Starting phenix.real_space_refine on Thu Mar 13 04:43:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xxr_38759/03_2025/8xxr_38759.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xxr_38759/03_2025/8xxr_38759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xxr_38759/03_2025/8xxr_38759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xxr_38759/03_2025/8xxr_38759.map" model { file = "/net/cci-nas-00/data/ceres_data/8xxr_38759/03_2025/8xxr_38759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xxr_38759/03_2025/8xxr_38759.cif" } resolution = 3.17 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= 1.000 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 58 5.16 5 C 5503 2.51 5 N 1474 2.21 5 O 1595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8630 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2277 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 8, 'TRANS': 284} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1652 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 205} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2550 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "G" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 383 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "S" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1768 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 5.02, per 1000 atoms: 0.58 Number of scatterers: 8630 At special positions: 0 Unit cell: (89.225, 121.388, 135.912, 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 58 16.00 O 1595 8.00 N 1474 7.00 C 5503 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 39 " - pdb=" SG CYS R 286 " distance=2.03 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 196 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 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: 2.15 Conformation dependent library (CDL) restraints added in 941.6 milliseconds 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 15 sheets defined 36.4% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'R' and resid 44 through 76 removed outlier: 4.412A pdb=" N SER R 76 " --> pdb=" O VAL R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 111 Proline residue: R 102 - end of helix Processing helix chain 'R' and resid 115 through 149 Processing helix chain 'R' and resid 153 through 160 removed outlier: 3.767A pdb=" N THR R 156 " --> pdb=" O ARG R 153 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG R 159 " --> pdb=" O THR R 156 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR R 160 " --> pdb=" O GLN R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 183 Proline residue: R 179 - end of helix Processing helix chain 'R' and resid 203 through 212 removed outlier: 3.651A pdb=" N TRP R 207 " --> pdb=" O ASN R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 220 through 240 Processing helix chain 'R' and resid 245 through 279 removed outlier: 3.808A pdb=" N ALA R 249 " --> pdb=" O GLN R 245 " (cutoff:3.500A) Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 285 through 305 removed outlier: 3.605A pdb=" N ASP R 297 " --> pdb=" O ASP R 293 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU R 305 " --> pdb=" O ILE R 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 315 Proline residue: R 311 - end of helix Processing helix chain 'R' and resid 318 through 329 removed outlier: 3.607A pdb=" N ARG R 322 " --> pdb=" O GLY R 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.517A pdb=" N TRP A 212 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.958A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 6 through 26 removed outlier: 3.554A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.623A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.691A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.875A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 208 through 212 removed outlier: 4.018A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 184 through 187 removed outlier: 3.778A pdb=" N ALA R 195 " --> pdb=" O VAL R 187 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 188 Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 188 removed outlier: 9.974A pdb=" N ALA A 221 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ASP A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.562A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.046A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 73 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.530A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 153 removed outlier: 4.547A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.603A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.562A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.538A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.605A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER S 71 " --> pdb=" O PHE S 80 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.648A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 130 removed outlier: 3.619A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.324A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.324A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1209 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: 2.28 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1498 1.32 - 1.45: 2345 1.45 - 1.57: 4881 1.57 - 1.70: 1 1.70 - 1.82: 81 Bond restraints: 8806 Sorted by residual: bond pdb=" C PRO S 75 " pdb=" O PRO S 75 " ideal model delta sigma weight residual 1.237 1.201 0.037 1.20e-02 6.94e+03 9.32e+00 bond pdb=" N LEU A 250 " pdb=" CA LEU A 250 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.53e+00 bond pdb=" CB PRO B 94 " pdb=" CG PRO B 94 " ideal model delta sigma weight residual 1.492 1.604 -0.112 5.00e-02 4.00e+02 5.04e+00 bond pdb=" N ASN R 66 " pdb=" CA ASN R 66 " ideal model delta sigma weight residual 1.458 1.486 -0.029 1.33e-02 5.65e+03 4.60e+00 bond pdb=" C ASP B 76 " pdb=" O ASP B 76 " ideal model delta sigma weight residual 1.236 1.210 0.026 1.47e-02 4.63e+03 3.09e+00 ... (remaining 8801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 11808 1.90 - 3.79: 121 3.79 - 5.69: 18 5.69 - 7.58: 5 7.58 - 9.48: 2 Bond angle restraints: 11954 Sorted by residual: angle pdb=" N THR B 102 " pdb=" CA THR B 102 " pdb=" C THR B 102 " ideal model delta sigma weight residual 107.23 115.24 -8.01 1.67e+00 3.59e-01 2.30e+01 angle pdb=" CA GLN B 32 " pdb=" CB GLN B 32 " pdb=" CG GLN B 32 " ideal model delta sigma weight residual 114.10 121.43 -7.33 2.00e+00 2.50e-01 1.34e+01 angle pdb=" CA PRO B 94 " pdb=" N PRO B 94 " pdb=" CD PRO B 94 " ideal model delta sigma weight residual 112.00 106.91 5.09 1.40e+00 5.10e-01 1.32e+01 angle pdb=" C ASN R 66 " pdb=" CA ASN R 66 " pdb=" CB ASN R 66 " ideal model delta sigma weight residual 110.31 117.40 -7.09 2.09e+00 2.29e-01 1.15e+01 angle pdb=" CB GLN B 32 " pdb=" CG GLN B 32 " pdb=" CD GLN B 32 " ideal model delta sigma weight residual 112.60 118.16 -5.56 1.70e+00 3.46e-01 1.07e+01 ... (remaining 11949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4614 17.92 - 35.84: 484 35.84 - 53.76: 104 53.76 - 71.68: 5 71.68 - 89.60: 6 Dihedral angle restraints: 5213 sinusoidal: 1955 harmonic: 3258 Sorted by residual: dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 139.65 -46.65 1 1.00e+01 1.00e-02 3.01e+01 dihedral pdb=" CB CYS R 39 " pdb=" SG CYS R 39 " pdb=" SG CYS R 286 " pdb=" CB CYS R 286 " ideal model delta sinusoidal sigma weight residual 93.00 61.09 31.91 1 1.00e+01 1.00e-02 1.45e+01 dihedral pdb=" C ASN R 66 " pdb=" N ASN R 66 " pdb=" CA ASN R 66 " pdb=" CB ASN R 66 " ideal model delta harmonic sigma weight residual -122.60 -131.58 8.98 0 2.50e+00 1.60e-01 1.29e+01 ... (remaining 5210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1049 0.043 - 0.085: 244 0.085 - 0.128: 87 0.128 - 0.171: 4 0.171 - 0.213: 4 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CA ASN R 66 " pdb=" N ASN R 66 " pdb=" C ASN R 66 " pdb=" CB ASN R 66 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA LEU A 250 " pdb=" N LEU A 250 " pdb=" C LEU A 250 " pdb=" CB LEU A 250 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.18e-01 chirality pdb=" CA TYR S 178 " pdb=" N TYR S 178 " pdb=" C TYR S 178 " pdb=" CB TYR S 178 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.18e-01 ... (remaining 1385 not shown) Planarity restraints: 1509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO B 236 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C THR B 87 " -0.028 2.00e-02 2.50e+03 pdb=" O THR B 87 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN B 88 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER R 193 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO R 194 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO R 194 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO R 194 " -0.022 5.00e-02 4.00e+02 ... (remaining 1506 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 727 2.74 - 3.28: 8309 3.28 - 3.82: 13921 3.82 - 4.36: 15833 4.36 - 4.90: 29314 Nonbonded interactions: 68104 Sorted by model distance: nonbonded pdb=" OD1 ASP S 211 " pdb=" OH TYR S 215 " model vdw 2.204 3.040 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.205 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.212 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.217 3.040 nonbonded pdb=" O GLY R 201 " pdb=" OG1 THR R 204 " model vdw 2.220 3.040 ... (remaining 68099 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 21.590 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 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 : 0.003 0.112 8806 Z= 0.184 Angle : 0.531 9.479 11954 Z= 0.290 Chirality : 0.042 0.213 1388 Planarity : 0.004 0.044 1509 Dihedral : 14.880 89.605 3099 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.43 % Allowed : 15.64 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.40 (0.26), residues: 1109 helix: 2.02 (0.27), residues: 383 sheet: -0.39 (0.30), residues: 294 loop : -0.81 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.002 0.001 HIS A 189 PHE 0.008 0.001 PHE R 233 TYR 0.024 0.001 TYR S 178 ARG 0.003 0.000 ARG S 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 250 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8133 (mp) REVERT: A 309 GLU cc_start: 0.7352 (mt-10) cc_final: 0.7136 (mt-10) outliers start: 4 outliers final: 3 residues processed: 122 average time/residue: 0.1745 time to fit residues: 31.1672 Evaluate side-chains 120 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 0.1980 chunk 52 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 ASN ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS B 91 HIS B 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.183354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.147149 restraints weight = 11249.155| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.88 r_work: 0.3624 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8806 Z= 0.190 Angle : 0.531 6.764 11954 Z= 0.286 Chirality : 0.042 0.199 1388 Planarity : 0.004 0.041 1509 Dihedral : 4.749 47.313 1220 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.17 % Allowed : 15.74 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.46 (0.26), residues: 1109 helix: 2.10 (0.27), residues: 387 sheet: -0.35 (0.29), residues: 301 loop : -0.86 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 PHE 0.010 0.001 PHE B 234 TYR 0.027 0.001 TYR S 178 ARG 0.006 0.000 ARG S 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8151 (mp) REVERT: B 59 TYR cc_start: 0.8587 (m-80) cc_final: 0.8247 (m-80) REVERT: B 76 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7942 (p0) REVERT: S 168 ARG cc_start: 0.7935 (mpt180) cc_final: 0.7391 (mpt180) outliers start: 20 outliers final: 11 residues processed: 142 average time/residue: 0.1596 time to fit residues: 33.7656 Evaluate side-chains 129 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 166 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 0.1980 chunk 67 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 ASN ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS B 220 GLN B 268 ASN S 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.180413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.144383 restraints weight = 11081.673| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.71 r_work: 0.3591 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8806 Z= 0.267 Angle : 0.562 7.338 11954 Z= 0.300 Chirality : 0.043 0.220 1388 Planarity : 0.004 0.040 1509 Dihedral : 4.609 44.784 1217 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.17 % Allowed : 18.24 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.40 (0.26), residues: 1109 helix: 2.06 (0.27), residues: 383 sheet: -0.37 (0.29), residues: 311 loop : -0.87 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 211 HIS 0.004 0.001 HIS B 91 PHE 0.014 0.001 PHE R 130 TYR 0.029 0.001 TYR S 178 ARG 0.006 0.000 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: A 250 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8299 (mp) REVERT: A 309 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7266 (mt-10) REVERT: A 349 ARG cc_start: 0.6784 (ttm110) cc_final: 0.6505 (tpp-160) REVERT: G 15 LEU cc_start: 0.7991 (tt) cc_final: 0.7739 (tt) REVERT: S 168 ARG cc_start: 0.7991 (mpt180) cc_final: 0.7680 (mpt180) REVERT: S 174 GLN cc_start: 0.8166 (mt0) cc_final: 0.7917 (pt0) REVERT: S 180 MET cc_start: 0.7161 (mmt) cc_final: 0.6758 (mmt) outliers start: 20 outliers final: 11 residues processed: 140 average time/residue: 0.1737 time to fit residues: 35.6680 Evaluate side-chains 134 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 166 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 95 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 25 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 ASN ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS R 206 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.190035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.151784 restraints weight = 11260.668| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.49 r_work: 0.3716 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8806 Z= 0.211 Angle : 0.526 7.623 11954 Z= 0.282 Chirality : 0.042 0.205 1388 Planarity : 0.003 0.040 1509 Dihedral : 4.216 36.242 1215 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.61 % Allowed : 18.68 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.26), residues: 1109 helix: 2.15 (0.27), residues: 383 sheet: -0.27 (0.29), residues: 288 loop : -0.86 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.003 0.001 HIS A 189 PHE 0.010 0.001 PHE R 130 TYR 0.027 0.001 TYR S 178 ARG 0.004 0.000 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 292 ILE cc_start: 0.7065 (OUTLIER) cc_final: 0.6679 (mm) REVERT: R 313 ILE cc_start: 0.7340 (OUTLIER) cc_final: 0.7130 (mt) REVERT: A 250 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8515 (mp) REVERT: A 309 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7190 (mt-10) REVERT: A 349 ARG cc_start: 0.6800 (ttm110) cc_final: 0.6404 (tpp-160) REVERT: G 15 LEU cc_start: 0.8110 (tt) cc_final: 0.7840 (tt) REVERT: S 168 ARG cc_start: 0.8034 (mpt180) cc_final: 0.7669 (mpt180) REVERT: S 174 GLN cc_start: 0.8069 (mt0) cc_final: 0.7828 (pt0) REVERT: S 180 MET cc_start: 0.7091 (mmt) cc_final: 0.6795 (mmt) outliers start: 24 outliers final: 16 residues processed: 140 average time/residue: 0.1746 time to fit residues: 35.7359 Evaluate side-chains 137 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 313 ILE Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 166 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 49 optimal weight: 0.0670 chunk 82 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 44 optimal weight: 0.0980 chunk 54 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 129 ASN R 150 HIS B 220 GLN B 268 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.183755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.148372 restraints weight = 10937.077| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.60 r_work: 0.3653 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8806 Z= 0.140 Angle : 0.491 7.172 11954 Z= 0.264 Chirality : 0.041 0.179 1388 Planarity : 0.003 0.039 1509 Dihedral : 3.993 37.570 1215 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.26 % Allowed : 18.35 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.61 (0.26), residues: 1109 helix: 2.29 (0.27), residues: 383 sheet: -0.20 (0.29), residues: 289 loop : -0.85 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 189 PHE 0.009 0.001 PHE B 199 TYR 0.024 0.001 TYR S 178 ARG 0.002 0.000 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 313 ILE cc_start: 0.7149 (OUTLIER) cc_final: 0.6948 (mt) REVERT: A 24 LYS cc_start: 0.6708 (tptp) cc_final: 0.5931 (tmmt) REVERT: A 218 ASP cc_start: 0.8583 (m-30) cc_final: 0.7945 (p0) REVERT: A 273 ASP cc_start: 0.7546 (p0) cc_final: 0.7240 (t0) REVERT: A 291 TYR cc_start: 0.5225 (t80) cc_final: 0.4919 (t80) REVERT: A 309 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7016 (mt-10) REVERT: G 15 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7707 (tt) outliers start: 30 outliers final: 18 residues processed: 152 average time/residue: 0.1682 time to fit residues: 37.5492 Evaluate side-chains 140 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 313 ILE Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 174 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 53 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 150 HIS A 322 HIS B 220 GLN B 239 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.190331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.158135 restraints weight = 11126.782| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.48 r_work: 0.3740 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8806 Z= 0.188 Angle : 0.517 6.906 11954 Z= 0.276 Chirality : 0.042 0.196 1388 Planarity : 0.003 0.042 1509 Dihedral : 3.858 24.301 1213 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.61 % Allowed : 18.57 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.68 (0.26), residues: 1109 helix: 2.30 (0.27), residues: 383 sheet: -0.08 (0.30), residues: 279 loop : -0.81 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 189 PHE 0.010 0.001 PHE R 130 TYR 0.025 0.001 TYR S 178 ARG 0.004 0.000 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 250 MET cc_start: 0.8289 (mtt) cc_final: 0.7770 (mtt) REVERT: R 313 ILE cc_start: 0.7344 (OUTLIER) cc_final: 0.7136 (mt) REVERT: A 24 LYS cc_start: 0.6901 (tptp) cc_final: 0.6131 (tmmt) REVERT: A 218 ASP cc_start: 0.8439 (m-30) cc_final: 0.7971 (p0) REVERT: A 273 ASP cc_start: 0.7554 (p0) cc_final: 0.7335 (t0) REVERT: A 309 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7187 (mt-10) REVERT: A 318 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7902 (mm-30) REVERT: A 349 ARG cc_start: 0.6841 (ttm110) cc_final: 0.6528 (tpp-160) REVERT: G 15 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7825 (tt) outliers start: 24 outliers final: 15 residues processed: 141 average time/residue: 0.1819 time to fit residues: 36.9771 Evaluate side-chains 135 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 313 ILE Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 166 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 90 optimal weight: 0.0270 chunk 20 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 chunk 14 optimal weight: 0.0670 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 150 HIS B 220 GLN B 239 ASN B 268 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.193318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.160932 restraints weight = 11323.266| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 2.56 r_work: 0.3765 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8806 Z= 0.141 Angle : 0.495 7.097 11954 Z= 0.264 Chirality : 0.041 0.179 1388 Planarity : 0.003 0.040 1509 Dihedral : 3.731 22.887 1213 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.37 % Allowed : 18.35 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.78 (0.26), residues: 1109 helix: 2.39 (0.27), residues: 383 sheet: -0.00 (0.30), residues: 277 loop : -0.79 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.000 HIS A 189 PHE 0.009 0.001 PHE B 234 TYR 0.023 0.001 TYR S 178 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 250 MET cc_start: 0.8338 (mtt) cc_final: 0.7797 (mtt) REVERT: A 24 LYS cc_start: 0.6860 (tptp) cc_final: 0.6102 (tmmt) REVERT: A 55 ILE cc_start: 0.5753 (OUTLIER) cc_final: 0.5501 (mt) REVERT: A 273 ASP cc_start: 0.7604 (p0) cc_final: 0.7375 (t0) REVERT: A 291 TYR cc_start: 0.5297 (t80) cc_final: 0.4943 (t80) REVERT: A 309 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7201 (mt-10) REVERT: A 349 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.6475 (tpp-160) REVERT: G 15 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7817 (tt) outliers start: 31 outliers final: 21 residues processed: 146 average time/residue: 0.1731 time to fit residues: 36.5112 Evaluate side-chains 143 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 279 THR Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 166 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 0.7980 chunk 93 optimal weight: 0.0370 chunk 78 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 107 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 ASN R 150 HIS B 220 GLN B 239 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.193220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.160771 restraints weight = 11394.758| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.56 r_work: 0.3717 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8806 Z= 0.150 Angle : 0.494 7.114 11954 Z= 0.265 Chirality : 0.041 0.185 1388 Planarity : 0.003 0.042 1509 Dihedral : 3.716 22.816 1213 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.04 % Allowed : 19.65 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.79 (0.26), residues: 1109 helix: 2.27 (0.27), residues: 389 sheet: 0.01 (0.29), residues: 286 loop : -0.70 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS A 189 PHE 0.009 0.001 PHE B 234 TYR 0.024 0.001 TYR R 197 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 94 ASP cc_start: 0.5816 (t0) cc_final: 0.5450 (t0) REVERT: R 250 MET cc_start: 0.8245 (mtt) cc_final: 0.7719 (mtt) REVERT: A 24 LYS cc_start: 0.6775 (tptp) cc_final: 0.6004 (tmmt) REVERT: A 55 ILE cc_start: 0.5720 (OUTLIER) cc_final: 0.5498 (mt) REVERT: A 273 ASP cc_start: 0.7638 (p0) cc_final: 0.7382 (t0) REVERT: A 291 TYR cc_start: 0.5260 (t80) cc_final: 0.4923 (t80) REVERT: A 309 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7114 (mt-10) REVERT: A 349 ARG cc_start: 0.6722 (OUTLIER) cc_final: 0.6414 (tpp-160) REVERT: B 247 ASP cc_start: 0.8028 (t0) cc_final: 0.7824 (t0) REVERT: G 15 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7795 (tt) REVERT: S 168 ARG cc_start: 0.7863 (mpt180) cc_final: 0.7564 (mpt180) outliers start: 28 outliers final: 21 residues processed: 141 average time/residue: 0.1925 time to fit residues: 39.5334 Evaluate side-chains 139 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 279 THR Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 174 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 150 HIS A 245 HIS B 220 GLN B 239 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.183492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.150059 restraints weight = 11339.460| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.56 r_work: 0.3732 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8806 Z= 0.207 Angle : 0.530 7.302 11954 Z= 0.283 Chirality : 0.042 0.204 1388 Planarity : 0.003 0.042 1509 Dihedral : 3.842 24.101 1213 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.15 % Allowed : 19.87 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1109 helix: 2.31 (0.27), residues: 383 sheet: 0.05 (0.30), residues: 280 loop : -0.81 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 189 PHE 0.011 0.001 PHE R 130 TYR 0.026 0.001 TYR R 197 ARG 0.004 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 94 ASP cc_start: 0.6114 (t0) cc_final: 0.5701 (t0) REVERT: R 250 MET cc_start: 0.8313 (mtt) cc_final: 0.8039 (mtt) REVERT: A 218 ASP cc_start: 0.8465 (m-30) cc_final: 0.8011 (p0) REVERT: A 309 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7252 (mt-10) REVERT: A 318 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7935 (mm-30) REVERT: A 349 ARG cc_start: 0.6813 (OUTLIER) cc_final: 0.6509 (tpp-160) REVERT: B 247 ASP cc_start: 0.8118 (t0) cc_final: 0.7840 (t0) REVERT: G 15 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7842 (tt) REVERT: S 109 ASP cc_start: 0.8268 (p0) cc_final: 0.8021 (p0) REVERT: S 168 ARG cc_start: 0.7974 (mpt180) cc_final: 0.7651 (mpt180) outliers start: 29 outliers final: 24 residues processed: 135 average time/residue: 0.1799 time to fit residues: 34.9793 Evaluate side-chains 146 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 279 THR Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 180 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 150 HIS B 239 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.190868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.158829 restraints weight = 11192.193| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.50 r_work: 0.3727 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8806 Z= 0.178 Angle : 0.516 7.405 11954 Z= 0.277 Chirality : 0.042 0.195 1388 Planarity : 0.003 0.040 1509 Dihedral : 3.826 24.045 1213 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.71 % Allowed : 20.74 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.76 (0.26), residues: 1109 helix: 2.24 (0.27), residues: 390 sheet: 0.04 (0.29), residues: 280 loop : -0.76 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 189 PHE 0.011 0.001 PHE B 241 TYR 0.024 0.001 TYR S 178 ARG 0.003 0.000 ARG B 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 94 ASP cc_start: 0.6075 (t0) cc_final: 0.5660 (t0) REVERT: R 250 MET cc_start: 0.8312 (mtt) cc_final: 0.8039 (mtt) REVERT: A 24 LYS cc_start: 0.6905 (tptp) cc_final: 0.6127 (tmmt) REVERT: A 55 ILE cc_start: 0.5951 (OUTLIER) cc_final: 0.5696 (mt) REVERT: A 309 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7267 (mt-10) REVERT: A 318 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7882 (mm-30) REVERT: A 349 ARG cc_start: 0.6765 (OUTLIER) cc_final: 0.6468 (tpp-160) REVERT: B 247 ASP cc_start: 0.8064 (t0) cc_final: 0.7802 (t0) REVERT: G 15 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7960 (tt) REVERT: S 109 ASP cc_start: 0.8186 (p0) cc_final: 0.7966 (p0) REVERT: S 168 ARG cc_start: 0.7956 (mpt180) cc_final: 0.7623 (mpt180) outliers start: 25 outliers final: 20 residues processed: 134 average time/residue: 0.1834 time to fit residues: 35.4712 Evaluate side-chains 141 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 142 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 279 THR Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 174 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 96 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 150 HIS B 220 GLN B 239 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.190653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.157890 restraints weight = 11420.146| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.60 r_work: 0.3713 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8806 Z= 0.187 Angle : 0.521 8.162 11954 Z= 0.279 Chirality : 0.042 0.198 1388 Planarity : 0.003 0.041 1509 Dihedral : 3.854 24.290 1213 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.82 % Allowed : 20.30 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.75 (0.26), residues: 1109 helix: 2.23 (0.27), residues: 389 sheet: 0.03 (0.30), residues: 280 loop : -0.74 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.003 0.001 HIS A 189 PHE 0.010 0.001 PHE B 241 TYR 0.026 0.001 TYR R 197 ARG 0.003 0.000 ARG B 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4039.95 seconds wall clock time: 70 minutes 1.77 seconds (4201.77 seconds total)