1250 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.60 % Allowed : 18.31 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.26), residues: 1109 helix: 2.08 (0.28), residues: 363 sheet: 0.13 (0.30), residues: 294 loop : -1.11 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 111 TYR 0.019 0.001 TYR S 235 PHE 0.011 0.001 PHE A 197 TRP 0.010 0.001 TRP B 169 HIS 0.002 0.000 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 8760) covalent geometry : angle 0.51677 (11892) SS BOND : bond 0.00333 ( 5) SS BOND : angle 0.94404 ( 10) hydrogen bonds : bond 0.03879 ( 387) hydrogen bonds : angle 4.59337 ( 1104) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.236 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 49 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8299 (mm) REVERT: A 193 PHE cc_start: 0.5536 (OUTLIER) cc_final: 0.4621 (m-10) REVERT: A 267 GLU cc_start: 0.8207 (mp0) cc_final: 0.7620 (mp0) REVERT: A 269 TYR cc_start: 0.7416 (m-80) cc_final: 0.7071 (m-80) REVERT: A 277 PHE cc_start: 0.8545 (m-10) cc_final: 0.8037 (m-80) REVERT: B 32 GLN cc_start: 0.9079 (mt0) cc_final: 0.8720 (mt0) REVERT: B 262 MET cc_start: 0.8516 (mmm) cc_final: 0.7875 (tpp) REVERT: G 48 ASP cc_start: 0.8834 (t0) cc_final: 0.8473 (t0) REVERT: G 58 GLU cc_start: 0.8117 (pm20) cc_final: 0.7818 (pm20) outliers start: 23 outliers final: 14 residues processed: 135 average time/residue: 0.0863 time to fit residues: 15.5501 Evaluate side-chains 127 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 PHE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain C residue 256 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 0.0870 chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS A 189 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.120653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.080403 restraints weight = 14995.241| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.27 r_work: 0.2859 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8765 Z= 0.112 Angle : 0.510 7.301 11902 Z= 0.271 Chirality : 0.042 0.181 1355 Planarity : 0.004 0.051 1512 Dihedral : 6.005 49.831 1244 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.07 % Allowed : 17.06 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.26), residues: 1109 helix: 2.17 (0.28), residues: 369 sheet: 0.16 (0.30), residues: 299 loop : -1.04 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 160 TYR 0.018 0.001 TYR S 235 PHE 0.015 0.001 PHE A 38 TRP 0.008 0.001 TRP S 47 HIS 0.002 0.000 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8760) covalent geometry : angle 0.50960 (11892) SS BOND : bond 0.00347 ( 5) SS BOND : angle 0.85686 ( 10) hydrogen bonds : bond 0.03687 ( 387) hydrogen bonds : angle 4.37661 ( 1104) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 0.271 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 49 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8327 (mm) REVERT: A 109 MET cc_start: 0.7272 (tmm) cc_final: 0.7065 (tmm) REVERT: A 193 PHE cc_start: 0.5493 (OUTLIER) cc_final: 0.4561 (m-10) REVERT: A 259 HIS cc_start: 0.7959 (t70) cc_final: 0.7407 (t70) REVERT: A 269 TYR cc_start: 0.7505 (m-80) cc_final: 0.7153 (m-80) REVERT: A 277 PHE cc_start: 0.8590 (m-10) cc_final: 0.8040 (m-80) REVERT: A 294 TYR cc_start: 0.8198 (m-80) cc_final: 0.7832 (m-80) REVERT: A 296 PHE cc_start: 0.5312 (OUTLIER) cc_final: 0.4818 (p90) REVERT: B 262 MET cc_start: 0.8594 (mmm) cc_final: 0.8027 (tpp) REVERT: G 58 GLU cc_start: 0.8055 (pm20) cc_final: 0.7656 (pm20) outliers start: 36 outliers final: 21 residues processed: 145 average time/residue: 0.0794 time to fit residues: 15.5840 Evaluate side-chains 139 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 PHE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain C residue 256 ASN Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 48 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 82 optimal weight: 30.0000 chunk 34 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 86 optimal weight: 0.4980 chunk 43 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.120662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.080426 restraints weight = 14866.334| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.25 r_work: 0.2859 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8765 Z= 0.114 Angle : 0.517 7.326 11902 Z= 0.274 Chirality : 0.042 0.190 1355 Planarity : 0.004 0.053 1512 Dihedral : 5.756 50.078 1243 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.73 % Allowed : 17.18 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.26), residues: 1109 helix: 2.36 (0.28), residues: 363 sheet: 0.10 (0.30), residues: 306 loop : -1.00 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 313 TYR 0.021 0.001 TYR S 235 PHE 0.009 0.001 PHE A 240 TRP 0.008 0.001 TRP S 47 HIS 0.003 0.000 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8760) covalent geometry : angle 0.51641 (11892) SS BOND : bond 0.00355 ( 5) SS BOND : angle 0.81679 ( 10) hydrogen bonds : bond 0.03652 ( 387) hydrogen bonds : angle 4.30914 ( 1104) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.219 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 49 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8269 (mm) REVERT: A 109 MET cc_start: 0.7349 (tmm) cc_final: 0.7079 (tmm) REVERT: A 193 PHE cc_start: 0.5505 (OUTLIER) cc_final: 0.4652 (m-10) REVERT: A 213 TRP cc_start: 0.8199 (t60) cc_final: 0.7987 (t60) REVERT: A 259 HIS cc_start: 0.7962 (t70) cc_final: 0.7436 (t70) REVERT: A 277 PHE cc_start: 0.8656 (m-10) cc_final: 0.8069 (m-80) REVERT: A 294 TYR cc_start: 0.8321 (m-80) cc_final: 0.8006 (m-80) REVERT: A 296 PHE cc_start: 0.5317 (OUTLIER) cc_final: 0.4872 (p90) REVERT: B 262 MET cc_start: 0.8563 (mmm) cc_final: 0.8027 (tpp) REVERT: G 48 ASP cc_start: 0.8872 (t0) cc_final: 0.8378 (t0) REVERT: G 58 GLU cc_start: 0.8177 (pm20) cc_final: 0.7754 (pm20) outliers start: 33 outliers final: 24 residues processed: 143 average time/residue: 0.0911 time to fit residues: 17.2549 Evaluate side-chains 142 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 PHE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain C residue 256 ASN Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Chi-restraints excluded: chain S residue 244 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 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 306 GLN B 142 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.115929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.075749 restraints weight = 14871.633| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.21 r_work: 0.2792 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8765 Z= 0.218 Angle : 0.600 9.752 11902 Z= 0.317 Chirality : 0.045 0.232 1355 Planarity : 0.004 0.052 1512 Dihedral : 6.553 55.246 1243 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.18 % Allowed : 18.87 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.26), residues: 1109 helix: 2.08 (0.28), residues: 367 sheet: -0.01 (0.30), residues: 304 loop : -1.12 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 228 TYR 0.024 0.002 TYR S 235 PHE 0.021 0.002 PHE A 240 TRP 0.013 0.001 TRP S 36 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00520 ( 8760) covalent geometry : angle 0.59932 (11892) SS BOND : bond 0.00479 ( 5) SS BOND : angle 1.02956 ( 10) hydrogen bonds : bond 0.04598 ( 387) hydrogen bonds : angle 4.53061 ( 1104) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 0.365 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 49 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8318 (mm) REVERT: A 193 PHE cc_start: 0.5421 (OUTLIER) cc_final: 0.4538 (m-10) REVERT: A 259 HIS cc_start: 0.7892 (t70) cc_final: 0.7383 (t70) REVERT: A 277 PHE cc_start: 0.8637 (m-10) cc_final: 0.8035 (m-80) REVERT: A 296 PHE cc_start: 0.5425 (OUTLIER) cc_final: 0.5042 (p90) REVERT: C 247 MET cc_start: 0.9384 (mtp) cc_final: 0.9068 (mtt) REVERT: C 287 TYR cc_start: 0.8794 (m-80) cc_final: 0.8474 (m-80) REVERT: G 58 GLU cc_start: 0.8231 (pm20) cc_final: 0.7806 (pm20) outliers start: 37 outliers final: 28 residues processed: 142 average time/residue: 0.0893 time to fit residues: 17.1920 Evaluate side-chains 143 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 PHE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain C residue 256 ASN Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 58 optimal weight: 0.0050 chunk 8 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.117781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.076492 restraints weight = 15213.011| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.33 r_work: 0.2786 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8765 Z= 0.182 Angle : 0.583 9.106 11902 Z= 0.307 Chirality : 0.044 0.241 1355 Planarity : 0.004 0.052 1512 Dihedral : 6.324 50.274 1243 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.84 % Allowed : 19.21 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.26), residues: 1109 helix: 2.06 (0.28), residues: 367 sheet: -0.08 (0.29), residues: 307 loop : -1.12 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 228 TYR 0.022 0.002 TYR S 235 PHE 0.014 0.001 PHE A 240 TRP 0.012 0.001 TRP S 47 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 8760) covalent geometry : angle 0.58304 (11892) SS BOND : bond 0.00473 ( 5) SS BOND : angle 0.97253 ( 10) hydrogen bonds : bond 0.04277 ( 387) hydrogen bonds : angle 4.47165 ( 1104) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 0.228 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8318 (mm) REVERT: A 193 PHE cc_start: 0.5476 (OUTLIER) cc_final: 0.4555 (m-10) REVERT: A 277 PHE cc_start: 0.8670 (m-10) cc_final: 0.8053 (m-80) REVERT: A 296 PHE cc_start: 0.5494 (OUTLIER) cc_final: 0.5097 (p90) REVERT: C 313 ARG cc_start: 0.8760 (tpp80) cc_final: 0.8557 (tpp80) REVERT: B 262 MET cc_start: 0.8729 (mmm) cc_final: 0.7970 (tpp) REVERT: G 48 ASP cc_start: 0.8989 (t0) cc_final: 0.8601 (t0) REVERT: G 58 GLU cc_start: 0.8192 (pm20) cc_final: 0.7753 (pm20) outliers start: 34 outliers final: 28 residues processed: 140 average time/residue: 0.0910 time to fit residues: 17.0709 Evaluate side-chains 143 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 PHE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain C residue 256 ASN Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 73 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 106 optimal weight: 0.0670 overall best weight: 1.1920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.117320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.076930 restraints weight = 14746.316| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.21 r_work: 0.2810 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8765 Z= 0.150 Angle : 0.573 9.066 11902 Z= 0.300 Chirality : 0.044 0.232 1355 Planarity : 0.004 0.051 1512 Dihedral : 6.035 50.583 1243 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.62 % Allowed : 19.21 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.26), residues: 1109 helix: 2.07 (0.28), residues: 367 sheet: -0.03 (0.30), residues: 307 loop : -1.10 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 111 TYR 0.022 0.001 TYR S 235 PHE 0.012 0.001 PHE A 240 TRP 0.011 0.001 TRP S 47 HIS 0.003 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 8760) covalent geometry : angle 0.57147 (11892) SS BOND : bond 0.00465 ( 5) SS BOND : angle 1.34627 ( 10) hydrogen bonds : bond 0.04047 ( 387) hydrogen bonds : angle 4.43327 ( 1104) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.192 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 18 CYS cc_start: 0.6454 (OUTLIER) cc_final: 0.6068 (t) REVERT: A 49 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8306 (mm) REVERT: A 193 PHE cc_start: 0.5693 (OUTLIER) cc_final: 0.4740 (m-10) REVERT: A 223 HIS cc_start: 0.7616 (OUTLIER) cc_final: 0.7299 (m90) REVERT: A 259 HIS cc_start: 0.8069 (m90) cc_final: 0.7488 (t70) REVERT: A 277 PHE cc_start: 0.8677 (m-10) cc_final: 0.8054 (m-80) REVERT: A 296 PHE cc_start: 0.5466 (OUTLIER) cc_final: 0.5101 (p90) REVERT: B 262 MET cc_start: 0.8685 (mmm) cc_final: 0.8053 (tpp) REVERT: G 27 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.6788 (mtp85) REVERT: G 48 ASP cc_start: 0.8951 (t0) cc_final: 0.8599 (t0) REVERT: G 58 GLU cc_start: 0.8217 (pm20) cc_final: 0.7763 (pm20) outliers start: 32 outliers final: 25 residues processed: 139 average time/residue: 0.0878 time to fit residues: 16.5191 Evaluate side-chains 147 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 21 PHE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain C residue 256 ASN Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.6980 chunk 97 optimal weight: 0.0670 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 72 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.119150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.078776 restraints weight = 14822.378| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.22 r_work: 0.2847 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8765 Z= 0.116 Angle : 0.557 8.952 11902 Z= 0.291 Chirality : 0.043 0.234 1355 Planarity : 0.004 0.052 1512 Dihedral : 5.513 51.987 1243 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.39 % Allowed : 19.55 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.26), residues: 1109 helix: 2.14 (0.28), residues: 368 sheet: 0.05 (0.30), residues: 307 loop : -1.05 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 313 TYR 0.021 0.001 TYR S 235 PHE 0.012 0.001 PHE A 232 TRP 0.010 0.001 TRP S 47 HIS 0.003 0.000 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8760) covalent geometry : angle 0.55685 (11892) SS BOND : bond 0.00379 ( 5) SS BOND : angle 1.05629 ( 10) hydrogen bonds : bond 0.03536 ( 387) hydrogen bonds : angle 4.29176 ( 1104) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.303 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 18 CYS cc_start: 0.6357 (OUTLIER) cc_final: 0.6006 (t) REVERT: A 49 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8306 (mm) REVERT: A 193 PHE cc_start: 0.5747 (OUTLIER) cc_final: 0.4746 (m-10) REVERT: A 223 HIS cc_start: 0.7624 (OUTLIER) cc_final: 0.7406 (m90) REVERT: A 259 HIS cc_start: 0.7983 (m90) cc_final: 0.7537 (t70) REVERT: A 277 PHE cc_start: 0.8680 (m-10) cc_final: 0.8051 (m-80) REVERT: A 296 PHE cc_start: 0.5429 (OUTLIER) cc_final: 0.5071 (p90) REVERT: B 262 MET cc_start: 0.8665 (mmm) cc_final: 0.8037 (tpp) REVERT: G 27 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.6738 (mtp85) REVERT: G 48 ASP cc_start: 0.8920 (t0) cc_final: 0.8593 (t0) REVERT: G 58 GLU cc_start: 0.8245 (pm20) cc_final: 0.7782 (pm20) outliers start: 30 outliers final: 23 residues processed: 140 average time/residue: 0.0808 time to fit residues: 15.2682 Evaluate side-chains 144 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 21 PHE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 223 HIS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain C residue 256 ASN Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 101 optimal weight: 9.9990 chunk 36 optimal weight: 0.7980 chunk 68 optimal weight: 0.0030 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.119255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.078823 restraints weight = 14675.776| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.21 r_work: 0.2846 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8765 Z= 0.118 Angle : 0.560 8.986 11902 Z= 0.292 Chirality : 0.043 0.231 1355 Planarity : 0.004 0.052 1512 Dihedral : 5.203 52.217 1243 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.39 % Allowed : 19.44 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.26), residues: 1109 helix: 2.15 (0.28), residues: 367 sheet: 0.08 (0.30), residues: 307 loop : -1.09 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 160 TYR 0.020 0.001 TYR S 235 PHE 0.015 0.001 PHE A 232 TRP 0.009 0.001 TRP B 82 HIS 0.002 0.000 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8760) covalent geometry : angle 0.55984 (11892) SS BOND : bond 0.00367 ( 5) SS BOND : angle 0.92656 ( 10) hydrogen bonds : bond 0.03600 ( 387) hydrogen bonds : angle 4.26943 ( 1104) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.258 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 18 CYS cc_start: 0.6403 (OUTLIER) cc_final: 0.6083 (t) REVERT: A 49 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8240 (mm) REVERT: A 193 PHE cc_start: 0.5746 (OUTLIER) cc_final: 0.4797 (m-10) REVERT: A 213 TRP cc_start: 0.8112 (t60) cc_final: 0.7758 (t60) REVERT: A 259 HIS cc_start: 0.7959 (m90) cc_final: 0.7723 (t70) REVERT: A 277 PHE cc_start: 0.8686 (m-10) cc_final: 0.8054 (m-80) REVERT: A 296 PHE cc_start: 0.5411 (OUTLIER) cc_final: 0.5072 (p90) REVERT: B 262 MET cc_start: 0.8662 (mmm) cc_final: 0.8029 (tpp) REVERT: G 27 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.6714 (mtp85) REVERT: G 48 ASP cc_start: 0.8926 (t0) cc_final: 0.8623 (t0) REVERT: G 58 GLU cc_start: 0.8235 (pm20) cc_final: 0.7769 (pm20) outliers start: 30 outliers final: 23 residues processed: 141 average time/residue: 0.0825 time to fit residues: 15.6458 Evaluate side-chains 148 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 21 PHE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 193 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain C residue 256 ASN Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 78 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.120780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.079004 restraints weight = 14972.211| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.34 r_work: 0.2835 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8765 Z= 0.123 Angle : 0.566 8.830 11902 Z= 0.296 Chirality : 0.043 0.230 1355 Planarity : 0.004 0.051 1512 Dihedral : 4.795 49.930 1241 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.28 % Allowed : 19.55 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.26), residues: 1109 helix: 2.18 (0.28), residues: 366 sheet: 0.09 (0.30), residues: 307 loop : -1.05 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 160 TYR 0.020 0.001 TYR S 235 PHE 0.014 0.001 PHE A 232 TRP 0.009 0.001 TRP B 82 HIS 0.002 0.000 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8760) covalent geometry : angle 0.56561 (11892) SS BOND : bond 0.00393 ( 5) SS BOND : angle 0.93595 ( 10) hydrogen bonds : bond 0.03604 ( 387) hydrogen bonds : angle 4.27536 ( 1104) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1853.90 seconds wall clock time: 32 minutes 23.90 seconds (1943.90 seconds total)