Starting phenix.real_space_refine on Wed Feb 14 08:19:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hoc_34925/02_2024/8hoc_34925_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hoc_34925/02_2024/8hoc_34925.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hoc_34925/02_2024/8hoc_34925_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hoc_34925/02_2024/8hoc_34925_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hoc_34925/02_2024/8hoc_34925_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hoc_34925/02_2024/8hoc_34925.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hoc_34925/02_2024/8hoc_34925.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hoc_34925/02_2024/8hoc_34925_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hoc_34925/02_2024/8hoc_34925_updated.pdb" } resolution = 3.0 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= -0.004 sd= 0.105 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 60 5.16 5 C 5707 2.51 5 N 1497 2.21 5 O 1654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 20": "OD1" <-> "OD2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 231": "OD1" <-> "OD2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8918 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1811 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2280 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 10, 'TRANS': 265} Chain breaks: 1 Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'ITF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.35, per 1000 atoms: 0.60 Number of scatterers: 8918 At special positions: 0 Unit cell: (94.64, 121.68, 131.04, 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 60 16.00 O 1654 8.00 N 1497 7.00 C 5707 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 87 " - pdb=" SG CYS R 164 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 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 - 3.50 Amino acid : False - 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: 3.47 Conformation dependent library (CDL) restraints added in 1.9 seconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 12 sheets defined 33.7% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 4.199A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.895A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 310 removed outlier: 3.639A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.759A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 41 Processing helix chain 'R' and resid 14 through 42 Processing helix chain 'R' and resid 51 through 76 removed outlier: 4.601A pdb=" N ILE R 69 " --> pdb=" O GLY R 65 " (cutoff:3.500A) Proline residue: R 70 - end of helix Proline residue: R 74 - end of helix Processing helix chain 'R' and resid 84 through 117 removed outlier: 3.884A pdb=" N VAL R 88 " --> pdb=" O LYS R 84 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE R 89 " --> pdb=" O GLU R 85 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE R 105 " --> pdb=" O SER R 101 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL R 106 " --> pdb=" O VAL R 102 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU R 107 " --> pdb=" O TYR R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 123 Processing helix chain 'R' and resid 129 through 156 removed outlier: 4.167A pdb=" N ASN R 147 " --> pdb=" O ALA R 143 " (cutoff:3.500A) Proline residue: R 149 - end of helix removed outlier: 4.710A pdb=" N SER R 156 " --> pdb=" O LEU R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 204 removed outlier: 4.837A pdb=" N VAL R 185 " --> pdb=" O LEU R 181 " (cutoff:3.500A) Proline residue: R 186 - end of helix Processing helix chain 'R' and resid 293 through 328 removed outlier: 3.922A pdb=" N LEU R 308 " --> pdb=" O SER R 304 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) Proline residue: R 318 - end of helix removed outlier: 3.796A pdb=" N PHE R 328 " --> pdb=" O ILE R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 357 removed outlier: 3.826A pdb=" N GLN R 347 " --> pdb=" O ALA R 343 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TRP R 348 " --> pdb=" O PHE R 344 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER R 351 " --> pdb=" O GLN R 347 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE R 352 " --> pdb=" O TRP R 348 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL R 353 " --> pdb=" O PHE R 349 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN R 354 " --> pdb=" O ASN R 350 " (cutoff:3.500A) Proline residue: R 355 - end of helix Processing helix chain 'R' and resid 365 through 373 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 324 removed outlier: 6.915A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR A 324 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 268 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.940A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.910A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.930A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.065A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.731A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.805A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.261A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 143 through 147 removed outlier: 4.187A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 214 through 219 removed outlier: 3.659A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1125 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: 2.81 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2844 1.34 - 1.46: 2255 1.46 - 1.58: 3935 1.58 - 1.70: 0 1.70 - 1.82: 87 Bond restraints: 9121 Sorted by residual: bond pdb=" C ASP S 74 " pdb=" N PRO S 75 " ideal model delta sigma weight residual 1.335 1.357 -0.021 1.36e-02 5.41e+03 2.48e+00 bond pdb=" N ARG A 205 " pdb=" CA ARG A 205 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.29e-02 6.01e+03 8.74e-01 bond pdb=" CA GLU R 182 " pdb=" CB GLU R 182 " ideal model delta sigma weight residual 1.529 1.541 -0.012 1.40e-02 5.10e+03 7.20e-01 bond pdb=" CA ARG A 205 " pdb=" C ARG A 205 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.34e-02 5.57e+03 6.17e-01 bond pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 1.457 1.467 -0.010 1.29e-02 6.01e+03 5.50e-01 ... (remaining 9116 not shown) Histogram of bond angle deviations from ideal: 98.89 - 105.91: 141 105.91 - 112.93: 4890 112.93 - 119.95: 3069 119.95 - 126.97: 4143 126.97 - 133.98: 112 Bond angle restraints: 12355 Sorted by residual: angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 121.54 129.79 -8.25 1.91e+00 2.74e-01 1.87e+01 angle pdb=" C LEU R 181 " pdb=" N GLU R 182 " pdb=" CA GLU R 182 " ideal model delta sigma weight residual 122.67 117.29 5.38 1.59e+00 3.96e-01 1.14e+01 angle pdb=" C ASP S 73 " pdb=" N ASP S 74 " pdb=" CA ASP S 74 " ideal model delta sigma weight residual 121.80 128.62 -6.82 2.44e+00 1.68e-01 7.81e+00 angle pdb=" N ASP A 261 " pdb=" CA ASP A 261 " pdb=" C ASP A 261 " ideal model delta sigma weight residual 114.56 111.25 3.31 1.27e+00 6.20e-01 6.79e+00 angle pdb=" C ASN S 77 " pdb=" N THR S 78 " pdb=" CA THR S 78 " ideal model delta sigma weight residual 122.29 118.13 4.16 1.65e+00 3.67e-01 6.35e+00 ... (remaining 12350 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.28: 4766 15.28 - 30.55: 476 30.55 - 45.83: 103 45.83 - 61.10: 18 61.10 - 76.38: 10 Dihedral angle restraints: 5373 sinusoidal: 2096 harmonic: 3277 Sorted by residual: dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 155.42 24.58 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA LEU A 273 " pdb=" C LEU A 273 " pdb=" N PHE A 274 " pdb=" CA PHE A 274 " ideal model delta harmonic sigma weight residual 180.00 162.69 17.31 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASP B 212 " pdb=" CB ASP B 212 " pdb=" CG ASP B 212 " pdb=" OD1 ASP B 212 " ideal model delta sinusoidal sigma weight residual -30.00 -85.54 55.54 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 5370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 861 0.030 - 0.060: 338 0.060 - 0.090: 114 0.090 - 0.120: 58 0.120 - 0.151: 10 Chirality restraints: 1381 Sorted by residual: chirality pdb=" CA GLU R 182 " pdb=" N GLU R 182 " pdb=" C GLU R 182 " pdb=" CB GLU R 182 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 1378 not shown) Planarity restraints: 1556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 180 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C PHE R 180 " 0.033 2.00e-02 2.50e+03 pdb=" O PHE R 180 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU R 181 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET G 38 " 0.008 2.00e-02 2.50e+03 1.57e-02 2.46e+00 pdb=" C MET G 38 " -0.027 2.00e-02 2.50e+03 pdb=" O MET G 38 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA G 39 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY R 148 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.16e+00 pdb=" N PRO R 149 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO R 149 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 149 " 0.021 5.00e-02 4.00e+02 ... (remaining 1553 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1505 2.77 - 3.30: 8229 3.30 - 3.83: 14026 3.83 - 4.37: 16523 4.37 - 4.90: 30058 Nonbonded interactions: 70341 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.234 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.309 2.440 nonbonded pdb=" O LEU A 232 " pdb=" ND2 ASN A 241 " model vdw 2.327 2.520 nonbonded pdb=" NH2 ARG R 49 " pdb=" O TYR R 122 " model vdw 2.331 2.520 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.343 2.440 ... (remaining 70336 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.920 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: 4.030 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 29.820 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 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 : 0.002 0.021 9121 Z= 0.129 Angle : 0.519 8.250 12355 Z= 0.283 Chirality : 0.040 0.151 1381 Planarity : 0.003 0.037 1556 Dihedral : 13.067 76.381 3250 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: 0.94 (0.26), residues: 1111 helix: 2.25 (0.28), residues: 380 sheet: 0.03 (0.32), residues: 276 loop : -0.34 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.015 0.001 PHE R 322 TYR 0.008 0.001 TYR S 178 ARG 0.002 0.000 ARG S 179 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.042 Fit side-chains REVERT: R 154 SER cc_start: 0.7490 (p) cc_final: 0.7243 (p) REVERT: S 211 ASP cc_start: 0.7887 (m-30) cc_final: 0.7378 (m-30) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 1.1160 time to fit residues: 193.6681 Evaluate side-chains 128 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 0.3980 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.0670 chunk 64 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.0714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9121 Z= 0.144 Angle : 0.490 7.150 12355 Z= 0.255 Chirality : 0.040 0.154 1381 Planarity : 0.003 0.036 1556 Dihedral : 4.083 57.819 1222 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.65 % Allowed : 9.59 % Favored : 88.76 % 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: 0.96 (0.26), residues: 1111 helix: 2.19 (0.27), residues: 388 sheet: -0.01 (0.32), residues: 280 loop : -0.25 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.010 0.001 PHE A 189 TYR 0.007 0.001 TYR S 178 ARG 0.003 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 1.011 Fit side-chains REVERT: R 154 SER cc_start: 0.7554 (p) cc_final: 0.7297 (p) REVERT: R 182 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7342 (pm20) REVERT: S 211 ASP cc_start: 0.7988 (m-30) cc_final: 0.7433 (m-30) outliers start: 16 outliers final: 7 residues processed: 136 average time/residue: 1.1208 time to fit residues: 163.8097 Evaluate side-chains 133 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 182 GLU Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 9121 Z= 0.242 Angle : 0.539 7.686 12355 Z= 0.282 Chirality : 0.042 0.145 1381 Planarity : 0.004 0.050 1556 Dihedral : 4.383 59.020 1222 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.58 % Allowed : 11.44 % Favored : 85.98 % 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: 0.82 (0.26), residues: 1111 helix: 2.09 (0.27), residues: 388 sheet: -0.01 (0.32), residues: 272 loop : -0.40 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.016 0.002 PHE R 168 TYR 0.016 0.001 TYR S 163 ARG 0.003 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 1.144 Fit side-chains REVERT: A 25 GLU cc_start: 0.7490 (tm-30) cc_final: 0.7258 (tm-30) REVERT: A 231 ASP cc_start: 0.8358 (t0) cc_final: 0.7970 (t0) REVERT: A 270 LYS cc_start: 0.8577 (mttm) cc_final: 0.8289 (mmtm) REVERT: B 262 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7635 (ttm) REVERT: R 154 SER cc_start: 0.7644 (p) cc_final: 0.7405 (p) REVERT: S 211 ASP cc_start: 0.8064 (m-30) cc_final: 0.7518 (m-30) outliers start: 25 outliers final: 10 residues processed: 143 average time/residue: 1.2139 time to fit residues: 185.7529 Evaluate side-chains 138 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9980 chunk 75 optimal weight: 0.0370 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 0.0070 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9121 Z= 0.202 Angle : 0.522 7.915 12355 Z= 0.273 Chirality : 0.041 0.143 1381 Planarity : 0.004 0.051 1556 Dihedral : 4.318 58.346 1222 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.89 % Allowed : 13.92 % Favored : 83.20 % 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: 0.81 (0.26), residues: 1111 helix: 2.11 (0.27), residues: 387 sheet: -0.07 (0.32), residues: 274 loop : -0.40 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.011 0.001 PHE A 189 TYR 0.011 0.001 TYR S 163 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 1.070 Fit side-chains REVERT: A 25 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7249 (tm-30) REVERT: A 231 ASP cc_start: 0.8336 (t0) cc_final: 0.7936 (t0) REVERT: A 270 LYS cc_start: 0.8586 (mttm) cc_final: 0.8305 (mmtm) REVERT: B 262 MET cc_start: 0.7892 (ttm) cc_final: 0.7665 (ttm) REVERT: R 154 SER cc_start: 0.7626 (p) cc_final: 0.7371 (p) REVERT: S 211 ASP cc_start: 0.8126 (m-30) cc_final: 0.7553 (m-30) outliers start: 28 outliers final: 15 residues processed: 139 average time/residue: 1.2353 time to fit residues: 183.5177 Evaluate side-chains 138 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9121 Z= 0.232 Angle : 0.548 9.192 12355 Z= 0.284 Chirality : 0.042 0.141 1381 Planarity : 0.004 0.051 1556 Dihedral : 4.367 57.854 1222 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.89 % Allowed : 15.36 % Favored : 81.75 % 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: 1111 helix: 2.07 (0.27), residues: 387 sheet: -0.09 (0.32), residues: 274 loop : -0.45 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE R 168 TYR 0.015 0.001 TYR S 163 ARG 0.004 0.000 ARG R 334 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 125 time to evaluate : 0.985 Fit side-chains REVERT: A 231 ASP cc_start: 0.8339 (t0) cc_final: 0.7982 (t0) REVERT: A 234 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7452 (tt) REVERT: A 270 LYS cc_start: 0.8619 (mttm) cc_final: 0.8348 (mmtm) REVERT: B 262 MET cc_start: 0.7860 (ttm) cc_final: 0.7617 (ttm) REVERT: G 38 MET cc_start: 0.8034 (mtm) cc_final: 0.7819 (mtp) REVERT: R 154 SER cc_start: 0.8082 (p) cc_final: 0.7878 (p) REVERT: S 171 GLN cc_start: 0.8186 (mt0) cc_final: 0.7926 (mt0) REVERT: S 211 ASP cc_start: 0.8066 (m-30) cc_final: 0.7549 (m-30) outliers start: 28 outliers final: 16 residues processed: 136 average time/residue: 1.3694 time to fit residues: 198.7874 Evaluate side-chains 140 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 0.0170 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9121 Z= 0.169 Angle : 0.517 8.354 12355 Z= 0.268 Chirality : 0.040 0.142 1381 Planarity : 0.004 0.052 1556 Dihedral : 4.239 55.063 1222 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.89 % Allowed : 15.88 % Favored : 81.24 % 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: 0.84 (0.26), residues: 1111 helix: 2.18 (0.27), residues: 384 sheet: -0.11 (0.31), residues: 279 loop : -0.36 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.010 0.001 PHE A 189 TYR 0.011 0.001 TYR B 124 ARG 0.005 0.000 ARG R 334 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 1.047 Fit side-chains REVERT: A 25 GLU cc_start: 0.7378 (tm-30) cc_final: 0.7166 (tm-30) REVERT: A 231 ASP cc_start: 0.8337 (t0) cc_final: 0.8000 (t0) REVERT: A 234 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7482 (tt) REVERT: A 270 LYS cc_start: 0.8613 (mttm) cc_final: 0.8357 (mmtm) REVERT: B 262 MET cc_start: 0.7888 (ttm) cc_final: 0.7623 (ttm) REVERT: G 22 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8210 (tm-30) REVERT: G 38 MET cc_start: 0.7978 (mtm) cc_final: 0.7752 (mtp) REVERT: R 150 MET cc_start: 0.7735 (tpt) cc_final: 0.7454 (mmm) REVERT: S 171 GLN cc_start: 0.8191 (mt0) cc_final: 0.7953 (mt0) REVERT: S 211 ASP cc_start: 0.8121 (m-30) cc_final: 0.7598 (m-30) outliers start: 28 outliers final: 18 residues processed: 143 average time/residue: 1.2748 time to fit residues: 194.5617 Evaluate side-chains 146 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 89 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9121 Z= 0.178 Angle : 0.521 9.007 12355 Z= 0.270 Chirality : 0.041 0.146 1381 Planarity : 0.004 0.052 1556 Dihedral : 4.208 53.823 1222 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.30 % Allowed : 16.29 % Favored : 80.41 % 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: 0.87 (0.26), residues: 1111 helix: 2.20 (0.27), residues: 384 sheet: -0.07 (0.31), residues: 277 loop : -0.36 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.010 0.001 PHE A 189 TYR 0.011 0.001 TYR B 124 ARG 0.002 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 1.073 Fit side-chains REVERT: A 25 GLU cc_start: 0.7381 (tm-30) cc_final: 0.7169 (tm-30) REVERT: A 231 ASP cc_start: 0.8313 (t0) cc_final: 0.7999 (t0) REVERT: A 234 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7559 (tt) REVERT: A 270 LYS cc_start: 0.8613 (mttm) cc_final: 0.8364 (mmtm) REVERT: B 262 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7595 (ttm) REVERT: G 22 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8216 (tm-30) REVERT: G 38 MET cc_start: 0.7931 (mtm) cc_final: 0.7704 (mtp) REVERT: R 49 ARG cc_start: 0.6756 (OUTLIER) cc_final: 0.6442 (ttp-170) REVERT: R 182 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8093 (pm20) REVERT: S 171 GLN cc_start: 0.8194 (mt0) cc_final: 0.7955 (mt0) REVERT: S 211 ASP cc_start: 0.8135 (m-30) cc_final: 0.7580 (m-30) outliers start: 32 outliers final: 16 residues processed: 141 average time/residue: 1.2321 time to fit residues: 185.4797 Evaluate side-chains 141 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 49 ARG Chi-restraints excluded: chain R residue 182 GLU Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9121 Z= 0.294 Angle : 0.592 9.420 12355 Z= 0.306 Chirality : 0.043 0.144 1381 Planarity : 0.004 0.061 1556 Dihedral : 4.469 54.454 1222 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.20 % Allowed : 17.11 % Favored : 79.69 % 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: 0.65 (0.26), residues: 1111 helix: 1.98 (0.27), residues: 387 sheet: -0.14 (0.32), residues: 274 loop : -0.50 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.017 0.002 PHE R 168 TYR 0.022 0.002 TYR S 163 ARG 0.002 0.000 ARG R 334 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 125 time to evaluate : 1.076 Fit side-chains REVERT: A 231 ASP cc_start: 0.8384 (t0) cc_final: 0.8130 (t0) REVERT: A 270 LYS cc_start: 0.8651 (mttm) cc_final: 0.8392 (mmtm) REVERT: B 262 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7647 (ttm) REVERT: G 22 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8238 (tm-30) REVERT: R 49 ARG cc_start: 0.6824 (OUTLIER) cc_final: 0.6492 (ttp-170) REVERT: R 182 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8188 (pm20) REVERT: S 171 GLN cc_start: 0.8194 (mt0) cc_final: 0.7921 (mt0) REVERT: S 211 ASP cc_start: 0.8080 (m-30) cc_final: 0.7558 (m-30) outliers start: 31 outliers final: 17 residues processed: 140 average time/residue: 1.2496 time to fit residues: 186.4813 Evaluate side-chains 141 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 49 ARG Chi-restraints excluded: chain R residue 182 GLU Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.6980 chunk 101 optimal weight: 0.1980 chunk 59 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9121 Z= 0.164 Angle : 0.536 8.734 12355 Z= 0.279 Chirality : 0.041 0.141 1381 Planarity : 0.004 0.056 1556 Dihedral : 4.255 51.497 1222 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.47 % Allowed : 18.14 % Favored : 79.38 % 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: 0.83 (0.26), residues: 1111 helix: 2.17 (0.27), residues: 382 sheet: -0.01 (0.32), residues: 272 loop : -0.43 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 PHE 0.010 0.001 PHE A 189 TYR 0.010 0.001 TYR B 124 ARG 0.016 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 1.017 Fit side-chains REVERT: A 231 ASP cc_start: 0.8324 (t0) cc_final: 0.8112 (t0) REVERT: A 270 LYS cc_start: 0.8637 (mttm) cc_final: 0.8393 (mmtm) REVERT: B 61 MET cc_start: 0.8860 (ppp) cc_final: 0.8537 (ptm) REVERT: B 262 MET cc_start: 0.7841 (ttm) cc_final: 0.7582 (ttm) REVERT: G 22 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8242 (tm-30) REVERT: R 49 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.6432 (ttp-170) REVERT: S 171 GLN cc_start: 0.8210 (mt0) cc_final: 0.7935 (mt0) REVERT: S 211 ASP cc_start: 0.8051 (m-30) cc_final: 0.7531 (m-30) outliers start: 24 outliers final: 15 residues processed: 133 average time/residue: 1.1998 time to fit residues: 170.7231 Evaluate side-chains 136 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 49 ARG Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 0.3980 chunk 100 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9121 Z= 0.218 Angle : 0.565 9.435 12355 Z= 0.292 Chirality : 0.042 0.144 1381 Planarity : 0.004 0.059 1556 Dihedral : 4.294 51.333 1222 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.06 % Allowed : 18.76 % Favored : 79.18 % 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: 1111 helix: 2.08 (0.27), residues: 384 sheet: -0.09 (0.32), residues: 274 loop : -0.45 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE R 168 TYR 0.012 0.001 TYR B 124 ARG 0.011 0.000 ARG S 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 1.066 Fit side-chains REVERT: A 231 ASP cc_start: 0.8371 (t0) cc_final: 0.8169 (t0) REVERT: A 270 LYS cc_start: 0.8639 (mttm) cc_final: 0.8394 (mmtm) REVERT: B 262 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7605 (ttm) REVERT: G 22 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8259 (tm-30) REVERT: R 49 ARG cc_start: 0.6759 (OUTLIER) cc_final: 0.6448 (ttp-170) REVERT: S 171 GLN cc_start: 0.8173 (mt0) cc_final: 0.7892 (mt0) REVERT: S 211 ASP cc_start: 0.8069 (m-30) cc_final: 0.7542 (m-30) outliers start: 20 outliers final: 15 residues processed: 128 average time/residue: 1.2775 time to fit residues: 174.1504 Evaluate side-chains 134 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 30 MET Chi-restraints excluded: chain R residue 49 ARG Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 0.0060 chunk 63 optimal weight: 0.0770 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.148609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110888 restraints weight = 10995.931| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.37 r_work: 0.3155 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9121 Z= 0.160 Angle : 0.534 9.176 12355 Z= 0.277 Chirality : 0.041 0.148 1381 Planarity : 0.004 0.057 1556 Dihedral : 4.162 49.070 1222 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.75 % Allowed : 19.18 % Favored : 79.07 % 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: 0.85 (0.26), residues: 1111 helix: 2.18 (0.27), residues: 382 sheet: -0.00 (0.32), residues: 273 loop : -0.42 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.011 0.001 PHE A 189 TYR 0.009 0.001 TYR B 124 ARG 0.016 0.000 ARG S 148 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3589.67 seconds wall clock time: 64 minutes 27.96 seconds (3867.96 seconds total)