Starting phenix.real_space_refine on Fri Nov 15 15:50:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6r_36012/11_2024/8j6r_36012.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6r_36012/11_2024/8j6r_36012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6r_36012/11_2024/8j6r_36012.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6r_36012/11_2024/8j6r_36012.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6r_36012/11_2024/8j6r_36012.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6r_36012/11_2024/8j6r_36012.cif" } resolution = 2.76 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= 0.002 sd= 0.034 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 69 5.16 5 C 5811 2.51 5 N 1554 2.21 5 O 1686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9120 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: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "S" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1795 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Chain: "R" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2420 Classifications: {'peptide': 295} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 284} Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'FI7': 1, 'NAG': 1} Classifications: {'undetermined': 2, 'water': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.45, per 1000 atoms: 0.60 Number of scatterers: 9120 At special positions: 0 Unit cell: (108.498, 122.694, 112.554, 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 69 16.00 O 1686 8.00 N 1554 7.00 C 5811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.04 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " 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 Links applied NAG-ASN " NAG R 402 " - " ASN R 17 " Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.1 seconds 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 37.9% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.387A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.691A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 removed outlier: 4.512A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.242A 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 87 through 91 removed outlier: 3.648A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.581A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 23 through 55 removed outlier: 4.010A pdb=" N VAL R 27 " --> pdb=" O ASP R 23 " (cutoff:3.500A) Proline residue: R 31 - end of helix Processing helix chain 'R' and resid 60 through 78 Processing helix chain 'R' and resid 79 through 89 removed outlier: 3.923A pdb=" N LEU R 83 " --> pdb=" O CYS R 79 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG R 89 " --> pdb=" O ASP R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 130 removed outlier: 3.756A pdb=" N CYS R 100 " --> pdb=" O GLY R 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 139 removed outlier: 3.615A pdb=" N ILE R 139 " --> pdb=" O LEU R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 160 Processing helix chain 'R' and resid 161 through 163 No H-bonds generated for 'chain 'R' and resid 161 through 163' Processing helix chain 'R' and resid 187 through 218 removed outlier: 3.798A pdb=" N LEU R 194 " --> pdb=" O GLU R 190 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Proline residue: R 200 - end of helix Processing helix chain 'R' and resid 219 through 222 removed outlier: 4.105A pdb=" N ARG R 222 " --> pdb=" O GLN R 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 219 through 222' Processing helix chain 'R' and resid 223 through 261 Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 265 through 268 removed outlier: 3.863A pdb=" N VAL R 268 " --> pdb=" O ASN R 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 265 through 268' Processing helix chain 'R' and resid 269 through 295 removed outlier: 3.812A pdb=" N PHE R 277 " --> pdb=" O ASP R 273 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER R 287 " --> pdb=" O THR R 283 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.699A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.569A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.970A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.104A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.558A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.850A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.599A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.581A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.961A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.961A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141 removed outlier: 3.786A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.540A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 10 through 11 removed outlier: 4.034A pdb=" N CYS R 18 " --> pdb=" O LEU R 11 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 169 through 170 442 hydrogen bonds defined for protein. 1227 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: 2.61 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2928 1.34 - 1.46: 2278 1.46 - 1.58: 4012 1.58 - 1.71: 1 1.71 - 1.83: 100 Bond restraints: 9319 Sorted by residual: bond pdb=" C20 FI7 R 401 " pdb=" N19 FI7 R 401 " ideal model delta sigma weight residual 1.396 1.486 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C07 FI7 R 401 " pdb=" C08 FI7 R 401 " ideal model delta sigma weight residual 1.466 1.546 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C04 FI7 R 401 " pdb=" C05 FI7 R 401 " ideal model delta sigma weight residual 1.483 1.563 -0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C05 FI7 R 401 " pdb=" O16 FI7 R 401 " ideal model delta sigma weight residual 1.330 1.406 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C17 FI7 R 401 " pdb=" N19 FI7 R 401 " ideal model delta sigma weight residual 1.348 1.420 -0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 9314 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 12395 2.03 - 4.06: 168 4.06 - 6.08: 38 6.08 - 8.11: 7 8.11 - 10.14: 2 Bond angle restraints: 12610 Sorted by residual: angle pdb=" C MET R 167 " pdb=" N PRO R 168 " pdb=" CA PRO R 168 " ideal model delta sigma weight residual 127.00 136.86 -9.86 2.40e+00 1.74e-01 1.69e+01 angle pdb=" C ASP R 14 " pdb=" N LYS R 15 " pdb=" CA LYS R 15 " ideal model delta sigma weight residual 121.54 129.12 -7.58 1.91e+00 2.74e-01 1.57e+01 angle pdb=" C MET R 167 " pdb=" N PRO R 168 " pdb=" CD PRO R 168 " ideal model delta sigma weight residual 120.60 112.67 7.93 2.20e+00 2.07e-01 1.30e+01 angle pdb=" C02 FI7 R 401 " pdb=" C17 FI7 R 401 " pdb=" N19 FI7 R 401 " ideal model delta sigma weight residual 113.44 123.58 -10.14 3.00e+00 1.11e-01 1.14e+01 angle pdb=" N HIS R 184 " pdb=" CA HIS R 184 " pdb=" C HIS R 184 " ideal model delta sigma weight residual 111.30 115.76 -4.46 1.36e+00 5.41e-01 1.08e+01 ... (remaining 12605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 4976 16.57 - 33.13: 451 33.13 - 49.70: 102 49.70 - 66.26: 17 66.26 - 82.83: 7 Dihedral angle restraints: 5553 sinusoidal: 2218 harmonic: 3335 Sorted by residual: dihedral pdb=" CB CYS R 100 " pdb=" SG CYS R 100 " pdb=" SG CYS R 177 " pdb=" CB CYS R 177 " ideal model delta sinusoidal sigma weight residual 93.00 138.69 -45.69 1 1.00e+01 1.00e-02 2.89e+01 dihedral pdb=" CB CYS R 18 " pdb=" SG CYS R 18 " pdb=" SG CYS R 183 " pdb=" CB CYS R 183 " ideal model delta sinusoidal sigma weight residual 93.00 53.83 39.17 1 1.00e+01 1.00e-02 2.16e+01 dihedral pdb=" CA PHE A 323 " pdb=" C PHE A 323 " pdb=" N THR A 324 " pdb=" CA THR A 324 " ideal model delta harmonic sigma weight residual -180.00 -160.03 -19.97 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 5550 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.244: 1411 0.244 - 0.489: 0 0.489 - 0.733: 0 0.733 - 0.977: 0 0.977 - 1.222: 1 Chirality restraints: 1412 Sorted by residual: chirality pdb=" C1 NAG R 402 " pdb=" ND2 ASN R 17 " pdb=" C2 NAG R 402 " pdb=" O5 NAG R 402 " both_signs ideal model delta sigma weight residual False -2.40 -1.18 -1.22 2.00e-01 2.50e+01 3.73e+01 chirality pdb=" CA TRP R 59 " pdb=" N TRP R 59 " pdb=" C TRP R 59 " pdb=" CB TRP R 59 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA TYR S 190 " pdb=" N TYR S 190 " pdb=" C TYR S 190 " pdb=" CB TYR S 190 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1409 not shown) Planarity restraints: 1595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 402 " 0.350 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG R 402 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG R 402 " 0.154 2.00e-02 2.50e+03 pdb=" N2 NAG R 402 " -0.533 2.00e-02 2.50e+03 pdb=" O7 NAG R 402 " 0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.059 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO S 75 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN R 17 " 0.026 2.00e-02 2.50e+03 2.89e-02 1.05e+01 pdb=" CG ASN R 17 " -0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN R 17 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN R 17 " -0.047 2.00e-02 2.50e+03 pdb=" C1 NAG R 402 " 0.035 2.00e-02 2.50e+03 ... (remaining 1592 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 137 2.67 - 3.23: 8076 3.23 - 3.79: 13912 3.79 - 4.34: 18688 4.34 - 4.90: 32033 Nonbonded interactions: 72846 Sorted by model distance: nonbonded pdb=" O GLU R 196 " pdb=" CG PRO R 200 " model vdw 2.116 3.440 nonbonded pdb=" O GLU R 196 " pdb=" CD PRO R 200 " model vdw 2.125 3.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.208 3.040 nonbonded pdb=" O LYS R 60 " pdb=" N ARG R 63 " model vdw 2.228 3.120 nonbonded pdb=" O LEU B 30 " pdb=" OG1 THR B 34 " model vdw 2.280 3.040 ... (remaining 72841 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: 0.360 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.990 Find NCS groups from input model: 0.110 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:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 9319 Z= 0.270 Angle : 0.625 10.140 12610 Z= 0.325 Chirality : 0.055 1.222 1412 Planarity : 0.009 0.300 1594 Dihedral : 13.554 82.831 3382 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.25), residues: 1137 helix: 1.31 (0.27), residues: 387 sheet: 0.50 (0.31), residues: 295 loop : -0.53 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 59 HIS 0.004 0.001 HIS R 161 PHE 0.015 0.001 PHE R 52 TYR 0.016 0.001 TYR S 190 ARG 0.004 0.000 ARG R 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 1.095 Fit side-chains REVERT: A 25 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6707 (mm-30) REVERT: A 28 GLU cc_start: 0.6756 (mp0) cc_final: 0.6365 (mp0) REVERT: A 270 LYS cc_start: 0.8072 (mtmm) cc_final: 0.7775 (mttm) REVERT: A 337 ASP cc_start: 0.7542 (m-30) cc_final: 0.7334 (m-30) REVERT: B 89 LYS cc_start: 0.8421 (mttp) cc_final: 0.8198 (mttt) REVERT: B 254 ASP cc_start: 0.7008 (t70) cc_final: 0.6596 (t0) REVERT: B 268 ASN cc_start: 0.7227 (m110) cc_final: 0.7021 (m110) REVERT: S 219 LEU cc_start: 0.8014 (tt) cc_final: 0.7812 (tt) REVERT: R 22 ARG cc_start: 0.6712 (mtm-85) cc_final: 0.6482 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 1.2697 time to fit residues: 278.5949 Evaluate side-chains 190 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.6980 chunk 84 optimal weight: 0.2980 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.0040 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.0470 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.3890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN S 186 GLN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9319 Z= 0.150 Angle : 0.515 6.593 12610 Z= 0.278 Chirality : 0.041 0.171 1412 Planarity : 0.004 0.068 1594 Dihedral : 5.455 40.144 1290 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.91 % Allowed : 8.84 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.91 (0.26), residues: 1137 helix: 1.69 (0.27), residues: 393 sheet: 0.65 (0.31), residues: 284 loop : -0.32 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 59 HIS 0.006 0.001 HIS R 161 PHE 0.009 0.001 PHE B 234 TYR 0.022 0.001 TYR S 190 ARG 0.006 0.000 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.949 Fit side-chains REVERT: A 190 THR cc_start: 0.8440 (t) cc_final: 0.8192 (m) REVERT: A 337 ASP cc_start: 0.7554 (m-30) cc_final: 0.7334 (m-30) REVERT: B 158 VAL cc_start: 0.8589 (p) cc_final: 0.8316 (t) REVERT: B 254 ASP cc_start: 0.6958 (t70) cc_final: 0.6666 (t0) REVERT: B 268 ASN cc_start: 0.7257 (m110) cc_final: 0.7037 (m110) REVERT: R 146 ILE cc_start: 0.6798 (OUTLIER) cc_final: 0.6414 (mp) REVERT: R 195 LEU cc_start: 0.7861 (tm) cc_final: 0.7608 (tt) REVERT: R 196 GLU cc_start: 0.7618 (pt0) cc_final: 0.7316 (pp20) outliers start: 19 outliers final: 9 residues processed: 196 average time/residue: 1.1861 time to fit residues: 248.6345 Evaluate side-chains 195 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 185 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 146 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.0010 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 100 optimal weight: 0.0570 overall best weight: 0.6506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN B 340 ASN R 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9319 Z= 0.173 Angle : 0.500 6.233 12610 Z= 0.270 Chirality : 0.041 0.182 1412 Planarity : 0.004 0.064 1594 Dihedral : 5.271 40.635 1290 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.21 % Allowed : 11.06 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1137 helix: 1.81 (0.28), residues: 393 sheet: 0.69 (0.31), residues: 292 loop : -0.40 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.004 0.001 HIS A 188 PHE 0.009 0.001 PHE R 117 TYR 0.024 0.001 TYR S 190 ARG 0.004 0.000 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.998 Fit side-chains REVERT: A 190 THR cc_start: 0.8475 (t) cc_final: 0.8271 (m) REVERT: A 337 ASP cc_start: 0.7583 (m-30) cc_final: 0.7336 (m-30) REVERT: B 158 VAL cc_start: 0.8559 (p) cc_final: 0.8344 (t) REVERT: B 254 ASP cc_start: 0.6960 (t70) cc_final: 0.6651 (t0) REVERT: B 268 ASN cc_start: 0.7285 (m110) cc_final: 0.7070 (m110) REVERT: R 83 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6690 (mp) REVERT: R 146 ILE cc_start: 0.6819 (OUTLIER) cc_final: 0.6451 (mp) outliers start: 22 outliers final: 13 residues processed: 201 average time/residue: 1.2147 time to fit residues: 261.8901 Evaluate side-chains 207 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 146 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 0.0980 chunk 53 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN ** B 340 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: 0.7242 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9319 Z= 0.336 Angle : 0.590 7.913 12610 Z= 0.313 Chirality : 0.045 0.239 1412 Planarity : 0.004 0.065 1594 Dihedral : 5.640 41.312 1290 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.81 % Allowed : 12.56 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.70 (0.25), residues: 1137 helix: 1.53 (0.27), residues: 393 sheet: 0.68 (0.30), residues: 292 loop : -0.58 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.006 0.002 HIS A 188 PHE 0.019 0.002 PHE R 117 TYR 0.026 0.002 TYR B 105 ARG 0.005 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 1.056 Fit side-chains REVERT: A 270 LYS cc_start: 0.7953 (mttp) cc_final: 0.7731 (mttp) REVERT: A 337 ASP cc_start: 0.7628 (m-30) cc_final: 0.7397 (m-30) REVERT: B 254 ASP cc_start: 0.6992 (t70) cc_final: 0.6666 (t70) REVERT: B 268 ASN cc_start: 0.7282 (m110) cc_final: 0.7075 (m-40) REVERT: R 83 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6477 (mp) REVERT: R 146 ILE cc_start: 0.6820 (OUTLIER) cc_final: 0.6453 (mp) outliers start: 28 outliers final: 18 residues processed: 218 average time/residue: 1.2389 time to fit residues: 288.0017 Evaluate side-chains 217 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 192 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 92 optimal weight: 0.4980 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 0.0570 chunk 97 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9319 Z= 0.172 Angle : 0.509 6.406 12610 Z= 0.274 Chirality : 0.042 0.185 1412 Planarity : 0.004 0.063 1594 Dihedral : 5.367 38.284 1290 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.51 % Allowed : 14.47 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.90 (0.26), residues: 1137 helix: 1.77 (0.27), residues: 393 sheet: 0.67 (0.30), residues: 294 loop : -0.46 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 256 HIS 0.004 0.001 HIS A 188 PHE 0.009 0.001 PHE A 189 TYR 0.023 0.001 TYR S 190 ARG 0.008 0.000 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 1.112 Fit side-chains REVERT: A 270 LYS cc_start: 0.7924 (mttp) cc_final: 0.7723 (mttp) REVERT: A 337 ASP cc_start: 0.7659 (m-30) cc_final: 0.7406 (m-30) REVERT: B 254 ASP cc_start: 0.6962 (t70) cc_final: 0.6639 (t70) REVERT: S 83 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7665 (ptm) REVERT: S 140 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7522 (mtm) REVERT: R 83 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6545 (mp) REVERT: R 146 ILE cc_start: 0.6803 (OUTLIER) cc_final: 0.6433 (mp) outliers start: 25 outliers final: 16 residues processed: 200 average time/residue: 1.2669 time to fit residues: 270.8793 Evaluate side-chains 208 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 146 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 9319 Z= 0.433 Angle : 0.638 8.085 12610 Z= 0.338 Chirality : 0.047 0.253 1412 Planarity : 0.005 0.065 1594 Dihedral : 5.825 41.898 1290 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.12 % Allowed : 15.08 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.25), residues: 1137 helix: 1.36 (0.27), residues: 391 sheet: 0.56 (0.29), residues: 297 loop : -0.66 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.007 0.002 HIS B 142 PHE 0.021 0.002 PHE R 276 TYR 0.024 0.002 TYR S 190 ARG 0.011 0.001 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 1.018 Fit side-chains REVERT: A 260 THR cc_start: 0.8105 (m) cc_final: 0.7781 (p) REVERT: A 337 ASP cc_start: 0.7650 (m-30) cc_final: 0.7409 (m-30) REVERT: B 254 ASP cc_start: 0.7010 (t70) cc_final: 0.6680 (t70) REVERT: R 83 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6474 (mp) REVERT: R 146 ILE cc_start: 0.6797 (OUTLIER) cc_final: 0.6433 (mp) outliers start: 31 outliers final: 21 residues processed: 223 average time/residue: 1.1910 time to fit residues: 283.4045 Evaluate side-chains 227 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 233 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 0.0370 chunk 79 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 82 GLN S 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9319 Z= 0.181 Angle : 0.520 6.090 12610 Z= 0.282 Chirality : 0.042 0.187 1412 Planarity : 0.004 0.059 1594 Dihedral : 5.431 38.875 1290 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.71 % Allowed : 16.48 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.25), residues: 1137 helix: 1.66 (0.27), residues: 393 sheet: 0.62 (0.30), residues: 297 loop : -0.51 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 256 HIS 0.004 0.001 HIS A 188 PHE 0.009 0.001 PHE B 241 TYR 0.022 0.001 TYR S 190 ARG 0.012 0.001 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.961 Fit side-chains REVERT: A 270 LYS cc_start: 0.7919 (mttp) cc_final: 0.7710 (mttm) REVERT: A 337 ASP cc_start: 0.7668 (m-30) cc_final: 0.7430 (m-30) REVERT: B 254 ASP cc_start: 0.6947 (t70) cc_final: 0.6635 (t70) REVERT: B 285 LEU cc_start: 0.8597 (tp) cc_final: 0.8379 (tt) REVERT: S 140 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7539 (mtm) REVERT: R 83 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6499 (mp) REVERT: R 146 ILE cc_start: 0.6799 (OUTLIER) cc_final: 0.6432 (mp) outliers start: 27 outliers final: 17 residues processed: 210 average time/residue: 1.2741 time to fit residues: 284.4756 Evaluate side-chains 214 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 146 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 82 GLN S 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9319 Z= 0.294 Angle : 0.577 8.503 12610 Z= 0.309 Chirality : 0.044 0.225 1412 Planarity : 0.004 0.060 1594 Dihedral : 5.699 42.441 1290 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.02 % Allowed : 16.58 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.67 (0.25), residues: 1137 helix: 1.52 (0.27), residues: 392 sheet: 0.58 (0.29), residues: 297 loop : -0.55 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.016 0.002 PHE R 117 TYR 0.026 0.002 TYR S 190 ARG 0.013 0.001 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 1.058 Fit side-chains REVERT: A 337 ASP cc_start: 0.7678 (m-30) cc_final: 0.7430 (m-30) REVERT: B 254 ASP cc_start: 0.6971 (t70) cc_final: 0.6651 (t70) REVERT: S 38 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7450 (ptt-90) REVERT: R 83 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6436 (mp) REVERT: R 146 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.6456 (mp) REVERT: R 212 ILE cc_start: 0.7442 (OUTLIER) cc_final: 0.7115 (mm) outliers start: 30 outliers final: 18 residues processed: 213 average time/residue: 1.2986 time to fit residues: 294.2169 Evaluate side-chains 218 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 212 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 78 optimal weight: 0.0870 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN S 82 GLN S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9319 Z= 0.178 Angle : 0.524 9.057 12610 Z= 0.285 Chirality : 0.042 0.183 1412 Planarity : 0.004 0.058 1594 Dihedral : 5.390 39.491 1290 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.91 % Allowed : 16.78 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1137 helix: 1.68 (0.27), residues: 393 sheet: 0.61 (0.30), residues: 299 loop : -0.47 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.009 0.001 PHE B 241 TYR 0.020 0.001 TYR S 190 ARG 0.014 0.000 ARG R 270 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 1.040 Fit side-chains REVERT: A 20 ASP cc_start: 0.7239 (m-30) cc_final: 0.7033 (m-30) REVERT: A 337 ASP cc_start: 0.7664 (m-30) cc_final: 0.7408 (m-30) REVERT: B 254 ASP cc_start: 0.6920 (t70) cc_final: 0.6616 (t70) REVERT: B 308 LEU cc_start: 0.8669 (mt) cc_final: 0.8422 (mp) REVERT: S 140 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7533 (mtm) REVERT: R 83 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.6422 (mp) REVERT: R 146 ILE cc_start: 0.6812 (OUTLIER) cc_final: 0.6446 (mp) REVERT: R 212 ILE cc_start: 0.7371 (OUTLIER) cc_final: 0.7093 (mm) outliers start: 29 outliers final: 16 residues processed: 205 average time/residue: 1.2671 time to fit residues: 277.6717 Evaluate side-chains 211 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 292 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 102 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 82 GLN R 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9319 Z= 0.206 Angle : 0.541 10.063 12610 Z= 0.293 Chirality : 0.042 0.196 1412 Planarity : 0.004 0.060 1594 Dihedral : 5.442 40.994 1290 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.71 % Allowed : 16.88 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 (0.25), residues: 1137 helix: 1.68 (0.27), residues: 394 sheet: 0.62 (0.30), residues: 297 loop : -0.47 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 PHE 0.010 0.001 PHE R 117 TYR 0.022 0.001 TYR S 190 ARG 0.015 0.000 ARG R 270 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 1.114 Fit side-chains REVERT: A 337 ASP cc_start: 0.7659 (m-30) cc_final: 0.7430 (m-30) REVERT: B 254 ASP cc_start: 0.6936 (t70) cc_final: 0.6621 (t70) REVERT: B 285 LEU cc_start: 0.8581 (tp) cc_final: 0.8369 (tt) REVERT: R 83 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6399 (mp) REVERT: R 146 ILE cc_start: 0.6824 (OUTLIER) cc_final: 0.6459 (mp) REVERT: R 212 ILE cc_start: 0.7392 (OUTLIER) cc_final: 0.7108 (mm) outliers start: 27 outliers final: 20 residues processed: 206 average time/residue: 1.3394 time to fit residues: 294.3641 Evaluate side-chains 212 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 292 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 91 optimal weight: 0.1980 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.145191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.123572 restraints weight = 12183.989| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.95 r_work: 0.3493 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9319 Z= 0.189 Angle : 0.534 10.997 12610 Z= 0.288 Chirality : 0.042 0.188 1412 Planarity : 0.004 0.060 1594 Dihedral : 5.343 40.236 1290 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.51 % Allowed : 18.09 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.86 (0.26), residues: 1137 helix: 1.72 (0.27), residues: 394 sheet: 0.62 (0.30), residues: 298 loop : -0.45 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.009 0.001 PHE B 241 TYR 0.021 0.001 TYR S 190 ARG 0.015 0.000 ARG R 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4676.13 seconds wall clock time: 83 minutes 59.15 seconds (5039.15 seconds total)