Starting phenix.real_space_refine on Thu Feb 13 16:46:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j6r_36012/02_2025/8j6r_36012.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j6r_36012/02_2025/8j6r_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/cci-nas-00/data/ceres_data/8j6r_36012/02_2025/8j6r_36012.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j6r_36012/02_2025/8j6r_36012.map" model { file = "/net/cci-nas-00/data/ceres_data/8j6r_36012/02_2025/8j6r_36012.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j6r_36012/02_2025/8j6r_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-5592/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: 7.18, per 1000 atoms: 0.79 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: 2.30 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: 1.14 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: 2.65 Time building geometry restraints manager: 2.71 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.210 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 23.160 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.560 ------------------------------------------------------------------------------- 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 : 0.971 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: 1.2173 time to fit residues: 266.5176 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 : 0.926 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.148190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.126393 restraints weight = 12263.827| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.98 r_work: 0.3524 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 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 : 0.926 Fit side-chains REVERT: A 190 THR cc_start: 0.8576 (t) cc_final: 0.8306 (m) REVERT: A 337 ASP cc_start: 0.8066 (m-30) cc_final: 0.7856 (m-30) REVERT: A 347 ASN cc_start: 0.8199 (m-40) cc_final: 0.7927 (m110) REVERT: B 158 VAL cc_start: 0.8702 (p) cc_final: 0.8458 (t) REVERT: B 254 ASP cc_start: 0.7751 (t70) cc_final: 0.7414 (t0) REVERT: B 268 ASN cc_start: 0.7667 (m110) cc_final: 0.7387 (m110) REVERT: R 146 ILE cc_start: 0.7142 (OUTLIER) cc_final: 0.6749 (mp) REVERT: R 195 LEU cc_start: 0.7939 (tm) cc_final: 0.7701 (tt) REVERT: R 196 GLU cc_start: 0.8073 (pt0) cc_final: 0.7650 (pp20) outliers start: 19 outliers final: 9 residues processed: 196 average time/residue: 1.2247 time to fit residues: 256.4166 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 : 1.001 ------------------------------------------------------------------------------- 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 24 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 9 optimal weight: 0.1980 chunk 26 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 34 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.147047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.125293 restraints weight = 12449.783| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.98 r_work: 0.3514 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 9319 Z= 0.161 Angle : 0.493 6.237 12610 Z= 0.266 Chirality : 0.041 0.176 1412 Planarity : 0.004 0.063 1594 Dihedral : 5.229 40.444 1290 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.31 % Allowed : 10.95 % 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: 0.97 (0.26), residues: 1137 helix: 1.82 (0.28), residues: 393 sheet: 0.66 (0.31), residues: 279 loop : -0.34 (0.30), residues: 465 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 B 234 TYR 0.023 0.001 TYR S 190 ARG 0.004 0.000 ARG B 251 *********************** 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 211 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.976 Fit side-chains REVERT: A 190 THR cc_start: 0.8609 (t) cc_final: 0.8376 (m) REVERT: A 337 ASP cc_start: 0.8136 (m-30) cc_final: 0.7909 (m-30) REVERT: B 254 ASP cc_start: 0.7752 (t70) cc_final: 0.7403 (t0) REVERT: B 268 ASN cc_start: 0.7693 (m110) cc_final: 0.7421 (m110) REVERT: S 140 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8055 (mtm) REVERT: R 83 LEU cc_start: 0.7021 (OUTLIER) cc_final: 0.6687 (mp) REVERT: R 146 ILE cc_start: 0.7179 (OUTLIER) cc_final: 0.6788 (mp) REVERT: R 196 GLU cc_start: 0.8125 (pt0) cc_final: 0.7665 (pp20) outliers start: 23 outliers final: 13 residues processed: 198 average time/residue: 1.1974 time to fit residues: 253.5998 Evaluate side-chains 207 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 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 65 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.146459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.124606 restraints weight = 12353.369| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.01 r_work: 0.3500 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1393 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= 0.187 Angle : 0.510 6.584 12610 Z= 0.273 Chirality : 0.042 0.186 1412 Planarity : 0.004 0.061 1594 Dihedral : 5.271 39.090 1290 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.11 % Allowed : 13.37 % Favored : 84.52 % 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: 0.95 (0.26), residues: 1137 helix: 1.84 (0.28), residues: 393 sheet: 0.70 (0.30), residues: 293 loop : -0.45 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 PHE 0.010 0.001 PHE B 151 TYR 0.023 0.001 TYR S 190 ARG 0.005 0.000 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 214 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.998 Fit side-chains REVERT: A 28 GLU cc_start: 0.7501 (mp0) cc_final: 0.7301 (mp0) REVERT: A 190 THR cc_start: 0.8571 (t) cc_final: 0.8361 (m) REVERT: A 337 ASP cc_start: 0.8167 (m-30) cc_final: 0.7932 (m-30) REVERT: B 254 ASP cc_start: 0.7775 (t70) cc_final: 0.7419 (t0) REVERT: B 268 ASN cc_start: 0.7723 (m110) cc_final: 0.7480 (m-40) REVERT: S 140 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7938 (mtm) REVERT: R 83 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6661 (mp) REVERT: R 146 ILE cc_start: 0.7185 (OUTLIER) cc_final: 0.6803 (mp) outliers start: 21 outliers final: 12 residues processed: 202 average time/residue: 1.2540 time to fit residues: 269.9442 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 : 1.040 ------------------------------------------------------------------------------- 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 128 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 161 SER 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 146 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 98 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 84 optimal weight: 0.0270 chunk 67 optimal weight: 3.9990 chunk 10 optimal weight: 0.0770 chunk 20 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.146858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.125040 restraints weight = 12335.594| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.00 r_work: 0.3515 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9319 Z= 0.156 Angle : 0.490 6.693 12610 Z= 0.262 Chirality : 0.041 0.172 1412 Planarity : 0.004 0.059 1594 Dihedral : 5.151 38.377 1290 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.41 % Allowed : 14.37 % Favored : 83.22 % 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: 1.03 (0.26), residues: 1137 helix: 1.94 (0.27), residues: 394 sheet: 0.68 (0.30), residues: 293 loop : -0.39 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 188 HIS 0.004 0.001 HIS A 188 PHE 0.007 0.001 PHE B 199 TYR 0.022 0.001 TYR S 190 ARG 0.010 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 213 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 1.001 Fit side-chains REVERT: A 28 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7266 (mp0) REVERT: A 317 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7363 (pttm) REVERT: A 337 ASP cc_start: 0.8145 (m-30) cc_final: 0.7929 (m-30) REVERT: B 254 ASP cc_start: 0.7765 (t70) cc_final: 0.7403 (t0) REVERT: B 268 ASN cc_start: 0.7732 (m110) cc_final: 0.7497 (m-40) REVERT: S 83 MET cc_start: 0.8287 (mtp) cc_final: 0.8078 (ptm) REVERT: S 140 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7868 (mtm) REVERT: R 83 LEU cc_start: 0.6889 (OUTLIER) cc_final: 0.6584 (mp) REVERT: R 146 ILE cc_start: 0.7184 (OUTLIER) cc_final: 0.6799 (mp) outliers start: 24 outliers final: 13 residues processed: 201 average time/residue: 1.2728 time to fit residues: 272.5591 Evaluate side-chains 203 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU 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 197 ARG 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 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 91 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.145559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.123698 restraints weight = 12277.412| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.99 r_work: 0.3492 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9319 Z= 0.232 Angle : 0.529 6.342 12610 Z= 0.284 Chirality : 0.043 0.205 1412 Planarity : 0.004 0.059 1594 Dihedral : 5.393 39.165 1290 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.61 % Allowed : 14.77 % Favored : 82.61 % 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: 0.92 (0.26), residues: 1137 helix: 1.79 (0.27), residues: 394 sheet: 0.70 (0.30), residues: 294 loop : -0.46 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 PHE 0.013 0.001 PHE R 117 TYR 0.023 0.002 TYR S 190 ARG 0.007 0.000 ARG B 49 *********************** 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 220 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 1.032 Fit side-chains REVERT: A 28 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: A 337 ASP cc_start: 0.8197 (m-30) cc_final: 0.7969 (m-30) REVERT: B 254 ASP cc_start: 0.7791 (t70) cc_final: 0.7431 (t70) REVERT: B 268 ASN cc_start: 0.7722 (m110) cc_final: 0.7484 (m-40) REVERT: B 285 LEU cc_start: 0.8697 (tp) cc_final: 0.8495 (tt) REVERT: S 83 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.8048 (ptm) REVERT: R 83 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6591 (mp) REVERT: R 146 ILE cc_start: 0.7175 (OUTLIER) cc_final: 0.6800 (mp) outliers start: 26 outliers final: 16 residues processed: 205 average time/residue: 1.2946 time to fit residues: 282.4932 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 : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU 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 270 ILE Chi-restraints excluded: chain B residue 275 SER 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 83 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 0.9980 chunk 108 optimal weight: 0.4980 chunk 93 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.144872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.122961 restraints weight = 12321.401| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.99 r_work: 0.3483 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9319 Z= 0.245 Angle : 0.540 6.663 12610 Z= 0.289 Chirality : 0.043 0.211 1412 Planarity : 0.004 0.060 1594 Dihedral : 5.450 38.829 1290 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.51 % Allowed : 16.18 % Favored : 81.31 % 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: 0.87 (0.25), residues: 1137 helix: 1.72 (0.27), residues: 393 sheet: 0.67 (0.30), residues: 299 loop : -0.47 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 PHE 0.012 0.001 PHE R 117 TYR 0.023 0.002 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 221 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 0.775 Fit side-chains REVERT: A 28 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7314 (mp0) REVERT: A 337 ASP cc_start: 0.8183 (m-30) cc_final: 0.7940 (m-30) REVERT: B 254 ASP cc_start: 0.7800 (t70) cc_final: 0.7435 (t70) REVERT: B 268 ASN cc_start: 0.7728 (m110) cc_final: 0.7485 (m-40) REVERT: R 83 LEU cc_start: 0.6847 (OUTLIER) cc_final: 0.6538 (mp) REVERT: R 146 ILE cc_start: 0.7176 (OUTLIER) cc_final: 0.6799 (mp) outliers start: 25 outliers final: 15 residues processed: 209 average time/residue: 1.2569 time to fit residues: 279.6432 Evaluate side-chains 213 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 195 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 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 63 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 7 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.144641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.122628 restraints weight = 12439.941| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.99 r_work: 0.3473 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1774 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= 0.267 Angle : 0.558 8.084 12610 Z= 0.300 Chirality : 0.043 0.217 1412 Planarity : 0.004 0.059 1594 Dihedral : 5.551 39.475 1290 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.61 % Allowed : 16.48 % Favored : 80.90 % 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: 0.75 (0.25), residues: 1137 helix: 1.57 (0.27), residues: 394 sheet: 0.67 (0.30), residues: 297 loop : -0.55 (0.29), residues: 446 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 0.014 0.001 PHE R 117 TYR 0.022 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 223 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 0.940 Fit side-chains REVERT: A 28 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: A 337 ASP cc_start: 0.8204 (m-30) cc_final: 0.7970 (m-30) REVERT: B 254 ASP cc_start: 0.7799 (t70) cc_final: 0.7441 (t70) REVERT: B 268 ASN cc_start: 0.7694 (m110) cc_final: 0.7460 (m-40) REVERT: R 83 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6505 (mp) REVERT: R 146 ILE cc_start: 0.7193 (OUTLIER) cc_final: 0.6815 (mp) outliers start: 26 outliers final: 19 residues processed: 209 average time/residue: 1.2885 time to fit residues: 286.3780 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 : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU 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 44 GLN 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 300 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.145855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.123988 restraints weight = 12218.679| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.97 r_work: 0.3490 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1790 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= 0.195 Angle : 0.527 9.200 12610 Z= 0.286 Chirality : 0.042 0.192 1412 Planarity : 0.004 0.058 1594 Dihedral : 5.375 38.542 1290 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.31 % Allowed : 16.88 % 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: 0.85 (0.25), residues: 1137 helix: 1.70 (0.27), residues: 394 sheet: 0.66 (0.30), residues: 299 loop : -0.49 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 256 HIS 0.003 0.001 HIS A 188 PHE 0.009 0.001 PHE A 189 TYR 0.022 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 215 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 1.101 Fit side-chains REVERT: A 28 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: A 337 ASP cc_start: 0.8179 (m-30) cc_final: 0.7953 (m-30) REVERT: B 254 ASP cc_start: 0.7763 (t70) cc_final: 0.7405 (t70) REVERT: B 268 ASN cc_start: 0.7717 (m110) cc_final: 0.7488 (m-40) REVERT: S 140 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7947 (mtm) REVERT: R 83 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6461 (mp) REVERT: R 146 ILE cc_start: 0.7153 (OUTLIER) cc_final: 0.6772 (mp) outliers start: 23 outliers final: 17 residues processed: 205 average time/residue: 1.2862 time to fit residues: 280.4939 Evaluate side-chains 212 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN 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 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 195 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 0.8980 chunk 102 optimal weight: 0.0970 chunk 40 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 10 optimal weight: 0.0770 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 111 optimal weight: 0.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.146969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.125023 restraints weight = 12415.596| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.98 r_work: 0.3506 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 9319 Z= 0.161 Angle : 0.522 10.547 12610 Z= 0.280 Chirality : 0.042 0.176 1412 Planarity : 0.004 0.057 1594 Dihedral : 5.200 38.021 1290 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.31 % Allowed : 17.39 % 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: 0.99 (0.26), residues: 1137 helix: 1.84 (0.27), residues: 393 sheet: 0.69 (0.30), residues: 298 loop : -0.39 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 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 0.015 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 210 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.924 Fit side-chains REVERT: A 28 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: A 317 LYS cc_start: 0.7987 (pttm) cc_final: 0.7691 (ptpp) REVERT: A 337 ASP cc_start: 0.8157 (m-30) cc_final: 0.7924 (m-30) REVERT: B 254 ASP cc_start: 0.7746 (t70) cc_final: 0.7417 (t70) REVERT: B 268 ASN cc_start: 0.7721 (m110) cc_final: 0.7499 (m-40) REVERT: S 83 MET cc_start: 0.8375 (mtp) cc_final: 0.8174 (ptm) REVERT: S 140 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7925 (mtm) REVERT: R 83 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6465 (mp) REVERT: R 146 ILE cc_start: 0.7160 (OUTLIER) cc_final: 0.6780 (mp) outliers start: 23 outliers final: 14 residues processed: 200 average time/residue: 1.3105 time to fit residues: 279.0273 Evaluate side-chains 202 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 108 optimal weight: 0.3980 chunk 105 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.146224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.124344 restraints weight = 12429.062| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.98 r_work: 0.3495 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9319 Z= 0.190 Angle : 0.536 11.028 12610 Z= 0.287 Chirality : 0.042 0.188 1412 Planarity : 0.004 0.059 1594 Dihedral : 5.264 38.804 1290 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.21 % Allowed : 17.79 % Favored : 80.00 % 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: 0.97 (0.26), residues: 1137 helix: 1.81 (0.27), residues: 395 sheet: 0.61 (0.30), residues: 302 loop : -0.36 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.009 0.001 PHE R 117 TYR 0.022 0.001 TYR S 190 ARG 0.014 0.000 ARG R 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8229.52 seconds wall clock time: 145 minutes 48.55 seconds (8748.55 seconds total)