Starting phenix.real_space_refine on Thu Feb 13 03:03:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xxr_38759/02_2025/8xxr_38759.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xxr_38759/02_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_38759/02_2025/8xxr_38759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xxr_38759/02_2025/8xxr_38759.map" model { file = "/net/cci-nas-00/data/ceres_data/8xxr_38759/02_2025/8xxr_38759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xxr_38759/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.09, per 1000 atoms: 0.59 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 1.0 seconds 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: 1.14 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: 2.66 Time building geometry restraints manager: 2.48 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: 0.590 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.430 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.510 ------------------------------------------------------------------------------- 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 : 1.168 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: 0.1777 time to fit residues: 31.8186 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 : 1.015 ------------------------------------------------------------------------------- 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 = 0.147148 restraints weight = 11249.156| |-----------------------------------------------------------------------------| 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 : 0.940 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: 0.8249 (m-80) REVERT: B 76 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7941 (p0) REVERT: S 168 ARG cc_start: 0.7935 (mpt180) cc_final: 0.7390 (mpt180) outliers start: 20 outliers final: 11 residues processed: 142 average time/residue: 0.1693 time to fit residues: 35.5841 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 : 1.024 ------------------------------------------------------------------------------- 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: 0.0770 chunk 67 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- 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 = 0.4185 r_free = 0.4185 target = 0.181105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.147835 restraints weight = 11306.771| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.41 r_work: 0.3668 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8806 Z= 0.315 Angle : 0.594 7.465 11954 Z= 0.316 Chirality : 0.044 0.233 1388 Planarity : 0.004 0.041 1509 Dihedral : 4.732 44.460 1217 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.61 % Allowed : 17.59 % Favored : 79.80 % 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: 0.32 (0.26), residues: 1109 helix: 1.95 (0.27), residues: 383 sheet: -0.38 (0.29), residues: 310 loop : -0.91 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 211 HIS 0.004 0.001 HIS R 150 PHE 0.015 0.002 PHE R 130 TYR 0.030 0.002 TYR S 178 ARG 0.007 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 150 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.6910 (tptp) cc_final: 0.6187 (tmmt) REVERT: A 250 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8362 (mp) REVERT: A 309 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7343 (mt-10) REVERT: B 76 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.8029 (p0) REVERT: G 15 LEU cc_start: 0.8089 (tt) cc_final: 0.7827 (tt) REVERT: S 168 ARG cc_start: 0.8081 (mpt180) cc_final: 0.7799 (mtt90) REVERT: S 174 GLN cc_start: 0.8141 (mt0) cc_final: 0.7909 (pt0) REVERT: S 180 MET cc_start: 0.7184 (mmt) cc_final: 0.6783 (mmt) outliers start: 24 outliers final: 15 residues processed: 140 average time/residue: 0.1899 time to fit residues: 37.9063 Evaluate side-chains 140 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 SER 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 57 THR 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: 0.5980 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 7 optimal weight: 0.4980 chunk 25 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS R 206 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.192213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.158832 restraints weight = 11415.474| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.52 r_work: 0.3734 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8806 Z= 0.190 Angle : 0.521 7.797 11954 Z= 0.279 Chirality : 0.042 0.199 1388 Planarity : 0.003 0.040 1509 Dihedral : 4.505 45.506 1217 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.28 % Allowed : 18.57 % Favored : 79.15 % 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: 292 loop : -0.86 (0.30), residues: 434 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 0.010 0.001 PHE R 130 TYR 0.028 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 147 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 292 ILE cc_start: 0.7042 (OUTLIER) cc_final: 0.6649 (mm) REVERT: R 313 ILE cc_start: 0.7346 (OUTLIER) cc_final: 0.7140 (mt) REVERT: A 250 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8466 (mp) REVERT: A 309 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7204 (mt-10) REVERT: B 76 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7931 (p0) REVERT: G 15 LEU cc_start: 0.8096 (tt) cc_final: 0.7835 (tt) REVERT: S 168 ARG cc_start: 0.8034 (mpt180) cc_final: 0.7672 (mpt180) REVERT: S 174 GLN cc_start: 0.8069 (mt0) cc_final: 0.7825 (pt0) REVERT: S 180 MET cc_start: 0.7051 (mmt) cc_final: 0.6754 (mmt) outliers start: 21 outliers final: 14 residues processed: 140 average time/residue: 0.1632 time to fit residues: 34.0657 Evaluate side-chains 136 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 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 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 76 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 28 ILE 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: 3.9990 chunk 104 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS A 322 HIS B 220 GLN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.190356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.150406 restraints weight = 11452.187| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.59 r_work: 0.3686 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1629 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= 0.258 Angle : 0.558 7.528 11954 Z= 0.298 Chirality : 0.043 0.220 1388 Planarity : 0.003 0.041 1509 Dihedral : 4.559 44.418 1217 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.80 % Allowed : 17.92 % 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: 0.39 (0.26), residues: 1109 helix: 2.02 (0.27), residues: 383 sheet: -0.34 (0.30), residues: 286 loop : -0.86 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS R 150 PHE 0.012 0.001 PHE R 130 TYR 0.029 0.001 TYR S 178 ARG 0.004 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 166 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.6989 (tptp) cc_final: 0.6268 (tmmt) REVERT: A 218 ASP cc_start: 0.8496 (m-30) cc_final: 0.8024 (p0) REVERT: A 273 ASP cc_start: 0.7509 (p0) cc_final: 0.7275 (t0) REVERT: A 309 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7243 (mt-10) REVERT: A 318 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8047 (mm-30) REVERT: B 76 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7965 (p0) REVERT: G 15 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7821 (tt) outliers start: 35 outliers final: 21 residues processed: 153 average time/residue: 0.1949 time to fit residues: 42.3635 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 : 1.032 ------------------------------------------------------------------------------- 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 237 THR Chi-restraints excluded: chain R residue 238 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain A residue 38 LEU 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 A residue 318 GLU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 76 ASP 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 268 ASN Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL 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: 0.0030 chunk 90 optimal weight: 2.9990 chunk 52 optimal weight: 0.0030 chunk 62 optimal weight: 0.1980 chunk 26 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.3600 ------------------------------------------------------------------------------- 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 A 245 HIS B 220 GLN B 268 ASN ** S 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.192113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.154127 restraints weight = 11141.014| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.45 r_work: 0.3760 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8806 Z= 0.142 Angle : 0.507 8.830 11954 Z= 0.271 Chirality : 0.041 0.183 1388 Planarity : 0.003 0.040 1509 Dihedral : 4.182 45.701 1215 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.28 % Allowed : 19.11 % Favored : 78.61 % 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: 0.59 (0.26), residues: 1109 helix: 2.25 (0.27), residues: 383 sheet: -0.23 (0.29), residues: 289 loop : -0.83 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 189 PHE 0.009 0.001 PHE B 241 TYR 0.025 0.001 TYR S 178 ARG 0.003 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 149 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.6874 (tptp) cc_final: 0.6104 (tmmt) REVERT: A 55 ILE cc_start: 0.5746 (OUTLIER) cc_final: 0.5492 (mt) REVERT: A 218 ASP cc_start: 0.8463 (m-30) cc_final: 0.7967 (p0) REVERT: A 309 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7155 (mt-10) REVERT: B 76 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7989 (p0) REVERT: B 118 ASP cc_start: 0.8197 (m-30) cc_final: 0.7786 (m-30) REVERT: G 15 LEU cc_start: 0.8026 (tt) cc_final: 0.7797 (tt) outliers start: 21 outliers final: 13 residues processed: 144 average time/residue: 0.1774 time to fit residues: 37.6301 Evaluate side-chains 131 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 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 290 GLU Chi-restraints excluded: chain B residue 76 ASP 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 S residue 91 THR 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: 2.9990 chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 7 optimal weight: 0.0970 chunk 6 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 = 0.4218 r_free = 0.4218 target = 0.184897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.151851 restraints weight = 11280.919| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 2.56 r_work: 0.3719 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1826 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= 0.172 Angle : 0.517 7.000 11954 Z= 0.276 Chirality : 0.041 0.193 1388 Planarity : 0.003 0.040 1509 Dihedral : 4.134 44.853 1215 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.61 % Allowed : 20.20 % Favored : 77.20 % 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: 0.66 (0.26), residues: 1109 helix: 2.27 (0.27), residues: 383 sheet: -0.07 (0.30), residues: 280 loop : -0.84 (0.29), residues: 446 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 0.025 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 146 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 94 ASP cc_start: 0.5905 (t0) cc_final: 0.5619 (t0) REVERT: R 250 MET cc_start: 0.8303 (mtt) cc_final: 0.7751 (mtt) REVERT: A 24 LYS cc_start: 0.6892 (tptp) cc_final: 0.6119 (tmmt) REVERT: A 55 ILE cc_start: 0.5852 (OUTLIER) cc_final: 0.5598 (mt) REVERT: A 309 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7212 (mt-10) REVERT: B 76 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7976 (p0) REVERT: B 118 ASP cc_start: 0.8202 (m-30) cc_final: 0.7825 (m-30) REVERT: G 15 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7828 (tt) outliers start: 24 outliers final: 16 residues processed: 141 average time/residue: 0.1754 time to fit residues: 36.1633 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 : 0.971 ------------------------------------------------------------------------------- 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 214 LEU 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 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 B residue 76 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 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 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: 6.9990 chunk 93 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 0.0770 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 overall best weight: 1.1742 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.191347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.151170 restraints weight = 11633.820| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.60 r_work: 0.3697 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8806 Z= 0.228 Angle : 0.544 7.025 11954 Z= 0.290 Chirality : 0.043 0.212 1388 Planarity : 0.003 0.041 1509 Dihedral : 4.288 43.721 1215 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.93 % Allowed : 19.33 % Favored : 77.74 % 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: 0.59 (0.26), residues: 1109 helix: 2.22 (0.27), residues: 383 sheet: -0.15 (0.30), residues: 287 loop : -0.85 (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 0.013 0.001 PHE R 130 TYR 0.028 0.001 TYR S 178 ARG 0.004 0.000 ARG S 168 *********************** 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 157 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 94 ASP cc_start: 0.6186 (t0) cc_final: 0.5902 (t0) REVERT: R 250 MET cc_start: 0.8323 (mtt) cc_final: 0.7807 (mtt) REVERT: A 24 LYS cc_start: 0.6963 (tptp) cc_final: 0.6233 (tmmt) REVERT: A 211 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7318 (mmtt) REVERT: A 218 ASP cc_start: 0.8455 (m-30) cc_final: 0.8063 (p0) REVERT: A 309 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7252 (mt-10) REVERT: A 318 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7907 (mm-30) REVERT: B 76 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.8043 (p0) REVERT: B 118 ASP cc_start: 0.8238 (m-30) cc_final: 0.7911 (m-30) REVERT: G 15 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7811 (tt) REVERT: S 180 MET cc_start: 0.7596 (tpt) cc_final: 0.7265 (tpt) outliers start: 27 outliers final: 19 residues processed: 152 average time/residue: 0.1945 time to fit residues: 41.8180 Evaluate side-chains 146 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 238 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 279 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 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 91 THR Chi-restraints excluded: chain S residue 166 LEU 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: 0.8980 chunk 81 optimal weight: 0.0770 chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 = 0.4260 r_free = 0.4260 target = 0.190824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.158190 restraints weight = 11341.542| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.57 r_work: 0.3702 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.1961 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= 0.172 Angle : 0.530 7.972 11954 Z= 0.282 Chirality : 0.042 0.196 1388 Planarity : 0.003 0.041 1509 Dihedral : 4.201 44.029 1215 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.71 % Allowed : 20.85 % Favored : 76.44 % 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: 0.66 (0.26), residues: 1109 helix: 2.26 (0.27), residues: 384 sheet: -0.02 (0.30), residues: 280 loop : -0.87 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 189 PHE 0.011 0.001 PHE R 164 TYR 0.028 0.001 TYR R 197 ARG 0.003 0.000 ARG A 349 *********************** 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 143 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 250 MET cc_start: 0.8384 (mtt) cc_final: 0.7843 (mtt) REVERT: A 24 LYS cc_start: 0.6926 (tptp) cc_final: 0.6148 (tmmt) REVERT: A 55 ILE cc_start: 0.6020 (OUTLIER) cc_final: 0.5787 (mt) REVERT: A 211 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7301 (mmtt) REVERT: A 218 ASP cc_start: 0.8465 (m-30) cc_final: 0.7988 (p0) REVERT: A 309 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7291 (mt-10) REVERT: B 76 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.8014 (p0) REVERT: B 118 ASP cc_start: 0.8224 (m-30) cc_final: 0.7920 (m-30) REVERT: G 15 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7803 (tt) outliers start: 25 outliers final: 17 residues processed: 138 average time/residue: 0.1828 time to fit residues: 36.5823 Evaluate side-chains 137 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 238 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 279 THR Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 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 91 THR Chi-restraints excluded: chain S residue 166 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 71 optimal weight: 0.2980 chunk 80 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4260 r_free = 0.4260 target = 0.191285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.158079 restraints weight = 11268.121| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.50 r_work: 0.3719 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2017 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= 0.177 Angle : 0.544 9.717 11954 Z= 0.285 Chirality : 0.042 0.195 1388 Planarity : 0.003 0.041 1509 Dihedral : 4.185 43.961 1215 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.61 % Allowed : 20.63 % Favored : 76.76 % 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: 0.66 (0.26), residues: 1109 helix: 2.25 (0.27), residues: 383 sheet: -0.05 (0.30), residues: 281 loop : -0.83 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS R 150 PHE 0.013 0.001 PHE B 241 TYR 0.026 0.001 TYR S 178 ARG 0.006 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 144 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 250 MET cc_start: 0.8379 (mtt) cc_final: 0.7854 (mtt) REVERT: A 24 LYS cc_start: 0.6926 (tptp) cc_final: 0.6148 (tmmt) REVERT: A 211 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7298 (mmtt) REVERT: A 218 ASP cc_start: 0.8452 (m-30) cc_final: 0.7974 (p0) REVERT: A 249 MET cc_start: 0.7539 (tpp) cc_final: 0.7293 (tpp) REVERT: A 309 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7276 (mt-10) REVERT: B 118 ASP cc_start: 0.8273 (m-30) cc_final: 0.7962 (m-30) REVERT: G 15 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7936 (tt) REVERT: S 180 MET cc_start: 0.7551 (mmm) cc_final: 0.7332 (tpp) outliers start: 24 outliers final: 17 residues processed: 139 average time/residue: 0.1719 time to fit residues: 35.2468 Evaluate side-chains 135 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 238 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 279 THR Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 191 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 91 THR Chi-restraints excluded: chain S residue 166 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 96 optimal weight: 0.0770 chunk 30 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 35 optimal weight: 0.0870 chunk 105 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4275 r_free = 0.4275 target = 0.192964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.154941 restraints weight = 11442.262| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.48 r_work: 0.3751 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8806 Z= 0.144 Angle : 0.529 9.577 11954 Z= 0.278 Chirality : 0.041 0.180 1388 Planarity : 0.003 0.041 1509 Dihedral : 3.862 23.318 1213 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.95 % Allowed : 21.61 % Favored : 76.44 % 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: 0.73 (0.26), residues: 1109 helix: 2.24 (0.27), residues: 390 sheet: 0.03 (0.30), residues: 279 loop : -0.79 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS R 150 PHE 0.009 0.001 PHE B 234 TYR 0.024 0.001 TYR R 197 ARG 0.003 0.000 ARG S 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4320.08 seconds wall clock time: 77 minutes 23.65 seconds (4643.65 seconds total)