Starting phenix.real_space_refine on Sun May 11 18:38:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zfa_60054/05_2025/8zfa_60054_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zfa_60054/05_2025/8zfa_60054.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zfa_60054/05_2025/8zfa_60054.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zfa_60054/05_2025/8zfa_60054.map" model { file = "/net/cci-nas-00/data/ceres_data/8zfa_60054/05_2025/8zfa_60054_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zfa_60054/05_2025/8zfa_60054_neut.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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 53 5.16 5 C 5272 2.51 5 N 1453 2.21 5 O 1535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8313 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1861 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 8, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 2483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2483 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 6, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 85 Chain: "G" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 355 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 1922 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 258} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 229 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 142 Chain: "S" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1692 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Time building chain proxies: 5.22, per 1000 atoms: 0.63 Number of scatterers: 8313 At special positions: 0 Unit cell: (86.92, 124.02, 125.08, 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 53 16.00 O 1535 8.00 N 1453 7.00 C 5272 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 966.6 milliseconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 37.8% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 6 through 39 removed outlier: 3.810A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 243 through 249 removed outlier: 3.844A pdb=" N ASN A 249 " --> pdb=" O GLN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.677A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 18 through 47 Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 50 through 79 removed outlier: 4.143A pdb=" N VAL R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TYR R 55 " --> pdb=" O GLU R 51 " (cutoff:3.500A) Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 90 through 121 removed outlier: 3.989A pdb=" N ALA R 105 " --> pdb=" O LEU R 101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS R 121 " --> pdb=" O LEU R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 150 removed outlier: 4.035A pdb=" N SER R 133 " --> pdb=" O ARG R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 191 removed outlier: 4.224A pdb=" N VAL R 184 " --> pdb=" O ALA R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 209 Processing helix chain 'R' and resid 210 through 212 No H-bonds generated for 'chain 'R' and resid 210 through 212' Processing helix chain 'R' and resid 216 through 228 removed outlier: 3.866A pdb=" N ARG R 222 " --> pdb=" O ARG R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 239 Processing helix chain 'R' and resid 239 through 253 Processing helix chain 'R' and resid 264 through 283 Proline residue: R 273 - end of helix removed outlier: 3.795A pdb=" N ALA R 277 " --> pdb=" O PRO R 273 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU R 279 " --> pdb=" O TYR R 275 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA R 280 " --> pdb=" O HIS R 276 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU R 281 " --> pdb=" O ALA R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 294 Proline residue: R 290 - end of helix Processing helix chain 'R' and resid 297 through 307 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.848A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.647A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.908A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 224 removed outlier: 4.900A pdb=" N VAL A 234 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N GLY A 47 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N ALA A 253 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG A 42 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE A 255 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 44 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL A 257 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU A 46 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ASP A 259 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE A 254 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N PHE A 290 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE A 256 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN A 292 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL A 258 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.503A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.785A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.482A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.580A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.545A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.339A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.891A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.748A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.090A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195 removed outlier: 5.677A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.53 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1348 1.30 - 1.43: 2298 1.43 - 1.55: 4771 1.55 - 1.68: 3 1.68 - 1.81: 72 Bond restraints: 8492 Sorted by residual: bond pdb=" C ARG A 385 " pdb=" O ARG A 385 " ideal model delta sigma weight residual 1.236 1.169 0.068 1.26e-02 6.30e+03 2.89e+01 bond pdb=" C SER R 171 " pdb=" O SER R 171 " ideal model delta sigma weight residual 1.233 1.184 0.049 1.35e-02 5.49e+03 1.30e+01 bond pdb=" C GLY R 88 " pdb=" O GLY R 88 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.35e-02 5.49e+03 1.09e+01 bond pdb=" CA VAL R 82 " pdb=" C VAL R 82 " ideal model delta sigma weight residual 1.522 1.485 0.037 1.21e-02 6.83e+03 9.36e+00 bond pdb=" C THR R 166 " pdb=" O THR R 166 " ideal model delta sigma weight residual 1.233 1.194 0.039 1.36e-02 5.41e+03 8.23e+00 ... (remaining 8487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 11475 2.98 - 5.96: 79 5.96 - 8.94: 12 8.94 - 11.93: 2 11.93 - 14.91: 4 Bond angle restraints: 11572 Sorted by residual: angle pdb=" N GLU R 170 " pdb=" CA GLU R 170 " pdb=" C GLU R 170 " ideal model delta sigma weight residual 110.48 123.76 -13.28 1.48e+00 4.57e-01 8.05e+01 angle pdb=" N PRO R 87 " pdb=" CA PRO R 87 " pdb=" C PRO R 87 " ideal model delta sigma weight residual 112.47 99.30 13.17 2.06e+00 2.36e-01 4.09e+01 angle pdb=" CA CYS R 168 " pdb=" CB CYS R 168 " pdb=" SG CYS R 168 " ideal model delta sigma weight residual 114.40 99.77 14.63 2.30e+00 1.89e-01 4.04e+01 angle pdb=" N SER R 171 " pdb=" CA SER R 171 " pdb=" C SER R 171 " ideal model delta sigma weight residual 107.71 119.35 -11.64 1.90e+00 2.77e-01 3.75e+01 angle pdb=" N CYS R 168 " pdb=" CA CYS R 168 " pdb=" C CYS R 168 " ideal model delta sigma weight residual 108.67 117.66 -8.99 1.55e+00 4.16e-01 3.36e+01 ... (remaining 11567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 4508 16.07 - 32.15: 379 32.15 - 48.22: 68 48.22 - 64.30: 9 64.30 - 80.37: 7 Dihedral angle restraints: 4971 sinusoidal: 1698 harmonic: 3273 Sorted by residual: dihedral pdb=" N CYS R 168 " pdb=" C CYS R 168 " pdb=" CA CYS R 168 " pdb=" CB CYS R 168 " ideal model delta harmonic sigma weight residual 122.80 145.89 -23.09 0 2.50e+00 1.60e-01 8.53e+01 dihedral pdb=" CB CYS R 90 " pdb=" SG CYS R 90 " pdb=" SG CYS R 168 " pdb=" CB CYS R 168 " ideal model delta sinusoidal sigma weight residual -86.00 -5.63 -80.37 1 1.00e+01 1.00e-02 7.99e+01 dihedral pdb=" C CYS R 168 " pdb=" N CYS R 168 " pdb=" CA CYS R 168 " pdb=" CB CYS R 168 " ideal model delta harmonic sigma weight residual -122.60 -144.92 22.32 0 2.50e+00 1.60e-01 7.97e+01 ... (remaining 4968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 1325 0.197 - 0.395: 4 0.395 - 0.592: 2 0.592 - 0.790: 0 0.790 - 0.987: 1 Chirality restraints: 1332 Sorted by residual: chirality pdb=" CA CYS R 168 " pdb=" N CYS R 168 " pdb=" C CYS R 168 " pdb=" CB CYS R 168 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.44e+01 chirality pdb=" CA GLU R 170 " pdb=" N GLU R 170 " pdb=" C GLU R 170 " pdb=" CB GLU R 170 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.42e+00 chirality pdb=" CA ASP R 81 " pdb=" N ASP R 81 " pdb=" C ASP R 81 " pdb=" CB ASP R 81 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.17e+00 ... (remaining 1329 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 169 " -0.030 2.00e-02 2.50e+03 2.06e-02 8.45e+00 pdb=" CG TYR R 169 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR R 169 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR R 169 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR R 169 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR R 169 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR R 169 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR R 169 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 169 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.44e+00 pdb=" C TYR R 169 " -0.047 2.00e-02 2.50e+03 pdb=" O TYR R 169 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU R 170 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA S 40 " -0.044 5.00e-02 4.00e+02 6.72e-02 7.22e+00 pdb=" N PRO S 41 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO S 41 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO S 41 " -0.037 5.00e-02 4.00e+02 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 37 2.46 - 3.07: 5398 3.07 - 3.68: 12759 3.68 - 4.29: 18529 4.29 - 4.90: 31522 Nonbonded interactions: 68245 Sorted by model distance: nonbonded pdb=" O PRO R 20 " pdb=" CD2 TYR R 24 " model vdw 1.845 3.340 nonbonded pdb=" O ASP R 81 " pdb=" OD1 ASP R 81 " model vdw 1.994 3.040 nonbonded pdb=" O ASP R 75 " pdb=" CG ARG R 79 " model vdw 2.083 3.440 nonbonded pdb=" O LEU A 5 " pdb=" NZ LYS A 10 " model vdw 2.182 3.120 nonbonded pdb=" NH2 ARG S 98 " pdb=" OD2 ASP S 109 " model vdw 2.196 3.120 ... (remaining 68240 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.480 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 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 : 0.004 0.068 8494 Z= 0.208 Angle : 0.743 14.907 11576 Z= 0.415 Chirality : 0.058 0.987 1332 Planarity : 0.006 0.067 1488 Dihedral : 12.498 75.287 2859 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.50 % Allowed : 0.12 % Favored : 99.38 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1114 helix: 1.44 (0.27), residues: 391 sheet: -0.24 (0.31), residues: 268 loop : -0.67 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 244 HIS 0.008 0.001 HIS A 230 PHE 0.015 0.002 PHE B 234 TYR 0.048 0.001 TYR R 169 ARG 0.008 0.000 ARG R 79 Details of bonding type rmsd hydrogen bonds : bond 0.17164 ( 434) hydrogen bonds : angle 6.76189 ( 1245) SS BOND : bond 0.00306 ( 2) SS BOND : angle 6.85176 ( 4) covalent geometry : bond 0.00381 ( 8492) covalent geometry : angle 0.73178 (11572) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 205 time to evaluate : 0.922 Fit side-chains REVERT: A 33 ASP cc_start: 0.6780 (m-30) cc_final: 0.6464 (m-30) REVERT: A 219 GLU cc_start: 0.6790 (tm-30) cc_final: 0.6528 (tm-30) REVERT: A 289 LEU cc_start: 0.8387 (pt) cc_final: 0.8168 (pt) REVERT: B 132 ASN cc_start: 0.7715 (p0) cc_final: 0.7413 (p0) REVERT: B 258 ASP cc_start: 0.6228 (t0) cc_final: 0.5963 (t0) REVERT: R 64 LEU cc_start: 0.6715 (mm) cc_final: 0.6512 (mm) REVERT: R 116 TYR cc_start: 0.7890 (t80) cc_final: 0.7492 (t80) REVERT: R 124 ARG cc_start: 0.7440 (mtm-85) cc_final: 0.7085 (mtt-85) REVERT: R 193 LEU cc_start: 0.7169 (tp) cc_final: 0.6931 (tm) REVERT: R 287 LEU cc_start: 0.7703 (tt) cc_final: 0.7464 (tp) outliers start: 4 outliers final: 3 residues processed: 209 average time/residue: 1.1475 time to fit residues: 255.0274 Evaluate side-chains 173 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 170 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain R residue 81 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.0020 chunk 83 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN B 88 ASN B 220 GLN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.140550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.121567 restraints weight = 12075.205| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.91 r_work: 0.3469 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8494 Z= 0.180 Angle : 0.618 6.922 11576 Z= 0.327 Chirality : 0.044 0.139 1332 Planarity : 0.006 0.056 1488 Dihedral : 5.519 73.906 1228 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.47 % Allowed : 9.44 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.26), residues: 1114 helix: 1.89 (0.27), residues: 388 sheet: -0.39 (0.31), residues: 267 loop : -0.47 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 211 HIS 0.007 0.001 HIS A 357 PHE 0.022 0.002 PHE B 235 TYR 0.014 0.002 TYR B 59 ARG 0.007 0.001 ARG R 220 Details of bonding type rmsd hydrogen bonds : bond 0.04527 ( 434) hydrogen bonds : angle 5.07079 ( 1245) SS BOND : bond 0.00863 ( 2) SS BOND : angle 0.97632 ( 4) covalent geometry : bond 0.00411 ( 8492) covalent geometry : angle 0.61748 (11572) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 0.815 Fit side-chains REVERT: A 33 ASP cc_start: 0.7488 (m-30) cc_final: 0.7145 (m-30) REVERT: A 219 GLU cc_start: 0.7351 (tm-30) cc_final: 0.7072 (tm-30) REVERT: A 220 THR cc_start: 0.8535 (m) cc_final: 0.7829 (t) REVERT: A 221 LYS cc_start: 0.7566 (mtmm) cc_final: 0.7237 (mtmm) REVERT: A 289 LEU cc_start: 0.8504 (pt) cc_final: 0.8158 (pt) REVERT: A 381 ASP cc_start: 0.7767 (t70) cc_final: 0.7491 (t0) REVERT: B 59 TYR cc_start: 0.7597 (OUTLIER) cc_final: 0.7320 (t80) REVERT: B 132 ASN cc_start: 0.8074 (p0) cc_final: 0.7764 (p0) REVERT: B 258 ASP cc_start: 0.7175 (t0) cc_final: 0.6636 (t0) REVERT: B 325 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7396 (tpp) REVERT: B 340 ASN cc_start: 0.7148 (t0) cc_final: 0.6926 (t0) REVERT: R 116 TYR cc_start: 0.8629 (t80) cc_final: 0.8176 (t80) REVERT: R 124 ARG cc_start: 0.8063 (mtm-85) cc_final: 0.7781 (mtt-85) REVERT: S 98 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7974 (ttp-170) REVERT: S 192 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.6960 (ttp) outliers start: 36 outliers final: 13 residues processed: 184 average time/residue: 1.0940 time to fit residues: 214.5281 Evaluate side-chains 184 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 199 MET Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 98 ARG Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 72 optimal weight: 0.0770 chunk 101 optimal weight: 0.0070 chunk 32 optimal weight: 0.1980 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 69 optimal weight: 0.0980 chunk 45 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 overall best weight: 0.2156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN B 313 ASN S 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.142808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.123718 restraints weight = 12228.341| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.94 r_work: 0.3498 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8494 Z= 0.119 Angle : 0.554 7.375 11576 Z= 0.290 Chirality : 0.042 0.136 1332 Planarity : 0.005 0.054 1488 Dihedral : 4.421 43.953 1224 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.48 % Allowed : 13.04 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.26), residues: 1114 helix: 2.24 (0.27), residues: 388 sheet: -0.13 (0.31), residues: 262 loop : -0.60 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 PHE 0.019 0.002 PHE R 125 TYR 0.012 0.001 TYR R 76 ARG 0.007 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03843 ( 434) hydrogen bonds : angle 4.64845 ( 1245) SS BOND : bond 0.00402 ( 2) SS BOND : angle 0.78804 ( 4) covalent geometry : bond 0.00262 ( 8492) covalent geometry : angle 0.55378 (11572) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.814 Fit side-chains REVERT: A 33 ASP cc_start: 0.7470 (m-30) cc_final: 0.7019 (m-30) REVERT: A 36 VAL cc_start: 0.7663 (t) cc_final: 0.7338 (p) REVERT: A 219 GLU cc_start: 0.7388 (tm-30) cc_final: 0.7165 (tm-30) REVERT: A 221 LYS cc_start: 0.7555 (mtmm) cc_final: 0.7305 (mtmm) REVERT: A 289 LEU cc_start: 0.8536 (pt) cc_final: 0.8121 (pt) REVERT: A 338 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7389 (ptmt) REVERT: A 381 ASP cc_start: 0.7770 (t70) cc_final: 0.7501 (t0) REVERT: B 59 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.7382 (t80) REVERT: B 61 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8043 (pp-130) REVERT: B 132 ASN cc_start: 0.7955 (p0) cc_final: 0.7643 (p0) REVERT: B 237 ASN cc_start: 0.7744 (t0) cc_final: 0.7440 (t0) REVERT: B 258 ASP cc_start: 0.7131 (t0) cc_final: 0.6435 (t0) REVERT: B 325 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7331 (tpp) REVERT: B 340 ASN cc_start: 0.7122 (t0) cc_final: 0.6877 (t0) REVERT: R 116 TYR cc_start: 0.8658 (t80) cc_final: 0.7641 (t80) REVERT: R 124 ARG cc_start: 0.8077 (mtm-85) cc_final: 0.7778 (mtt-85) outliers start: 28 outliers final: 12 residues processed: 176 average time/residue: 1.1520 time to fit residues: 215.7623 Evaluate side-chains 185 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 199 MET Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 36 optimal weight: 0.1980 chunk 96 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 64 optimal weight: 0.3980 chunk 32 optimal weight: 0.3980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS B 75 GLN B 125 ASN B 220 GLN B 230 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.139707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.120808 restraints weight = 12146.682| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.91 r_work: 0.3453 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8494 Z= 0.176 Angle : 0.601 7.686 11576 Z= 0.314 Chirality : 0.043 0.163 1332 Planarity : 0.005 0.052 1488 Dihedral : 4.337 19.862 1222 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.22 % Allowed : 14.78 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1114 helix: 2.15 (0.26), residues: 384 sheet: -0.24 (0.31), residues: 258 loop : -0.67 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 211 HIS 0.006 0.001 HIS A 357 PHE 0.023 0.002 PHE R 107 TYR 0.016 0.001 TYR R 76 ARG 0.009 0.001 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.04321 ( 434) hydrogen bonds : angle 4.73949 ( 1245) SS BOND : bond 0.00277 ( 2) SS BOND : angle 0.70681 ( 4) covalent geometry : bond 0.00405 ( 8492) covalent geometry : angle 0.60067 (11572) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.876 Fit side-chains REVERT: A 33 ASP cc_start: 0.7457 (m-30) cc_final: 0.7135 (m-30) REVERT: A 36 VAL cc_start: 0.7840 (t) cc_final: 0.7525 (p) REVERT: A 221 LYS cc_start: 0.7665 (mtmm) cc_final: 0.7443 (mtmm) REVERT: A 289 LEU cc_start: 0.8580 (pt) cc_final: 0.8104 (pt) REVERT: A 338 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7415 (ptmt) REVERT: A 381 ASP cc_start: 0.7775 (t70) cc_final: 0.7503 (t0) REVERT: B 61 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8161 (pp-130) REVERT: B 132 ASN cc_start: 0.7966 (p0) cc_final: 0.7745 (p0) REVERT: B 143 THR cc_start: 0.8108 (m) cc_final: 0.7758 (p) REVERT: B 258 ASP cc_start: 0.7188 (t0) cc_final: 0.6436 (t0) REVERT: B 325 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7515 (tpp) REVERT: B 340 ASN cc_start: 0.7184 (t0) cc_final: 0.6901 (t0) REVERT: R 64 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.7081 (mm) REVERT: R 116 TYR cc_start: 0.8658 (t80) cc_final: 0.8244 (t80) REVERT: R 124 ARG cc_start: 0.8115 (mtm-85) cc_final: 0.7827 (mtt-85) outliers start: 34 outliers final: 14 residues processed: 178 average time/residue: 1.1477 time to fit residues: 217.4501 Evaluate side-chains 185 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 31 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 46 optimal weight: 0.0670 chunk 39 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 237 ASN S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.139349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.120700 restraints weight = 12027.615| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.90 r_work: 0.3449 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8494 Z= 0.192 Angle : 0.616 9.284 11576 Z= 0.319 Chirality : 0.044 0.140 1332 Planarity : 0.005 0.051 1488 Dihedral : 4.417 19.977 1222 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.72 % Allowed : 15.65 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.25), residues: 1114 helix: 2.05 (0.26), residues: 384 sheet: -0.34 (0.31), residues: 268 loop : -0.73 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 211 HIS 0.006 0.001 HIS A 357 PHE 0.023 0.002 PHE R 125 TYR 0.017 0.002 TYR R 76 ARG 0.009 0.001 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.04377 ( 434) hydrogen bonds : angle 4.73254 ( 1245) SS BOND : bond 0.00304 ( 2) SS BOND : angle 0.72905 ( 4) covalent geometry : bond 0.00440 ( 8492) covalent geometry : angle 0.61622 (11572) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 1.070 Fit side-chains REVERT: A 221 LYS cc_start: 0.7664 (mtmm) cc_final: 0.7443 (mtmm) REVERT: A 266 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7573 (mp) REVERT: A 289 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8000 (pt) REVERT: A 291 LEU cc_start: 0.7743 (mt) cc_final: 0.7429 (mt) REVERT: A 338 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7411 (ptmt) REVERT: A 381 ASP cc_start: 0.7692 (t70) cc_final: 0.7404 (t0) REVERT: B 61 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8162 (pp-130) REVERT: B 134 ARG cc_start: 0.7966 (ptt-90) cc_final: 0.7709 (ptt-90) REVERT: B 143 THR cc_start: 0.8159 (m) cc_final: 0.7809 (p) REVERT: B 258 ASP cc_start: 0.7206 (t0) cc_final: 0.6422 (t0) REVERT: B 325 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7555 (tpp) REVERT: B 340 ASN cc_start: 0.7128 (t0) cc_final: 0.6843 (t0) REVERT: R 64 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6851 (mm) REVERT: R 116 TYR cc_start: 0.8660 (t80) cc_final: 0.8199 (t80) REVERT: R 124 ARG cc_start: 0.8111 (mtm-85) cc_final: 0.7803 (mtt-85) outliers start: 38 outliers final: 20 residues processed: 190 average time/residue: 1.0863 time to fit residues: 220.2111 Evaluate side-chains 191 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 186 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 65 optimal weight: 0.7980 chunk 107 optimal weight: 0.2980 chunk 95 optimal weight: 0.8980 chunk 37 optimal weight: 0.0770 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 97 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS B 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.140262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.121673 restraints weight = 12076.280| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.90 r_work: 0.3468 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8494 Z= 0.154 Angle : 0.592 9.509 11576 Z= 0.305 Chirality : 0.043 0.145 1332 Planarity : 0.005 0.051 1488 Dihedral : 4.283 19.485 1222 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.10 % Allowed : 16.77 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1114 helix: 2.18 (0.26), residues: 384 sheet: -0.20 (0.31), residues: 261 loop : -0.85 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 211 HIS 0.004 0.001 HIS A 357 PHE 0.023 0.002 PHE R 125 TYR 0.015 0.001 TYR B 59 ARG 0.009 0.001 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.04058 ( 434) hydrogen bonds : angle 4.62035 ( 1245) SS BOND : bond 0.00304 ( 2) SS BOND : angle 0.70615 ( 4) covalent geometry : bond 0.00353 ( 8492) covalent geometry : angle 0.59220 (11572) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 0.889 Fit side-chains REVERT: A 36 VAL cc_start: 0.7835 (t) cc_final: 0.7542 (p) REVERT: A 221 LYS cc_start: 0.7666 (mtmm) cc_final: 0.7329 (mtmm) REVERT: A 223 GLN cc_start: 0.8406 (tt0) cc_final: 0.8198 (mt0) REVERT: A 289 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8000 (pt) REVERT: A 291 LEU cc_start: 0.7833 (mt) cc_final: 0.7504 (mt) REVERT: A 338 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7424 (ptmt) REVERT: A 381 ASP cc_start: 0.7678 (t70) cc_final: 0.7397 (t0) REVERT: B 61 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8124 (pp-130) REVERT: B 134 ARG cc_start: 0.8098 (ptt-90) cc_final: 0.7868 (ptt-90) REVERT: B 143 THR cc_start: 0.8162 (m) cc_final: 0.7826 (p) REVERT: B 258 ASP cc_start: 0.7213 (t0) cc_final: 0.6423 (t0) REVERT: B 325 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7480 (tpp) REVERT: B 340 ASN cc_start: 0.7098 (t0) cc_final: 0.6835 (t0) REVERT: R 64 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6799 (mm) REVERT: R 116 TYR cc_start: 0.8691 (t80) cc_final: 0.7779 (t80) REVERT: R 124 ARG cc_start: 0.8101 (mtm-85) cc_final: 0.7832 (mtt-85) REVERT: R 220 ARG cc_start: 0.7979 (tpp80) cc_final: 0.7736 (tpp80) outliers start: 33 outliers final: 18 residues processed: 187 average time/residue: 1.1501 time to fit residues: 229.0163 Evaluate side-chains 192 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 184 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 64 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 87 optimal weight: 0.0070 chunk 55 optimal weight: 2.9990 chunk 73 optimal weight: 0.0980 chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS B 125 ASN B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.140493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.121850 restraints weight = 12088.909| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.90 r_work: 0.3472 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8494 Z= 0.151 Angle : 0.591 9.044 11576 Z= 0.304 Chirality : 0.042 0.145 1332 Planarity : 0.005 0.051 1488 Dihedral : 4.243 19.045 1222 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.60 % Allowed : 18.63 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1114 helix: 2.25 (0.26), residues: 384 sheet: -0.12 (0.31), residues: 260 loop : -0.88 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.004 0.001 HIS A 357 PHE 0.023 0.002 PHE R 125 TYR 0.014 0.001 TYR R 76 ARG 0.009 0.001 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.03991 ( 434) hydrogen bonds : angle 4.57581 ( 1245) SS BOND : bond 0.00268 ( 2) SS BOND : angle 0.71856 ( 4) covalent geometry : bond 0.00345 ( 8492) covalent geometry : angle 0.59077 (11572) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.837 Fit side-chains REVERT: A 223 GLN cc_start: 0.8387 (tt0) cc_final: 0.8179 (mt0) REVERT: A 266 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7594 (mp) REVERT: A 289 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.7998 (pt) REVERT: A 291 LEU cc_start: 0.7832 (mt) cc_final: 0.7486 (mt) REVERT: A 338 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7419 (ptmt) REVERT: A 381 ASP cc_start: 0.7677 (t70) cc_final: 0.7408 (t0) REVERT: B 61 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8125 (pp-130) REVERT: B 134 ARG cc_start: 0.7996 (ptt-90) cc_final: 0.7780 (ptt-90) REVERT: B 143 THR cc_start: 0.8160 (m) cc_final: 0.7826 (p) REVERT: B 258 ASP cc_start: 0.7201 (t0) cc_final: 0.6392 (t0) REVERT: B 325 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7530 (tpp) REVERT: B 340 ASN cc_start: 0.7077 (t0) cc_final: 0.6830 (t0) REVERT: R 64 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6794 (mm) REVERT: R 116 TYR cc_start: 0.8707 (t80) cc_final: 0.7801 (t80) REVERT: R 124 ARG cc_start: 0.8088 (mtm-85) cc_final: 0.7815 (mtt-85) REVERT: S 18 ARG cc_start: 0.7332 (tpt170) cc_final: 0.7126 (tpt170) outliers start: 29 outliers final: 20 residues processed: 187 average time/residue: 1.0642 time to fit residues: 212.5598 Evaluate side-chains 198 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 26 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 89 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS B 125 ASN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.137988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.119364 restraints weight = 12088.243| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.89 r_work: 0.3431 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8494 Z= 0.250 Angle : 0.663 8.953 11576 Z= 0.345 Chirality : 0.046 0.149 1332 Planarity : 0.005 0.050 1488 Dihedral : 4.625 19.636 1222 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.72 % Allowed : 18.01 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.25), residues: 1114 helix: 1.79 (0.26), residues: 392 sheet: -0.21 (0.32), residues: 260 loop : -1.05 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 297 HIS 0.006 0.001 HIS A 357 PHE 0.026 0.003 PHE R 125 TYR 0.020 0.002 TYR R 76 ARG 0.009 0.001 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.04819 ( 434) hydrogen bonds : angle 4.87502 ( 1245) SS BOND : bond 0.00297 ( 2) SS BOND : angle 0.82222 ( 4) covalent geometry : bond 0.00576 ( 8492) covalent geometry : angle 0.66283 (11572) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 0.828 Fit side-chains REVERT: A 36 VAL cc_start: 0.7997 (t) cc_final: 0.7735 (p) REVERT: A 223 GLN cc_start: 0.8441 (tt0) cc_final: 0.8186 (mt0) REVERT: A 266 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7685 (mp) REVERT: A 289 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8015 (pt) REVERT: A 338 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7467 (ptmt) REVERT: A 344 GLU cc_start: 0.7864 (tp30) cc_final: 0.7532 (mm-30) REVERT: A 381 ASP cc_start: 0.7700 (t70) cc_final: 0.7420 (t0) REVERT: B 61 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8182 (pp-130) REVERT: B 143 THR cc_start: 0.8209 (m) cc_final: 0.7948 (p) REVERT: B 258 ASP cc_start: 0.7211 (t0) cc_final: 0.6411 (t0) REVERT: B 325 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7563 (tpp) REVERT: B 340 ASN cc_start: 0.7103 (t0) cc_final: 0.6805 (t0) REVERT: R 64 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6929 (mm) REVERT: R 116 TYR cc_start: 0.8667 (t80) cc_final: 0.8226 (t80) REVERT: R 124 ARG cc_start: 0.8137 (mtm-85) cc_final: 0.7880 (mtt-85) REVERT: S 18 ARG cc_start: 0.7483 (tpt170) cc_final: 0.7042 (tpt-90) REVERT: S 63 THR cc_start: 0.8414 (t) cc_final: 0.8118 (p) outliers start: 38 outliers final: 21 residues processed: 193 average time/residue: 1.0922 time to fit residues: 224.9915 Evaluate side-chains 204 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 137 VAL Chi-restraints excluded: chain R residue 199 MET Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 94 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 chunk 59 optimal weight: 0.1980 chunk 5 optimal weight: 3.9990 chunk 46 optimal weight: 0.0970 chunk 77 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 104 optimal weight: 0.0020 chunk 107 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 overall best weight: 0.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS B 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.141353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.122942 restraints weight = 12269.478| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.91 r_work: 0.3489 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8494 Z= 0.122 Angle : 0.579 8.666 11576 Z= 0.299 Chirality : 0.042 0.150 1332 Planarity : 0.005 0.052 1488 Dihedral : 4.228 18.230 1222 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.86 % Allowed : 20.12 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.25), residues: 1114 helix: 2.19 (0.26), residues: 385 sheet: -0.04 (0.32), residues: 248 loop : -1.01 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 PHE 0.023 0.002 PHE R 125 TYR 0.012 0.001 TYR B 59 ARG 0.010 0.001 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 434) hydrogen bonds : angle 4.52163 ( 1245) SS BOND : bond 0.00328 ( 2) SS BOND : angle 0.64941 ( 4) covalent geometry : bond 0.00269 ( 8492) covalent geometry : angle 0.57855 (11572) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.7842 (t) cc_final: 0.7530 (p) REVERT: A 223 GLN cc_start: 0.8359 (tt0) cc_final: 0.8158 (mt0) REVERT: A 266 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7560 (mp) REVERT: A 291 LEU cc_start: 0.7820 (mt) cc_final: 0.7471 (mt) REVERT: A 344 GLU cc_start: 0.7582 (tp30) cc_final: 0.7256 (mm-30) REVERT: A 381 ASP cc_start: 0.7623 (t70) cc_final: 0.7359 (t0) REVERT: B 61 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8067 (pp-130) REVERT: B 134 ARG cc_start: 0.7943 (ptt-90) cc_final: 0.7367 (ptt-90) REVERT: B 143 THR cc_start: 0.8169 (m) cc_final: 0.7856 (p) REVERT: B 258 ASP cc_start: 0.7198 (t0) cc_final: 0.6440 (t0) REVERT: B 340 ASN cc_start: 0.7007 (t0) cc_final: 0.6788 (t0) REVERT: R 64 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6751 (mm) REVERT: R 116 TYR cc_start: 0.8694 (t80) cc_final: 0.7607 (t80) REVERT: R 124 ARG cc_start: 0.8103 (mtm-85) cc_final: 0.7843 (mtt-85) REVERT: R 220 ARG cc_start: 0.7792 (tpp80) cc_final: 0.7249 (tpt90) outliers start: 23 outliers final: 14 residues processed: 180 average time/residue: 1.1189 time to fit residues: 214.4817 Evaluate side-chains 185 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 199 MET Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 12 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.138907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.120213 restraints weight = 12105.688| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.91 r_work: 0.3446 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8494 Z= 0.226 Angle : 0.668 12.674 11576 Z= 0.345 Chirality : 0.045 0.149 1332 Planarity : 0.006 0.060 1488 Dihedral : 4.598 19.009 1222 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.24 % Allowed : 21.74 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.25), residues: 1114 helix: 1.98 (0.26), residues: 387 sheet: -0.13 (0.31), residues: 259 loop : -0.99 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 297 HIS 0.006 0.001 HIS A 357 PHE 0.024 0.002 PHE R 125 TYR 0.019 0.002 TYR R 76 ARG 0.012 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04586 ( 434) hydrogen bonds : angle 4.77205 ( 1245) SS BOND : bond 0.00300 ( 2) SS BOND : angle 0.73536 ( 4) covalent geometry : bond 0.00522 ( 8492) covalent geometry : angle 0.66788 (11572) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 223 GLN cc_start: 0.8437 (tt0) cc_final: 0.8196 (mt0) REVERT: A 266 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7673 (mp) REVERT: A 289 LEU cc_start: 0.8608 (pt) cc_final: 0.8119 (pt) REVERT: A 301 VAL cc_start: 0.7472 (t) cc_final: 0.7267 (t) REVERT: A 344 GLU cc_start: 0.7800 (tp30) cc_final: 0.7478 (mm-30) REVERT: A 381 ASP cc_start: 0.7668 (t70) cc_final: 0.7391 (t0) REVERT: B 61 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8189 (pp-130) REVERT: B 134 ARG cc_start: 0.7887 (ptt-90) cc_final: 0.7632 (ptt-90) REVERT: B 143 THR cc_start: 0.8207 (m) cc_final: 0.7937 (p) REVERT: B 258 ASP cc_start: 0.7134 (t0) cc_final: 0.6380 (t0) REVERT: B 340 ASN cc_start: 0.7119 (t0) cc_final: 0.6840 (t0) REVERT: R 64 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6872 (mm) REVERT: R 116 TYR cc_start: 0.8675 (t80) cc_final: 0.8241 (t80) REVERT: R 124 ARG cc_start: 0.8133 (mtm-85) cc_final: 0.7876 (mtt-85) REVERT: R 206 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7795 (mt) REVERT: S 63 THR cc_start: 0.8429 (t) cc_final: 0.8135 (p) outliers start: 18 outliers final: 14 residues processed: 186 average time/residue: 1.0901 time to fit residues: 216.0816 Evaluate side-chains 193 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 199 MET Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 70 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 71 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** 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 = 0.3818 r_free = 0.3818 target = 0.138994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.120393 restraints weight = 12204.102| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.89 r_work: 0.3450 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8494 Z= 0.205 Angle : 0.657 12.653 11576 Z= 0.339 Chirality : 0.045 0.152 1332 Planarity : 0.005 0.056 1488 Dihedral : 4.599 18.773 1222 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.11 % Allowed : 20.87 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.25), residues: 1114 helix: 1.99 (0.26), residues: 384 sheet: -0.18 (0.31), residues: 259 loop : -1.03 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 211 HIS 0.005 0.001 HIS B 225 PHE 0.025 0.002 PHE R 125 TYR 0.017 0.002 TYR R 76 ARG 0.012 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04458 ( 434) hydrogen bonds : angle 4.75990 ( 1245) SS BOND : bond 0.00308 ( 2) SS BOND : angle 0.75818 ( 4) covalent geometry : bond 0.00472 ( 8492) covalent geometry : angle 0.65742 (11572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6921.83 seconds wall clock time: 119 minutes 40.01 seconds (7180.01 seconds total)