Starting phenix.real_space_refine on Wed Mar 12 21:25:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zfa_60054/03_2025/8zfa_60054_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zfa_60054/03_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_60054/03_2025/8zfa_60054.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zfa_60054/03_2025/8zfa_60054.map" model { file = "/net/cci-nas-00/data/ceres_data/8zfa_60054/03_2025/8zfa_60054_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zfa_60054/03_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.91, per 1000 atoms: 0.71 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: 2.28 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.07 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: 2.70 Time building geometry restraints manager: 2.68 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: 2.160 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.010 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:13.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.940 ------------------------------------------------------------------------------- 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 8492 Z= 0.253 Angle : 0.732 14.907 11572 Z= 0.411 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 *********************** 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 : 0.909 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: 1.2189 time to fit residues: 270.9810 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 : 0.902 ------------------------------------------------------------------------------- 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 = 46)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121595 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: 4.25 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 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 8492 Z= 0.270 Angle : 0.617 6.922 11572 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 *********************** 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 : 0.839 Fit side-chains REVERT: A 33 ASP cc_start: 0.7485 (m-30) cc_final: 0.7143 (m-30) REVERT: A 219 GLU cc_start: 0.7349 (tm-30) cc_final: 0.7071 (tm-30) REVERT: A 220 THR cc_start: 0.8535 (m) cc_final: 0.7830 (t) REVERT: A 221 LYS cc_start: 0.7566 (mtmm) cc_final: 0.7235 (mtmm) REVERT: A 289 LEU cc_start: 0.8499 (pt) cc_final: 0.8155 (pt) REVERT: A 381 ASP cc_start: 0.7766 (t70) cc_final: 0.7487 (t0) REVERT: B 59 TYR cc_start: 0.7594 (OUTLIER) cc_final: 0.7317 (t80) REVERT: B 132 ASN cc_start: 0.8075 (p0) cc_final: 0.7764 (p0) REVERT: B 258 ASP cc_start: 0.7170 (t0) cc_final: 0.6633 (t0) REVERT: B 325 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7392 (tpp) REVERT: B 340 ASN cc_start: 0.7143 (t0) cc_final: 0.6917 (t0) REVERT: R 116 TYR cc_start: 0.8627 (t80) cc_final: 0.8173 (t80) REVERT: R 124 ARG cc_start: 0.8063 (mtm-85) cc_final: 0.7782 (mtt-85) REVERT: S 98 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7973 (ttp-170) REVERT: S 192 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.6954 (ttp) outliers start: 36 outliers final: 13 residues processed: 184 average time/residue: 1.2069 time to fit residues: 236.8219 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 : 0.947 ------------------------------------------------------------------------------- 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: 0.0050 chunk 101 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 69 optimal weight: 0.0980 chunk 45 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 12 optimal weight: 0.0770 overall best weight: 0.2352 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.142560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.123497 restraints weight = 12222.376| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.94 r_work: 0.3493 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8492 Z= 0.180 Angle : 0.558 7.250 11572 Z= 0.292 Chirality : 0.042 0.136 1332 Planarity : 0.005 0.054 1488 Dihedral : 4.456 45.010 1224 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.48 % Allowed : 12.92 % Favored : 83.60 % 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: 0.73 (0.26), residues: 1114 helix: 2.22 (0.27), residues: 388 sheet: -0.15 (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 0.020 0.002 PHE R 125 TYR 0.013 0.001 TYR R 76 ARG 0.008 0.001 ARG A 380 *********************** 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 197 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 1.975 Fit side-chains REVERT: A 33 ASP cc_start: 0.7466 (m-30) cc_final: 0.7022 (m-30) REVERT: A 36 VAL cc_start: 0.7691 (t) cc_final: 0.7365 (p) REVERT: A 219 GLU cc_start: 0.7392 (tm-30) cc_final: 0.7172 (tm-30) REVERT: A 221 LYS cc_start: 0.7565 (mtmm) cc_final: 0.7317 (mtmm) REVERT: A 289 LEU cc_start: 0.8539 (pt) cc_final: 0.8119 (pt) REVERT: A 338 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7398 (ptmt) REVERT: A 381 ASP cc_start: 0.7771 (t70) cc_final: 0.7500 (t0) REVERT: B 59 TYR cc_start: 0.7588 (OUTLIER) cc_final: 0.7384 (t80) REVERT: B 61 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8057 (pp-130) REVERT: B 132 ASN cc_start: 0.7962 (p0) cc_final: 0.7648 (p0) REVERT: B 237 ASN cc_start: 0.7744 (t0) cc_final: 0.7434 (t0) REVERT: B 258 ASP cc_start: 0.7125 (t0) cc_final: 0.6428 (t0) REVERT: B 325 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7338 (tpp) REVERT: B 340 ASN cc_start: 0.7129 (t0) cc_final: 0.6881 (t0) REVERT: R 116 TYR cc_start: 0.8661 (t80) cc_final: 0.7651 (t80) REVERT: R 124 ARG cc_start: 0.8097 (mtm-85) cc_final: 0.7817 (mtt-85) outliers start: 28 outliers final: 13 residues processed: 175 average time/residue: 1.2077 time to fit residues: 225.9438 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 : 0.907 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 36 optimal weight: 0.4980 chunk 96 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 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: 0.9980 chunk 64 optimal weight: 0.1980 chunk 32 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 230 ASN S 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.139272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.120354 restraints weight = 12141.488| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.91 r_work: 0.3447 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8492 Z= 0.284 Angle : 0.613 7.911 11572 Z= 0.321 Chirality : 0.044 0.157 1332 Planarity : 0.005 0.052 1488 Dihedral : 4.410 20.131 1222 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.47 % Allowed : 15.03 % Favored : 80.50 % 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: 0.55 (0.25), residues: 1114 helix: 2.10 (0.26), residues: 384 sheet: -0.26 (0.31), residues: 258 loop : -0.68 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 211 HIS 0.007 0.001 HIS A 357 PHE 0.023 0.002 PHE R 107 TYR 0.018 0.002 TYR R 76 ARG 0.010 0.001 ARG B 137 *********************** 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 208 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.817 Fit side-chains REVERT: A 33 ASP cc_start: 0.7455 (m-30) cc_final: 0.7177 (m-30) REVERT: A 221 LYS cc_start: 0.7665 (mtmm) cc_final: 0.7435 (mtmm) REVERT: A 289 LEU cc_start: 0.8536 (pt) cc_final: 0.8040 (pt) REVERT: A 338 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7431 (ptmt) REVERT: A 381 ASP cc_start: 0.7711 (t70) cc_final: 0.7434 (t0) REVERT: B 61 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8182 (pp-130) REVERT: B 85 TYR cc_start: 0.8431 (m-10) cc_final: 0.8195 (m-10) REVERT: B 143 THR cc_start: 0.8109 (m) cc_final: 0.7774 (p) REVERT: B 186 ASP cc_start: 0.7659 (m-30) cc_final: 0.7435 (m-30) REVERT: B 258 ASP cc_start: 0.7196 (t0) cc_final: 0.6474 (t0) REVERT: B 325 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7517 (tpp) REVERT: B 340 ASN cc_start: 0.7182 (t0) cc_final: 0.6894 (t0) REVERT: R 64 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7098 (mm) REVERT: R 116 TYR cc_start: 0.8656 (t80) cc_final: 0.8249 (t80) REVERT: R 124 ARG cc_start: 0.8095 (mtm-85) cc_final: 0.7815 (mtt-85) outliers start: 36 outliers final: 15 residues processed: 183 average time/residue: 1.0904 time to fit residues: 212.7784 Evaluate side-chains 187 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 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 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 186 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 31 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 46 optimal weight: 0.0570 chunk 39 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 125 ASN B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.138785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.120192 restraints weight = 12004.444| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.89 r_work: 0.3448 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8492 Z= 0.330 Angle : 0.638 9.378 11572 Z= 0.331 Chirality : 0.045 0.142 1332 Planarity : 0.005 0.051 1488 Dihedral : 4.552 19.921 1222 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.72 % Allowed : 16.15 % 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: 0.42 (0.25), residues: 1114 helix: 1.97 (0.26), residues: 384 sheet: -0.31 (0.31), residues: 266 loop : -0.77 (0.29), residues: 464 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 0.022 0.002 PHE R 107 TYR 0.016 0.002 TYR B 59 ARG 0.009 0.001 ARG A 380 *********************** 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 214 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 0.910 Fit side-chains REVERT: A 36 VAL cc_start: 0.7919 (t) cc_final: 0.7655 (p) REVERT: A 221 LYS cc_start: 0.7647 (mtmm) cc_final: 0.7424 (mtmm) REVERT: A 289 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8020 (pt) REVERT: A 338 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7401 (ptmt) REVERT: A 381 ASP cc_start: 0.7686 (t70) cc_final: 0.7406 (t0) REVERT: B 61 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8194 (pp-130) REVERT: B 134 ARG cc_start: 0.7960 (ptt-90) cc_final: 0.7759 (ptt-90) REVERT: B 143 THR cc_start: 0.8178 (m) cc_final: 0.7873 (p) REVERT: B 186 ASP cc_start: 0.7683 (m-30) cc_final: 0.7447 (m-30) REVERT: B 212 ASP cc_start: 0.7793 (t0) cc_final: 0.7572 (t0) REVERT: B 258 ASP cc_start: 0.7181 (t0) cc_final: 0.6422 (t0) REVERT: B 325 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7571 (tpp) REVERT: B 340 ASN cc_start: 0.7174 (t0) cc_final: 0.6871 (t0) REVERT: R 64 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6845 (mm) REVERT: R 116 TYR cc_start: 0.8672 (t80) cc_final: 0.8222 (t80) REVERT: R 124 ARG cc_start: 0.8116 (mtm-85) cc_final: 0.7821 (mtt-85) outliers start: 38 outliers final: 21 residues processed: 192 average time/residue: 1.4440 time to fit residues: 295.5062 Evaluate side-chains 199 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 344 GLU 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 184 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 65 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 37 optimal weight: 0.2980 chunk 27 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 71 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.139202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.120639 restraints weight = 12100.084| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.91 r_work: 0.3455 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8492 Z= 0.275 Angle : 0.609 8.111 11572 Z= 0.317 Chirality : 0.044 0.147 1332 Planarity : 0.005 0.051 1488 Dihedral : 4.449 19.435 1222 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.35 % Allowed : 17.27 % Favored : 78.39 % 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: 0.45 (0.25), residues: 1114 helix: 2.03 (0.26), residues: 384 sheet: -0.21 (0.31), residues: 267 loop : -0.86 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.005 0.001 HIS B 225 PHE 0.020 0.002 PHE R 107 TYR 0.018 0.002 TYR R 76 ARG 0.009 0.001 ARG B 49 *********************** 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 217 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 182 time to evaluate : 0.955 Fit side-chains REVERT: A 36 VAL cc_start: 0.7926 (t) cc_final: 0.7626 (p) REVERT: A 223 GLN cc_start: 0.8443 (tt0) cc_final: 0.8192 (mt0) REVERT: A 289 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8020 (pt) REVERT: A 291 LEU cc_start: 0.7755 (mt) cc_final: 0.7422 (mt) REVERT: A 338 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7464 (ptmt) REVERT: A 344 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7307 (mm-30) REVERT: A 381 ASP cc_start: 0.7675 (t70) cc_final: 0.7396 (t0) REVERT: B 61 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8157 (pp-130) REVERT: B 134 ARG cc_start: 0.7981 (ptt-90) cc_final: 0.7762 (ptt-90) REVERT: B 143 THR cc_start: 0.8194 (m) cc_final: 0.7881 (p) REVERT: B 212 ASP cc_start: 0.7785 (t0) cc_final: 0.7567 (t0) REVERT: B 258 ASP cc_start: 0.7194 (t0) cc_final: 0.6395 (t0) REVERT: B 325 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7484 (tpp) REVERT: B 340 ASN cc_start: 0.7106 (t0) cc_final: 0.6819 (t0) REVERT: R 64 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6861 (mm) REVERT: R 116 TYR cc_start: 0.8687 (t80) cc_final: 0.7758 (t80) REVERT: R 124 ARG cc_start: 0.8116 (mtm-85) cc_final: 0.7825 (mtt-85) REVERT: S 18 ARG cc_start: 0.7373 (tpt170) cc_final: 0.7162 (tpt170) outliers start: 35 outliers final: 19 residues processed: 194 average time/residue: 1.2081 time to fit residues: 250.8978 Evaluate side-chains 200 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 344 GLU 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 64 optimal weight: 0.7980 chunk 66 optimal weight: 0.0980 chunk 22 optimal weight: 0.5980 chunk 87 optimal weight: 0.0980 chunk 55 optimal weight: 2.9990 chunk 73 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 105 optimal weight: 0.0980 overall best weight: 0.1780 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.142416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.123969 restraints weight = 12154.822| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.91 r_work: 0.3504 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8492 Z= 0.165 Angle : 0.572 9.841 11572 Z= 0.291 Chirality : 0.042 0.146 1332 Planarity : 0.005 0.052 1488 Dihedral : 4.097 18.243 1222 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.11 % Allowed : 19.25 % Favored : 77.64 % 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: 0.63 (0.26), residues: 1114 helix: 2.31 (0.26), residues: 386 sheet: -0.08 (0.31), residues: 257 loop : -0.91 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.003 0.001 HIS A 230 PHE 0.013 0.001 PHE R 107 TYR 0.012 0.001 TYR B 59 ARG 0.009 0.001 ARG A 380 *********************** 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 197 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.846 Fit side-chains REVERT: A 36 VAL cc_start: 0.7753 (t) cc_final: 0.7424 (p) REVERT: A 291 LEU cc_start: 0.7760 (mt) cc_final: 0.7377 (mt) REVERT: A 338 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7401 (ptmt) REVERT: A 381 ASP cc_start: 0.7638 (t70) cc_final: 0.7366 (t0) REVERT: B 61 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8040 (pp-130) REVERT: B 134 ARG cc_start: 0.7995 (ptt-90) cc_final: 0.7773 (ptt-90) REVERT: B 258 ASP cc_start: 0.7178 (t0) cc_final: 0.6412 (t0) REVERT: B 340 ASN cc_start: 0.7046 (t0) cc_final: 0.6831 (t0) REVERT: R 64 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6729 (mm) REVERT: R 116 TYR cc_start: 0.8684 (t80) cc_final: 0.7647 (t80) REVERT: R 124 ARG cc_start: 0.8014 (mtm-85) cc_final: 0.7732 (mtt-85) REVERT: R 220 ARG cc_start: 0.7744 (tpp80) cc_final: 0.7506 (tpt90) outliers start: 25 outliers final: 16 residues processed: 180 average time/residue: 1.1229 time to fit residues: 215.6200 Evaluate side-chains 188 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 275 SER 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 96 ARG Chi-restraints excluded: chain B residue 125 ASN 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 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 S residue 85 SER 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: 0.1980 chunk 84 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 92 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3833 r_free = 0.3833 target = 0.140077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121853 restraints weight = 12147.051| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.84 r_work: 0.3478 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8492 Z= 0.245 Angle : 0.606 11.312 11572 Z= 0.309 Chirality : 0.043 0.147 1332 Planarity : 0.005 0.051 1488 Dihedral : 4.208 18.086 1222 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.48 % Allowed : 19.25 % 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: 0.63 (0.25), residues: 1114 helix: 2.30 (0.26), residues: 384 sheet: -0.11 (0.31), residues: 262 loop : -0.86 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.005 0.001 HIS B 225 PHE 0.020 0.002 PHE R 107 TYR 0.016 0.001 TYR R 76 ARG 0.010 0.001 ARG B 137 *********************** 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 196 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.830 Fit side-chains REVERT: A 36 VAL cc_start: 0.7859 (t) cc_final: 0.7564 (p) REVERT: A 289 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8033 (pt) REVERT: A 338 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7450 (ptmt) REVERT: A 347 ARG cc_start: 0.8318 (ttp80) cc_final: 0.8107 (mtp-110) REVERT: A 381 ASP cc_start: 0.7628 (t70) cc_final: 0.7365 (t0) REVERT: B 61 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8118 (pp-130) REVERT: B 143 THR cc_start: 0.8160 (m) cc_final: 0.7850 (p) REVERT: B 258 ASP cc_start: 0.7212 (t0) cc_final: 0.6422 (t0) REVERT: B 340 ASN cc_start: 0.7073 (t0) cc_final: 0.6824 (t0) REVERT: R 116 TYR cc_start: 0.8699 (t80) cc_final: 0.7789 (t80) REVERT: R 124 ARG cc_start: 0.8114 (mtm-85) cc_final: 0.7850 (mtt-85) REVERT: R 220 ARG cc_start: 0.7896 (tpp80) cc_final: 0.7679 (tpt90) outliers start: 28 outliers final: 18 residues processed: 180 average time/residue: 1.1652 time to fit residues: 223.3767 Evaluate side-chains 190 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 96 ARG 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 94 optimal weight: 0.0770 chunk 36 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 104 optimal weight: 0.0970 chunk 107 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.140256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.121748 restraints weight = 12262.227| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.91 r_work: 0.3472 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8492 Z= 0.238 Angle : 0.627 13.458 11572 Z= 0.316 Chirality : 0.043 0.255 1332 Planarity : 0.005 0.057 1488 Dihedral : 4.272 18.162 1222 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.35 % Allowed : 19.88 % Favored : 76.77 % 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: 0.57 (0.25), residues: 1114 helix: 2.30 (0.26), residues: 382 sheet: -0.08 (0.31), residues: 255 loop : -0.97 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.004 0.001 HIS B 225 PHE 0.019 0.002 PHE R 107 TYR 0.016 0.001 TYR R 76 ARG 0.010 0.001 ARG A 380 *********************** 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 200 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 1.018 Fit side-chains REVERT: A 36 VAL cc_start: 0.7855 (t) cc_final: 0.7561 (p) REVERT: A 289 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8034 (pt) REVERT: A 338 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7447 (ptmt) REVERT: A 381 ASP cc_start: 0.7640 (t70) cc_final: 0.7365 (t0) REVERT: B 61 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8114 (pp-130) REVERT: B 134 ARG cc_start: 0.8062 (ptt-90) cc_final: 0.7531 (ptt-90) REVERT: B 143 THR cc_start: 0.8156 (m) cc_final: 0.7853 (p) REVERT: B 258 ASP cc_start: 0.7062 (t0) cc_final: 0.6343 (t0) REVERT: B 340 ASN cc_start: 0.7121 (t0) cc_final: 0.6895 (t0) REVERT: R 116 TYR cc_start: 0.8711 (t80) cc_final: 0.7812 (t80) REVERT: R 124 ARG cc_start: 0.8119 (mtm-85) cc_final: 0.7852 (mtt-85) REVERT: R 220 ARG cc_start: 0.7874 (tpp80) cc_final: 0.7654 (tpt90) outliers start: 27 outliers final: 20 residues processed: 186 average time/residue: 1.5541 time to fit residues: 311.6481 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 : 1.025 ------------------------------------------------------------------------------- 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 275 SER Chi-restraints excluded: chain A residue 289 LEU 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 96 ARG 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 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 82 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=1.00 ------------------------------------------------------------------------------- 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: 0.8980 chunk 37 optimal weight: 0.0970 chunk 52 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.139324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.120827 restraints weight = 12131.743| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.90 r_work: 0.3456 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8492 Z= 0.294 Angle : 0.666 14.540 11572 Z= 0.334 Chirality : 0.045 0.337 1332 Planarity : 0.005 0.056 1488 Dihedral : 4.468 19.059 1222 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.11 % Allowed : 20.50 % Favored : 76.40 % 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: 0.52 (0.25), residues: 1114 helix: 2.19 (0.26), residues: 382 sheet: -0.04 (0.31), residues: 253 loop : -0.97 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 211 HIS 0.005 0.001 HIS A 357 PHE 0.021 0.002 PHE R 107 TYR 0.019 0.002 TYR R 76 ARG 0.010 0.001 ARG A 380 ********************** 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 197 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.832 Fit side-chains REVERT: A 36 VAL cc_start: 0.7947 (t) cc_final: 0.7678 (p) REVERT: A 289 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8040 (pt) REVERT: A 338 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7435 (ptmt) REVERT: A 381 ASP cc_start: 0.7660 (t70) cc_final: 0.7393 (t0) REVERT: B 61 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8168 (pp-130) REVERT: B 143 THR cc_start: 0.8184 (m) cc_final: 0.7922 (p) REVERT: B 258 ASP cc_start: 0.6969 (t0) cc_final: 0.6247 (t0) REVERT: B 340 ASN cc_start: 0.7125 (t0) cc_final: 0.6874 (t0) REVERT: R 116 TYR cc_start: 0.8687 (t80) cc_final: 0.8245 (t80) REVERT: R 124 ARG cc_start: 0.8120 (mtm-85) cc_final: 0.7854 (mtt-85) REVERT: R 220 ARG cc_start: 0.7938 (tpp80) cc_final: 0.7715 (tpp80) REVERT: S 63 THR cc_start: 0.8371 (t) cc_final: 0.8077 (p) outliers start: 25 outliers final: 19 residues processed: 185 average time/residue: 1.2004 time to fit residues: 236.8474 Evaluate side-chains 187 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 1.214 ------------------------------------------------------------------------------- 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 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 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 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 82 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 57 optimal weight: 0.0470 chunk 80 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 75 optimal weight: 0.1980 chunk 19 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 71 optimal weight: 0.2980 overall best weight: 0.3478 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.140625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.122079 restraints weight = 12238.471| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.92 r_work: 0.3473 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8492 Z= 0.221 Angle : 0.645 15.012 11572 Z= 0.322 Chirality : 0.044 0.327 1332 Planarity : 0.005 0.051 1488 Dihedral : 4.351 18.346 1222 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.73 % Allowed : 21.37 % Favored : 75.90 % 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: 0.57 (0.25), residues: 1114 helix: 2.23 (0.26), residues: 382 sheet: -0.03 (0.31), residues: 253 loop : -0.93 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 43 HIS 0.004 0.001 HIS A 230 PHE 0.018 0.002 PHE R 107 TYR 0.015 0.001 TYR R 76 ARG 0.011 0.001 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7320.52 seconds wall clock time: 129 minutes 4.32 seconds (7744.32 seconds total)