Starting phenix.real_space_refine on Sat Aug 23 00:17:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iu2_35714/08_2025/8iu2_35714.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iu2_35714/08_2025/8iu2_35714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iu2_35714/08_2025/8iu2_35714.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iu2_35714/08_2025/8iu2_35714.map" model { file = "/net/cci-nas-00/data/ceres_data/8iu2_35714/08_2025/8iu2_35714.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iu2_35714/08_2025/8iu2_35714.cif" } resolution = 3.35 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= 0.001 sd= 0.012 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 67 5.16 5 C 5591 2.51 5 N 1481 2.21 5 O 1595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8734 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2338 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 280} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1589 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 2, 'TRANS': 206} Chain breaks: 2 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 7, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 62 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2598 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1751 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N TRP R 177 " occ=0.50 ... (12 atoms not shown) pdb=" CH2 TRP R 177 " occ=0.50 residue: pdb=" N PHE R 329 " occ=0.50 ... (9 atoms not shown) pdb=" CZ PHE R 329 " occ=0.50 Time building chain proxies: 2.28, per 1000 atoms: 0.26 Number of scatterers: 8734 At special positions: 0 Unit cell: (89.512, 123.58, 128.256, 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 67 16.00 O 1595 8.00 N 1481 7.00 C 5591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 126 " - pdb=" SG CYS R 203 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 445.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 17 sheets defined 36.1% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'R' and resid 49 through 81 removed outlier: 3.768A pdb=" N TYR R 53 " --> pdb=" O PRO R 49 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL R 74 " --> pdb=" O THR R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 117 removed outlier: 3.525A pdb=" N VAL R 93 " --> pdb=" O ASN R 89 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER R 107 " --> pdb=" O THR R 103 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE R 109 " --> pdb=" O ILE R 105 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER R 110 " --> pdb=" O ALA R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 122 through 157 Processing helix chain 'R' and resid 165 through 185 removed outlier: 4.010A pdb=" N ALA R 169 " --> pdb=" O ASP R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 190 Processing helix chain 'R' and resid 215 through 228 removed outlier: 3.549A pdb=" N ILE R 221 " --> pdb=" O GLN R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 228 through 253 removed outlier: 3.644A pdb=" N ILE R 246 " --> pdb=" O VAL R 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 294 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 300 through 323 removed outlier: 3.625A pdb=" N LEU R 306 " --> pdb=" O LEU R 302 " (cutoff:3.500A) Proline residue: R 307 - end of helix removed outlier: 4.035A pdb=" N THR R 315 " --> pdb=" O ALA R 311 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ILE R 316 " --> pdb=" O LYS R 312 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR R 317 " --> pdb=" O SER R 313 " (cutoff:3.500A) Proline residue: R 319 - end of helix Processing helix chain 'R' and resid 326 through 335 Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.581A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.524A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.605A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 352 removed outlier: 3.570A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.704A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.715A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.632A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 56 removed outlier: 3.626A pdb=" N SER S 55 " --> pdb=" O SER S 52 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 52 through 56' Processing sheet with id=AA1, first strand: chain 'R' and resid 194 through 197 removed outlier: 3.625A pdb=" N HIS R 197 " --> pdb=" O SER R 202 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N SER R 202 " --> pdb=" O HIS R 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 6.692A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.593A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 47 removed outlier: 3.613A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.782A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.613A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.586A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.805A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.478A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.783A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.619A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER S 71 " --> pdb=" O PHE S 80 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.747A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.747A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 141 through 142 Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 148 Processing sheet with id=AB7, first strand: chain 'S' and resid 155 through 157 removed outlier: 3.503A pdb=" N VAL S 155 " --> pdb=" O ILE S 216 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR S 213 " --> pdb=" O SER S 206 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 177 through 178 402 hydrogen bonds defined for protein. 1158 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: 1.47 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2221 1.33 - 1.45: 1926 1.45 - 1.57: 4697 1.57 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 8940 Sorted by residual: bond pdb=" N LEU R 306 " pdb=" CA LEU R 306 " ideal model delta sigma weight residual 1.462 1.495 -0.033 9.50e-03 1.11e+04 1.21e+01 bond pdb=" N VAL R 120 " pdb=" CA VAL R 120 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.08e-02 8.57e+03 1.11e+01 bond pdb=" N ASN R 318 " pdb=" CA ASN R 318 " ideal model delta sigma weight residual 1.461 1.492 -0.031 9.20e-03 1.18e+04 1.10e+01 bond pdb=" N GLY R 122 " pdb=" CA GLY R 122 " ideal model delta sigma weight residual 1.448 1.477 -0.028 8.80e-03 1.29e+04 1.04e+01 bond pdb=" N VAL A 34 " pdb=" CA VAL A 34 " ideal model delta sigma weight residual 1.458 1.493 -0.034 1.12e-02 7.97e+03 9.49e+00 ... (remaining 8935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 11559 2.53 - 5.06: 544 5.06 - 7.59: 40 7.59 - 10.12: 7 10.12 - 12.65: 3 Bond angle restraints: 12153 Sorted by residual: angle pdb=" N PRO R 186 " pdb=" CA PRO R 186 " pdb=" C PRO R 186 " ideal model delta sigma weight residual 110.70 119.15 -8.45 1.22e+00 6.72e-01 4.79e+01 angle pdb=" CA GLY R 122 " pdb=" C GLY R 122 " pdb=" O GLY R 122 " ideal model delta sigma weight residual 122.37 118.10 4.27 7.30e-01 1.88e+00 3.43e+01 angle pdb=" N THR A 329 " pdb=" CA THR A 329 " pdb=" C THR A 329 " ideal model delta sigma weight residual 113.02 106.70 6.32 1.20e+00 6.94e-01 2.78e+01 angle pdb=" CA ASP A 309 " pdb=" C ASP A 309 " pdb=" O ASP A 309 " ideal model delta sigma weight residual 121.99 116.44 5.55 1.14e+00 7.69e-01 2.37e+01 angle pdb=" CA PRO R 186 " pdb=" C PRO R 186 " pdb=" N PRO R 187 " ideal model delta sigma weight residual 117.93 123.41 -5.48 1.20e+00 6.94e-01 2.09e+01 ... (remaining 12148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 4956 17.23 - 34.45: 209 34.45 - 51.68: 50 51.68 - 68.91: 6 68.91 - 86.14: 4 Dihedral angle restraints: 5225 sinusoidal: 1933 harmonic: 3292 Sorted by residual: dihedral pdb=" CA ASP B 195 " pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta harmonic sigma weight residual -180.00 -147.47 -32.53 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA LEU A 353 " pdb=" C LEU A 353 " pdb=" N PHE A 354 " pdb=" CA PHE A 354 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA TYR S 190 " pdb=" C TYR S 190 " pdb=" N ARG S 191 " pdb=" CA ARG S 191 " ideal model delta harmonic sigma weight residual 180.00 155.63 24.37 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 5222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 862 0.061 - 0.123: 395 0.123 - 0.184: 96 0.184 - 0.245: 17 0.245 - 0.307: 5 Chirality restraints: 1375 Sorted by residual: chirality pdb=" CG LEU S 174 " pdb=" CB LEU S 174 " pdb=" CD1 LEU S 174 " pdb=" CD2 LEU S 174 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA VAL A 34 " pdb=" N VAL A 34 " pdb=" C VAL A 34 " pdb=" CB VAL A 34 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA TRP R 183 " pdb=" N TRP R 183 " pdb=" C TRP R 183 " pdb=" CB TRP R 183 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 1372 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP S 111 " 0.024 2.00e-02 2.50e+03 2.02e-02 1.02e+01 pdb=" CG TRP S 111 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP S 111 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP S 111 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP S 111 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP S 111 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP S 111 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 111 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 111 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP S 111 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 234 " 0.023 2.00e-02 2.50e+03 2.41e-02 1.01e+01 pdb=" CG PHE B 234 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE B 234 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE B 234 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 234 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 234 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 234 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 278 " 0.015 2.00e-02 2.50e+03 2.08e-02 7.59e+00 pdb=" CG PHE B 278 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE B 278 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE B 278 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 278 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE B 278 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 278 " 0.003 2.00e-02 2.50e+03 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2674 2.82 - 3.34: 7710 3.34 - 3.86: 13965 3.86 - 4.38: 15709 4.38 - 4.90: 28188 Nonbonded interactions: 68246 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.299 3.040 nonbonded pdb=" OG1 THR B 184 " pdb=" OD2 ASP B 205 " model vdw 2.314 3.040 nonbonded pdb=" O VAL R 104 " pdb=" OG SER R 107 " model vdw 2.328 3.040 nonbonded pdb=" OG SER A 293 " pdb=" OE1 GLU A 298 " model vdw 2.345 3.040 nonbonded pdb=" OG SER B 161 " pdb=" N GLY B 162 " model vdw 2.350 3.120 ... (remaining 68241 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=0.50 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: 4.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.150 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.076 8942 Z= 0.623 Angle : 1.186 12.651 12155 Z= 0.759 Chirality : 0.072 0.307 1375 Planarity : 0.006 0.068 1532 Dihedral : 10.944 86.136 3102 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.60 % Favored : 93.31 % Rotamer: Outliers : 1.64 % Allowed : 3.27 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -2.77 (0.23), residues: 1121 helix: 0.28 (0.24), residues: 390 sheet: -3.37 (0.28), residues: 267 loop : -2.67 (0.24), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 314 TYR 0.038 0.004 TYR S 227 PHE 0.055 0.004 PHE B 234 TRP 0.054 0.003 TRP S 111 HIS 0.013 0.003 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.01197 ( 8940) covalent geometry : angle 1.18612 (12153) SS BOND : bond 0.00045 ( 1) SS BOND : angle 1.03416 ( 2) hydrogen bonds : bond 0.19820 ( 394) hydrogen bonds : angle 7.45647 ( 1158) Misc. bond : bond 0.05556 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 231 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 54 HIS cc_start: 0.8695 (m-70) cc_final: 0.8483 (m90) REVERT: R 207 VAL cc_start: 0.8888 (t) cc_final: 0.8677 (m) REVERT: A 24 ARG cc_start: 0.7502 (mtm110) cc_final: 0.7108 (mtm-85) REVERT: A 346 ASN cc_start: 0.8593 (m110) cc_final: 0.8234 (m110) REVERT: B 44 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7257 (pm20) REVERT: B 86 THR cc_start: 0.9245 (p) cc_final: 0.9001 (p) REVERT: B 214 ARG cc_start: 0.7787 (mmt-90) cc_final: 0.7428 (mmt180) REVERT: B 215 GLU cc_start: 0.8714 (mp0) cc_final: 0.8507 (mp0) REVERT: B 295 ASN cc_start: 0.8850 (m-40) cc_final: 0.8633 (m-40) REVERT: B 304 ARG cc_start: 0.8379 (ttp-170) cc_final: 0.8096 (ptm160) REVERT: G 16 VAL cc_start: 0.8561 (p) cc_final: 0.8311 (m) REVERT: G 17 GLU cc_start: 0.8692 (tp30) cc_final: 0.8474 (tp30) REVERT: G 27 ARG cc_start: 0.8516 (mtt90) cc_final: 0.8235 (mtt90) REVERT: G 47 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8043 (mp0) REVERT: S 65 LYS cc_start: 0.8539 (tttt) cc_final: 0.8103 (tttp) REVERT: S 87 ARG cc_start: 0.8118 (ptp-170) cc_final: 0.7859 (mtm110) REVERT: S 234 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7616 (pt0) REVERT: S 244 LYS cc_start: 0.8170 (tttm) cc_final: 0.7802 (ttmm) outliers start: 15 outliers final: 6 residues processed: 244 average time/residue: 0.1205 time to fit residues: 38.3694 Evaluate side-chains 164 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 158 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 PHE Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 209 SER Chi-restraints excluded: chain R residue 312 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 0.0470 chunk 106 optimal weight: 2.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 94 ASN R 113 ASN ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 129 GLN R 331 ASN B 44 GLN B 91 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 268 ASN B 340 ASN G 5 ASN S 194 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.129114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.093850 restraints weight = 14072.617| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.86 r_work: 0.3062 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8942 Z= 0.131 Angle : 0.603 8.056 12155 Z= 0.313 Chirality : 0.043 0.158 1375 Planarity : 0.004 0.055 1532 Dihedral : 6.971 81.214 1242 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.84 % Allowed : 10.14 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: -1.46 (0.25), residues: 1121 helix: 1.83 (0.26), residues: 390 sheet: -2.84 (0.29), residues: 265 loop : -2.26 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 32 TYR 0.018 0.001 TYR R 194 PHE 0.014 0.001 PHE R 290 TRP 0.016 0.001 TRP S 111 HIS 0.003 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8940) covalent geometry : angle 0.60297 (12153) SS BOND : bond 0.00096 ( 1) SS BOND : angle 0.24102 ( 2) hydrogen bonds : bond 0.05207 ( 394) hydrogen bonds : angle 5.18466 ( 1158) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 54 HIS cc_start: 0.8637 (m-70) cc_final: 0.8436 (m90) REVERT: R 284 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.7329 (t80) REVERT: R 302 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7364 (mm) REVERT: A 17 LYS cc_start: 0.8814 (mttt) cc_final: 0.8375 (mtpt) REVERT: A 24 ARG cc_start: 0.7517 (mtm110) cc_final: 0.7177 (mtm-85) REVERT: A 256 ASN cc_start: 0.8833 (t0) cc_final: 0.8394 (t0) REVERT: A 332 VAL cc_start: 0.9091 (m) cc_final: 0.8757 (p) REVERT: A 346 ASN cc_start: 0.8742 (m110) cc_final: 0.8408 (m110) REVERT: B 42 ARG cc_start: 0.7733 (ttp80) cc_final: 0.7270 (ttp80) REVERT: B 44 GLN cc_start: 0.8000 (mm110) cc_final: 0.7436 (pm20) REVERT: B 156 GLN cc_start: 0.8245 (mt0) cc_final: 0.7803 (mt0) REVERT: B 215 GLU cc_start: 0.8803 (mp0) cc_final: 0.8491 (mp0) REVERT: G 17 GLU cc_start: 0.8645 (tp30) cc_final: 0.8427 (tp30) REVERT: G 27 ARG cc_start: 0.8587 (mtt90) cc_final: 0.8288 (mtt90) REVERT: G 47 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8240 (mp0) REVERT: S 65 LYS cc_start: 0.8553 (tttt) cc_final: 0.8097 (tttp) REVERT: S 234 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7823 (pt0) REVERT: S 244 LYS cc_start: 0.8355 (tttm) cc_final: 0.7953 (ttmm) outliers start: 26 outliers final: 15 residues processed: 208 average time/residue: 0.1196 time to fit residues: 32.6874 Evaluate side-chains 167 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 265 GLU Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 217 GLN B 44 GLN B 75 GLN B 220 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.124662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.089711 restraints weight = 14078.585| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.81 r_work: 0.2996 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8942 Z= 0.200 Angle : 0.605 8.000 12155 Z= 0.314 Chirality : 0.043 0.140 1375 Planarity : 0.004 0.054 1532 Dihedral : 6.502 79.896 1234 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.25 % Allowed : 12.32 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: -1.17 (0.25), residues: 1121 helix: 2.26 (0.26), residues: 388 sheet: -2.84 (0.27), residues: 281 loop : -2.09 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 160 TYR 0.020 0.002 TYR R 118 PHE 0.020 0.002 PHE B 234 TRP 0.031 0.002 TRP R 51 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 8940) covalent geometry : angle 0.60523 (12153) SS BOND : bond 0.00074 ( 1) SS BOND : angle 0.13314 ( 2) hydrogen bonds : bond 0.04845 ( 394) hydrogen bonds : angle 4.86922 ( 1158) Misc. bond : bond 0.00169 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: R 45 TYR cc_start: 0.7871 (m-80) cc_final: 0.7548 (m-80) REVERT: R 220 MET cc_start: 0.8925 (tpp) cc_final: 0.8716 (tpp) REVERT: R 302 LEU cc_start: 0.7785 (pt) cc_final: 0.7454 (mm) REVERT: A 17 LYS cc_start: 0.8891 (mttt) cc_final: 0.8422 (mtpt) REVERT: A 24 ARG cc_start: 0.7621 (mtm110) cc_final: 0.7181 (mtm-85) REVERT: A 256 ASN cc_start: 0.8884 (t0) cc_final: 0.8409 (t0) REVERT: A 332 VAL cc_start: 0.9174 (OUTLIER) cc_final: 0.8810 (p) REVERT: B 42 ARG cc_start: 0.7726 (ttp80) cc_final: 0.7031 (ttp80) REVERT: B 44 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7586 (pm20) REVERT: B 161 SER cc_start: 0.9361 (t) cc_final: 0.8688 (p) REVERT: B 301 LYS cc_start: 0.8656 (ptpt) cc_final: 0.8347 (mtpp) REVERT: G 27 ARG cc_start: 0.8601 (mtt90) cc_final: 0.8285 (mtt90) REVERT: G 47 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8258 (mp0) REVERT: S 65 LYS cc_start: 0.8616 (tttt) cc_final: 0.8138 (tttp) REVERT: S 160 ARG cc_start: 0.8088 (ttm-80) cc_final: 0.7443 (mmm-85) REVERT: S 234 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7920 (pt0) REVERT: S 244 LYS cc_start: 0.8388 (tttm) cc_final: 0.7961 (ttmm) outliers start: 39 outliers final: 28 residues processed: 187 average time/residue: 0.1102 time to fit residues: 27.8334 Evaluate side-chains 175 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 265 GLU Chi-restraints excluded: chain R residue 273 MET Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 294 ASN Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 48 optimal weight: 0.6980 chunk 100 optimal weight: 0.0370 chunk 59 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 94 ASN ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 294 ASN B 259 GLN S 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.128587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.094018 restraints weight = 14099.597| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.80 r_work: 0.3071 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8942 Z= 0.109 Angle : 0.540 9.860 12155 Z= 0.278 Chirality : 0.041 0.175 1375 Planarity : 0.004 0.046 1532 Dihedral : 6.073 75.432 1234 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.49 % Allowed : 15.05 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: -0.81 (0.26), residues: 1121 helix: 2.47 (0.27), residues: 388 sheet: -2.51 (0.27), residues: 281 loop : -1.90 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 218 TYR 0.024 0.001 TYR R 118 PHE 0.016 0.001 PHE S 68 TRP 0.040 0.001 TRP R 51 HIS 0.002 0.001 HIS R 54 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8940) covalent geometry : angle 0.53969 (12153) SS BOND : bond 0.00324 ( 1) SS BOND : angle 1.06815 ( 2) hydrogen bonds : bond 0.03939 ( 394) hydrogen bonds : angle 4.59437 ( 1158) Misc. bond : bond 0.00072 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 269 MET cc_start: 0.8958 (tpp) cc_final: 0.8686 (mmm) REVERT: R 302 LEU cc_start: 0.7690 (pt) cc_final: 0.7351 (mm) REVERT: R 331 ASN cc_start: 0.7964 (p0) cc_final: 0.7534 (p0) REVERT: A 17 LYS cc_start: 0.8777 (mttt) cc_final: 0.8335 (mtpt) REVERT: A 24 ARG cc_start: 0.7577 (mtm110) cc_final: 0.7120 (mtm-85) REVERT: A 256 ASN cc_start: 0.8822 (t0) cc_final: 0.8415 (t0) REVERT: A 332 VAL cc_start: 0.9123 (m) cc_final: 0.8777 (p) REVERT: B 17 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7712 (pt0) REVERT: B 42 ARG cc_start: 0.7738 (ttp80) cc_final: 0.7398 (ttp80) REVERT: B 161 SER cc_start: 0.9229 (t) cc_final: 0.8593 (p) REVERT: G 27 ARG cc_start: 0.8578 (mtt90) cc_final: 0.8151 (mtt90) REVERT: G 47 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8222 (mp0) REVERT: S 65 LYS cc_start: 0.8669 (tttt) cc_final: 0.8202 (tttp) REVERT: S 160 ARG cc_start: 0.7995 (ttm-80) cc_final: 0.7306 (mmm-85) REVERT: S 234 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7916 (pt0) REVERT: S 244 LYS cc_start: 0.8402 (tttm) cc_final: 0.7974 (ttmm) outliers start: 32 outliers final: 20 residues processed: 195 average time/residue: 0.1089 time to fit residues: 28.6386 Evaluate side-chains 183 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 294 ASN Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 0.0070 chunk 17 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 106 optimal weight: 0.0980 chunk 89 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.127599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.092818 restraints weight = 14130.541| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.79 r_work: 0.3053 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8942 Z= 0.126 Angle : 0.538 10.091 12155 Z= 0.276 Chirality : 0.041 0.142 1375 Planarity : 0.004 0.045 1532 Dihedral : 5.951 79.975 1234 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.03 % Allowed : 14.94 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: -0.72 (0.26), residues: 1121 helix: 2.44 (0.27), residues: 387 sheet: -2.42 (0.27), residues: 285 loop : -1.74 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 251 TYR 0.023 0.001 TYR R 118 PHE 0.017 0.001 PHE R 208 TRP 0.040 0.001 TRP R 51 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8940) covalent geometry : angle 0.53777 (12153) SS BOND : bond 0.00233 ( 1) SS BOND : angle 0.42430 ( 2) hydrogen bonds : bond 0.03992 ( 394) hydrogen bonds : angle 4.51107 ( 1158) Misc. bond : bond 0.00149 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 54 HIS cc_start: 0.8666 (m90) cc_final: 0.8333 (m90) REVERT: R 220 MET cc_start: 0.8887 (tpp) cc_final: 0.8556 (tpt) REVERT: R 302 LEU cc_start: 0.7680 (pt) cc_final: 0.7348 (mm) REVERT: R 331 ASN cc_start: 0.7920 (p0) cc_final: 0.7477 (p0) REVERT: A 17 LYS cc_start: 0.8789 (mttt) cc_final: 0.8345 (mtpt) REVERT: A 24 ARG cc_start: 0.7601 (mtm110) cc_final: 0.7114 (mtm-85) REVERT: A 256 ASN cc_start: 0.8820 (t0) cc_final: 0.8400 (t0) REVERT: A 332 VAL cc_start: 0.9155 (OUTLIER) cc_final: 0.8788 (p) REVERT: B 42 ARG cc_start: 0.7749 (ttp80) cc_final: 0.7387 (ttp80) REVERT: B 161 SER cc_start: 0.9252 (t) cc_final: 0.8609 (p) REVERT: B 262 MET cc_start: 0.8574 (mpp) cc_final: 0.7933 (mpp) REVERT: G 27 ARG cc_start: 0.8597 (mtt90) cc_final: 0.8176 (mtt90) REVERT: G 47 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8254 (mp0) REVERT: S 65 LYS cc_start: 0.8640 (tttt) cc_final: 0.8180 (tttp) REVERT: S 98 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8771 (ptt-90) REVERT: S 160 ARG cc_start: 0.8018 (ttm-80) cc_final: 0.7368 (mmm-85) REVERT: S 234 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7913 (pt0) REVERT: S 244 LYS cc_start: 0.8441 (tttm) cc_final: 0.8010 (ttmm) outliers start: 37 outliers final: 26 residues processed: 189 average time/residue: 0.1124 time to fit residues: 28.2844 Evaluate side-chains 177 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 265 GLU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 273 MET Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain R residue 335 GLN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 6 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.126611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.091713 restraints weight = 14083.939| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.78 r_work: 0.3027 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8942 Z= 0.144 Angle : 0.552 10.329 12155 Z= 0.282 Chirality : 0.042 0.152 1375 Planarity : 0.004 0.046 1532 Dihedral : 5.933 81.835 1234 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.03 % Allowed : 14.50 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: -0.63 (0.26), residues: 1121 helix: 2.44 (0.27), residues: 388 sheet: -2.34 (0.27), residues: 283 loop : -1.67 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 218 TYR 0.023 0.001 TYR R 118 PHE 0.018 0.001 PHE S 68 TRP 0.032 0.001 TRP R 51 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8940) covalent geometry : angle 0.55195 (12153) SS BOND : bond 0.00117 ( 1) SS BOND : angle 0.56002 ( 2) hydrogen bonds : bond 0.04074 ( 394) hydrogen bonds : angle 4.45966 ( 1158) Misc. bond : bond 0.00107 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 54 HIS cc_start: 0.8652 (m90) cc_final: 0.8313 (m90) REVERT: R 302 LEU cc_start: 0.7743 (pt) cc_final: 0.7417 (mm) REVERT: R 331 ASN cc_start: 0.7951 (p0) cc_final: 0.7554 (p0) REVERT: A 17 LYS cc_start: 0.8801 (mttt) cc_final: 0.8358 (mtpt) REVERT: A 24 ARG cc_start: 0.7619 (mtm110) cc_final: 0.7129 (mtm-85) REVERT: A 256 ASN cc_start: 0.8858 (t0) cc_final: 0.8432 (t0) REVERT: B 42 ARG cc_start: 0.7752 (ttp80) cc_final: 0.7123 (ttp80) REVERT: B 44 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7595 (pm20) REVERT: B 161 SER cc_start: 0.9275 (t) cc_final: 0.8627 (p) REVERT: B 262 MET cc_start: 0.8599 (mpp) cc_final: 0.8006 (mpp) REVERT: G 27 ARG cc_start: 0.8609 (mtt90) cc_final: 0.8324 (mtt90) REVERT: G 47 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8235 (mp0) REVERT: S 65 LYS cc_start: 0.8715 (tttt) cc_final: 0.8243 (tttp) REVERT: S 87 ARG cc_start: 0.8405 (mtm110) cc_final: 0.7927 (ptp-110) REVERT: S 98 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.8805 (ptt-90) REVERT: S 160 ARG cc_start: 0.7981 (ttm-80) cc_final: 0.7308 (mmm-85) REVERT: S 234 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7920 (pt0) REVERT: S 244 LYS cc_start: 0.8414 (tttm) cc_final: 0.7978 (ttmm) outliers start: 37 outliers final: 29 residues processed: 180 average time/residue: 0.1109 time to fit residues: 26.5929 Evaluate side-chains 178 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 265 GLU Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 273 MET Chi-restraints excluded: chain R residue 278 CYS Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 294 ASN Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain R residue 335 GLN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 71 optimal weight: 0.0770 chunk 105 optimal weight: 2.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 331 ASN A 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.128217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.093262 restraints weight = 14162.368| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.81 r_work: 0.3057 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8942 Z= 0.110 Angle : 0.536 11.856 12155 Z= 0.271 Chirality : 0.041 0.153 1375 Planarity : 0.004 0.045 1532 Dihedral : 5.827 83.666 1234 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.16 % Allowed : 15.81 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: -0.47 (0.26), residues: 1121 helix: 2.53 (0.27), residues: 387 sheet: -2.17 (0.28), residues: 283 loop : -1.57 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 50 TYR 0.024 0.001 TYR R 118 PHE 0.016 0.001 PHE S 68 TRP 0.023 0.001 TRP R 51 HIS 0.002 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8940) covalent geometry : angle 0.53624 (12153) SS BOND : bond 0.00150 ( 1) SS BOND : angle 0.45681 ( 2) hydrogen bonds : bond 0.03796 ( 394) hydrogen bonds : angle 4.33871 ( 1158) Misc. bond : bond 0.00136 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 54 HIS cc_start: 0.8635 (m90) cc_final: 0.8352 (m-70) REVERT: R 302 LEU cc_start: 0.7804 (pt) cc_final: 0.7460 (mm) REVERT: R 331 ASN cc_start: 0.7860 (OUTLIER) cc_final: 0.7588 (p0) REVERT: A 17 LYS cc_start: 0.8702 (mttt) cc_final: 0.8273 (mtpt) REVERT: A 24 ARG cc_start: 0.7474 (mtm110) cc_final: 0.7019 (mtm-85) REVERT: A 256 ASN cc_start: 0.8876 (t0) cc_final: 0.8464 (t0) REVERT: B 12 GLU cc_start: 0.8909 (tp30) cc_final: 0.8708 (tp30) REVERT: B 42 ARG cc_start: 0.7776 (ttp80) cc_final: 0.7067 (ttp80) REVERT: B 44 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7528 (pm20) REVERT: B 161 SER cc_start: 0.9242 (t) cc_final: 0.8607 (p) REVERT: B 262 MET cc_start: 0.8579 (mpp) cc_final: 0.8090 (mpp) REVERT: G 27 ARG cc_start: 0.8597 (mtt90) cc_final: 0.8291 (mtt90) REVERT: G 47 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8223 (mp0) REVERT: S 65 LYS cc_start: 0.8739 (tttt) cc_final: 0.8243 (tttp) REVERT: S 87 ARG cc_start: 0.8300 (mtm110) cc_final: 0.7821 (ptp-110) REVERT: S 160 ARG cc_start: 0.7931 (ttm-80) cc_final: 0.7235 (mmm-85) REVERT: S 234 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7854 (pt0) REVERT: S 235 TYR cc_start: 0.8862 (m-80) cc_final: 0.8595 (m-10) REVERT: S 244 LYS cc_start: 0.8328 (tttm) cc_final: 0.7879 (ttmm) outliers start: 29 outliers final: 22 residues processed: 178 average time/residue: 0.1016 time to fit residues: 24.5431 Evaluate side-chains 179 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 265 GLU Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 294 ASN Chi-restraints excluded: chain R residue 331 ASN Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain R residue 335 GLN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 64 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 113 ASN ** R 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS B 183 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.127974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.093319 restraints weight = 13989.522| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.77 r_work: 0.3051 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8942 Z= 0.120 Angle : 0.541 13.390 12155 Z= 0.272 Chirality : 0.041 0.148 1375 Planarity : 0.004 0.046 1532 Dihedral : 5.820 85.739 1234 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.05 % Allowed : 16.03 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: -0.39 (0.26), residues: 1121 helix: 2.55 (0.27), residues: 389 sheet: -2.08 (0.28), residues: 278 loop : -1.54 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 50 TYR 0.024 0.001 TYR R 118 PHE 0.023 0.001 PHE S 68 TRP 0.024 0.001 TRP R 51 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8940) covalent geometry : angle 0.54123 (12153) SS BOND : bond 0.00147 ( 1) SS BOND : angle 0.43281 ( 2) hydrogen bonds : bond 0.03743 ( 394) hydrogen bonds : angle 4.32808 ( 1158) Misc. bond : bond 0.00102 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 54 HIS cc_start: 0.8702 (m90) cc_final: 0.8356 (m-70) REVERT: R 220 MET cc_start: 0.8856 (tpp) cc_final: 0.8518 (tpt) REVERT: R 302 LEU cc_start: 0.7717 (pt) cc_final: 0.7391 (mm) REVERT: A 17 LYS cc_start: 0.8737 (mttt) cc_final: 0.8341 (mtpt) REVERT: A 24 ARG cc_start: 0.7558 (mtm110) cc_final: 0.7105 (mtm-85) REVERT: A 256 ASN cc_start: 0.8850 (t0) cc_final: 0.8465 (t0) REVERT: B 12 GLU cc_start: 0.8894 (tp30) cc_final: 0.8683 (tp30) REVERT: B 42 ARG cc_start: 0.7789 (ttp80) cc_final: 0.7397 (ttp80) REVERT: B 44 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7733 (pm20) REVERT: B 161 SER cc_start: 0.9215 (t) cc_final: 0.8599 (p) REVERT: B 215 GLU cc_start: 0.8749 (mp0) cc_final: 0.8480 (mp0) REVERT: B 262 MET cc_start: 0.8583 (mpp) cc_final: 0.8089 (mpp) REVERT: G 27 ARG cc_start: 0.8615 (mtt90) cc_final: 0.8332 (mtt90) REVERT: G 47 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8178 (mp0) REVERT: S 65 LYS cc_start: 0.8778 (tttt) cc_final: 0.8301 (tttp) REVERT: S 87 ARG cc_start: 0.8316 (mtm110) cc_final: 0.7918 (ptp-110) REVERT: S 160 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7310 (mmm-85) REVERT: S 234 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7925 (pt0) REVERT: S 235 TYR cc_start: 0.8825 (m-80) cc_final: 0.8617 (m-10) REVERT: S 244 LYS cc_start: 0.8416 (tttm) cc_final: 0.7967 (ttmm) outliers start: 28 outliers final: 22 residues processed: 176 average time/residue: 0.0992 time to fit residues: 23.6390 Evaluate side-chains 176 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 265 GLU Chi-restraints excluded: chain R residue 273 MET Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 335 GLN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 83 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 294 ASN R 331 ASN A 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.127165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.092367 restraints weight = 14142.150| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.80 r_work: 0.3038 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8942 Z= 0.132 Angle : 0.554 13.136 12155 Z= 0.278 Chirality : 0.041 0.147 1375 Planarity : 0.004 0.045 1532 Dihedral : 5.851 86.772 1234 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.05 % Allowed : 16.36 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: -0.33 (0.26), residues: 1121 helix: 2.60 (0.27), residues: 389 sheet: -2.08 (0.28), residues: 283 loop : -1.49 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 50 TYR 0.023 0.001 TYR R 118 PHE 0.018 0.001 PHE S 68 TRP 0.046 0.001 TRP R 51 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8940) covalent geometry : angle 0.55392 (12153) SS BOND : bond 0.00142 ( 1) SS BOND : angle 0.53027 ( 2) hydrogen bonds : bond 0.03830 ( 394) hydrogen bonds : angle 4.34945 ( 1158) Misc. bond : bond 0.00098 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: R 54 HIS cc_start: 0.8722 (m90) cc_final: 0.8355 (m-70) REVERT: R 200 LYS cc_start: 0.8402 (mttt) cc_final: 0.7978 (mmtt) REVERT: R 220 MET cc_start: 0.8757 (tpp) cc_final: 0.8520 (tpt) REVERT: R 302 LEU cc_start: 0.7732 (pt) cc_final: 0.7390 (mm) REVERT: R 331 ASN cc_start: 0.7844 (p0) cc_final: 0.7583 (p0) REVERT: A 17 LYS cc_start: 0.8740 (mttt) cc_final: 0.8342 (mtpt) REVERT: A 24 ARG cc_start: 0.7588 (mtm110) cc_final: 0.7126 (mtm-85) REVERT: A 256 ASN cc_start: 0.8853 (t0) cc_final: 0.8482 (t0) REVERT: B 12 GLU cc_start: 0.8895 (tp30) cc_final: 0.8686 (tp30) REVERT: B 42 ARG cc_start: 0.7808 (ttp80) cc_final: 0.7169 (ttp80) REVERT: B 44 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7554 (pm20) REVERT: B 161 SER cc_start: 0.9235 (t) cc_final: 0.8596 (p) REVERT: B 215 GLU cc_start: 0.8738 (mp0) cc_final: 0.8449 (mp0) REVERT: G 27 ARG cc_start: 0.8632 (mtt90) cc_final: 0.8352 (mtt90) REVERT: G 47 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8168 (mp0) REVERT: S 65 LYS cc_start: 0.8779 (tttt) cc_final: 0.8304 (tttp) REVERT: S 87 ARG cc_start: 0.8332 (mtm110) cc_final: 0.7930 (ptp-110) REVERT: S 160 ARG cc_start: 0.7993 (ttm-80) cc_final: 0.7312 (mmm-85) REVERT: S 234 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7896 (pt0) REVERT: S 235 TYR cc_start: 0.8830 (m-80) cc_final: 0.8630 (m-10) REVERT: S 244 LYS cc_start: 0.8413 (tttm) cc_final: 0.7961 (ttmm) outliers start: 28 outliers final: 26 residues processed: 176 average time/residue: 0.1036 time to fit residues: 24.8175 Evaluate side-chains 177 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 265 GLU Chi-restraints excluded: chain R residue 273 MET Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 294 ASN Chi-restraints excluded: chain R residue 335 GLN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 100 optimal weight: 0.1980 chunk 78 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.127132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.092233 restraints weight = 14064.436| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.80 r_work: 0.3034 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 8942 Z= 0.165 Angle : 0.876 59.199 12155 Z= 0.506 Chirality : 0.043 0.264 1375 Planarity : 0.004 0.047 1532 Dihedral : 5.862 86.781 1234 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.16 % Allowed : 16.14 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: -0.31 (0.26), residues: 1121 helix: 2.63 (0.27), residues: 389 sheet: -2.07 (0.28), residues: 283 loop : -1.48 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 50 TYR 0.022 0.001 TYR R 118 PHE 0.018 0.001 PHE S 68 TRP 0.041 0.001 TRP R 51 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8940) covalent geometry : angle 0.87594 (12153) SS BOND : bond 0.00112 ( 1) SS BOND : angle 0.51291 ( 2) hydrogen bonds : bond 0.03821 ( 394) hydrogen bonds : angle 4.38057 ( 1158) Misc. bond : bond 0.00072 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: R 54 HIS cc_start: 0.8701 (m90) cc_final: 0.8355 (m-70) REVERT: R 200 LYS cc_start: 0.8429 (mttt) cc_final: 0.7979 (mmtt) REVERT: R 220 MET cc_start: 0.8759 (tpp) cc_final: 0.8526 (tpt) REVERT: R 294 ASN cc_start: 0.7827 (OUTLIER) cc_final: 0.7585 (p0) REVERT: R 302 LEU cc_start: 0.7735 (pt) cc_final: 0.7385 (mm) REVERT: R 331 ASN cc_start: 0.7850 (p0) cc_final: 0.7578 (p0) REVERT: A 17 LYS cc_start: 0.8744 (mttt) cc_final: 0.8346 (mtpt) REVERT: A 24 ARG cc_start: 0.7579 (mtm110) cc_final: 0.7116 (mtm-85) REVERT: A 256 ASN cc_start: 0.8851 (t0) cc_final: 0.8505 (t0) REVERT: B 12 GLU cc_start: 0.8899 (tp30) cc_final: 0.8690 (tp30) REVERT: B 42 ARG cc_start: 0.7811 (ttp80) cc_final: 0.7169 (ttp80) REVERT: B 44 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7557 (pm20) REVERT: B 161 SER cc_start: 0.9230 (t) cc_final: 0.8593 (p) REVERT: B 215 GLU cc_start: 0.8731 (mp0) cc_final: 0.8436 (mp0) REVERT: G 27 ARG cc_start: 0.8629 (mtt90) cc_final: 0.8348 (mtt90) REVERT: G 47 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8146 (mp0) REVERT: S 65 LYS cc_start: 0.8784 (tttt) cc_final: 0.8307 (tttp) REVERT: S 87 ARG cc_start: 0.8325 (mtm110) cc_final: 0.7921 (ptp-110) REVERT: S 98 ARG cc_start: 0.9218 (OUTLIER) cc_final: 0.8632 (ptt-90) REVERT: S 160 ARG cc_start: 0.7992 (ttm-80) cc_final: 0.7309 (mmm-85) REVERT: S 234 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7887 (pt0) REVERT: S 244 LYS cc_start: 0.8409 (tttm) cc_final: 0.7957 (ttmm) outliers start: 29 outliers final: 26 residues processed: 172 average time/residue: 0.1079 time to fit residues: 25.0006 Evaluate side-chains 179 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 179 TRP Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 265 GLU Chi-restraints excluded: chain R residue 273 MET Chi-restraints excluded: chain R residue 279 VAL Chi-restraints excluded: chain R residue 294 ASN Chi-restraints excluded: chain R residue 335 GLN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 65 optimal weight: 3.9990 chunk 19 optimal weight: 0.0770 chunk 93 optimal weight: 0.1980 chunk 44 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 294 ASN ** 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 = 0.3658 r_free = 0.3658 target = 0.127137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.092293 restraints weight = 14034.799| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.79 r_work: 0.3033 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 8942 Z= 0.166 Angle : 0.864 55.228 12155 Z= 0.508 Chirality : 0.043 0.264 1375 Planarity : 0.004 0.047 1532 Dihedral : 5.862 86.781 1234 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.94 % Allowed : 16.47 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 aren not related in a simple way. whole: -0.31 (0.26), residues: 1121 helix: 2.63 (0.27), residues: 389 sheet: -2.07 (0.28), residues: 283 loop : -1.48 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 50 TYR 0.022 0.001 TYR R 118 PHE 0.018 0.001 PHE S 68 TRP 0.041 0.001 TRP R 51 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8940) covalent geometry : angle 0.86364 (12153) SS BOND : bond 0.00112 ( 1) SS BOND : angle 0.51291 ( 2) hydrogen bonds : bond 0.03821 ( 394) hydrogen bonds : angle 4.38057 ( 1158) Misc. bond : bond 0.00072 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2435.33 seconds wall clock time: 42 minutes 35.90 seconds (2555.90 seconds total)