Starting phenix.real_space_refine on Fri Nov 15 19:39:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6p_36010/11_2024/8j6p_36010.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6p_36010/11_2024/8j6p_36010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6p_36010/11_2024/8j6p_36010.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6p_36010/11_2024/8j6p_36010.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6p_36010/11_2024/8j6p_36010.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6p_36010/11_2024/8j6p_36010.cif" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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 5878 2.51 5 N 1555 2.21 5 O 1687 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: 9189 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 112 Unusual residues: {'CLR': 2, 'IX8': 1, 'NAG': 1, 'NIO': 1} Classifications: {'undetermined': 5, 'water': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.80, per 1000 atoms: 0.63 Number of scatterers: 9189 At special positions: 0 Unit cell: (106.02, 119.97, 113.46, 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 1687 8.00 N 1555 7.00 C 5878 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=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 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 405 " - " ASN R 17 " Time building additional restraints: 2.58 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: 31 helices and 13 sheets defined 38.7% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.657A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.560A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.436A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.120A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.751A 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 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.679A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.976A 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: 3.605A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 Processing helix chain 'R' and resid 23 through 54 removed outlier: 3.824A 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: 3.604A pdb=" N LEU R 83 " --> pdb=" O CYS R 79 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG R 89 " --> pdb=" O ASP R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 130 Processing helix chain 'R' and resid 134 through 139 removed outlier: 3.691A 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 165 removed outlier: 3.635A pdb=" N LYS R 164 " --> pdb=" O HIS R 161 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS R 165 " --> pdb=" O LEU R 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 161 through 165' Processing helix chain 'R' and resid 170 through 174 removed outlier: 3.986A pdb=" N GLY R 173 " --> pdb=" O GLN R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 218 removed outlier: 3.700A 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: 3.902A 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 267 No H-bonds generated for 'chain 'R' and resid 265 through 267' Processing helix chain 'R' and resid 268 through 295 removed outlier: 4.632A pdb=" N VAL R 272 " --> pdb=" O VAL R 268 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR R 283 " --> pdb=" O THR R 279 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR R 284 " --> pdb=" O LEU R 280 " (cutoff:3.500A) removed outlier: 3.849A 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: 5.970A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N THR A 324 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU A 268 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.614A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.752A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.476A 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: 6.730A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 6.730A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.523A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.378A 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: 3.769A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.223A 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: 6.107A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.374A 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 11 through 12 removed outlier: 6.702A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA S 40 " --> pdb=" O GLY S 44 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.976A 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 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.530A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1239 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: 2.75 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2259 1.33 - 1.46: 2385 1.46 - 1.58: 4650 1.58 - 1.71: 1 1.71 - 1.84: 100 Bond restraints: 9395 Sorted by residual: bond pdb=" C2 IX8 R 401 " pdb=" C25 IX8 R 401 " ideal model delta sigma weight residual 1.522 1.654 -0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" C4 IX8 R 401 " pdb=" N3 IX8 R 401 " ideal model delta sigma weight residual 1.341 1.442 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" C2 IX8 R 401 " pdb=" N3 IX8 R 401 " ideal model delta sigma weight residual 1.451 1.542 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C15 IX8 R 401 " pdb=" C16 IX8 R 401 " ideal model delta sigma weight residual 1.460 1.550 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C11 IX8 R 401 " pdb=" N10 IX8 R 401 " ideal model delta sigma weight residual 1.359 1.446 -0.087 2.00e-02 2.50e+03 1.88e+01 ... (remaining 9390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 12308 1.90 - 3.81: 318 3.81 - 5.71: 68 5.71 - 7.61: 22 7.61 - 9.52: 7 Bond angle restraints: 12723 Sorted by residual: angle pdb=" N THR A 329 " pdb=" CA THR A 329 " pdb=" C THR A 329 " ideal model delta sigma weight residual 111.36 119.06 -7.70 1.09e+00 8.42e-01 4.99e+01 angle pdb=" N LYS A 330 " pdb=" CA LYS A 330 " pdb=" C LYS A 330 " ideal model delta sigma weight residual 113.37 120.42 -7.05 1.38e+00 5.25e-01 2.61e+01 angle pdb=" N HIS R 55 " pdb=" CA HIS R 55 " pdb=" C HIS R 55 " ideal model delta sigma weight residual 111.28 115.97 -4.69 1.09e+00 8.42e-01 1.85e+01 angle pdb=" N HIS R 184 " pdb=" CA HIS R 184 " pdb=" C HIS R 184 " ideal model delta sigma weight residual 111.28 115.35 -4.07 1.09e+00 8.42e-01 1.39e+01 angle pdb=" C ILE R 169 " pdb=" N GLN R 170 " pdb=" CA GLN R 170 " ideal model delta sigma weight residual 122.68 127.90 -5.22 1.47e+00 4.63e-01 1.26e+01 ... (remaining 12718 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 5159 17.76 - 35.51: 434 35.51 - 53.26: 68 53.26 - 71.02: 9 71.02 - 88.77: 6 Dihedral angle restraints: 5676 sinusoidal: 2341 harmonic: 3335 Sorted by residual: 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 57.87 35.13 1 1.00e+01 1.00e-02 1.75e+01 dihedral pdb=" CA ASN R 17 " pdb=" C ASN R 17 " pdb=" N CYS R 18 " pdb=" CA CYS R 18 " ideal model delta harmonic sigma weight residual 180.00 159.49 20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA PHE R 197 " pdb=" C PHE R 197 " pdb=" N PHE R 198 " pdb=" CA PHE R 198 " ideal model delta harmonic sigma weight residual -180.00 -161.21 -18.79 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 5673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.259: 1424 0.259 - 0.518: 4 0.518 - 0.777: 0 0.777 - 1.036: 0 1.036 - 1.295: 1 Chirality restraints: 1429 Sorted by residual: chirality pdb=" C1 NAG R 405 " pdb=" ND2 ASN R 17 " pdb=" C2 NAG R 405 " pdb=" O5 NAG R 405 " both_signs ideal model delta sigma weight residual False -2.40 -1.10 -1.30 2.00e-01 2.50e+01 4.19e+01 chirality pdb=" C2 IX8 R 401 " pdb=" C1 IX8 R 401 " pdb=" C25 IX8 R 401 " pdb=" N3 IX8 R 401 " both_signs ideal model delta sigma weight residual False 2.42 2.87 -0.45 2.00e-01 2.50e+01 5.07e+00 chirality pdb=" C13 CLR R 404 " pdb=" C12 CLR R 404 " pdb=" C14 CLR R 404 " pdb=" C17 CLR R 404 " both_signs ideal model delta sigma weight residual False -2.93 -2.64 -0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 1426 not shown) Planarity restraints: 1597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 405 " -0.314 2.00e-02 2.50e+03 2.66e-01 8.81e+02 pdb=" C7 NAG R 405 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG R 405 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG R 405 " 0.459 2.00e-02 2.50e+03 pdb=" O7 NAG R 405 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.055 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO S 75 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN R 17 " -0.025 2.00e-02 2.50e+03 2.65e-02 8.78e+00 pdb=" CG ASN R 17 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN R 17 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN R 17 " 0.042 2.00e-02 2.50e+03 pdb=" C1 NAG R 405 " -0.032 2.00e-02 2.50e+03 ... (remaining 1594 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 175 2.68 - 3.23: 8234 3.23 - 3.79: 15201 3.79 - 4.34: 20936 4.34 - 4.90: 34502 Nonbonded interactions: 79048 Sorted by model distance: nonbonded pdb=" OE1 GLN A 52 " pdb=" ND2 ASN A 331 " model vdw 2.120 3.120 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 175 " model vdw 2.230 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.243 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.255 3.040 nonbonded pdb=" OH TYR R 284 " pdb=" O1 NIO R 403 " model vdw 2.283 3.040 ... (remaining 79043 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: 0.510 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.820 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: 0.010 Load rotamer database and sin/cos tables:12.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 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 : 0.005 0.132 9395 Z= 0.319 Angle : 0.783 9.515 12723 Z= 0.407 Chirality : 0.063 1.295 1429 Planarity : 0.009 0.266 1596 Dihedral : 13.098 88.774 3505 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.73 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: -0.04 (0.24), residues: 1137 helix: 0.56 (0.25), residues: 388 sheet: 0.09 (0.30), residues: 280 loop : -0.45 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 59 HIS 0.005 0.001 HIS S 232 PHE 0.027 0.002 PHE R 52 TYR 0.023 0.002 TYR S 190 ARG 0.006 0.000 ARG S 202 *********************** 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 172 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 1.054 Fit side-chains REVERT: A 8 GLU cc_start: 0.7017 (mt-10) cc_final: 0.5788 (mt-10) REVERT: A 21 ARG cc_start: 0.7616 (ttm110) cc_final: 0.7357 (ttp-170) REVERT: A 208 ARG cc_start: 0.7878 (ttp-110) cc_final: 0.7623 (ttm110) REVERT: A 330 LYS cc_start: 0.7276 (mttt) cc_final: 0.6958 (mtpp) REVERT: B 42 ARG cc_start: 0.7179 (tpt170) cc_final: 0.6836 (tpt170) REVERT: S 238 THR cc_start: 0.8179 (m) cc_final: 0.7722 (p) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 1.2496 time to fit residues: 229.6576 Evaluate side-chains 127 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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: 0.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 340 ASN S 186 GLN R 112 GLN R 141 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9395 Z= 0.248 Angle : 0.588 7.208 12723 Z= 0.313 Chirality : 0.043 0.202 1429 Planarity : 0.005 0.076 1596 Dihedral : 5.977 50.521 1413 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.71 % Allowed : 8.94 % Favored : 89.35 % 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: 1.50 (0.26), residues: 389 sheet: 0.28 (0.30), residues: 291 loop : -0.20 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.004 0.001 HIS S 232 PHE 0.014 0.002 PHE R 117 TYR 0.033 0.002 TYR S 190 ARG 0.007 0.001 ARG S 72 *********************** 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 152 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 1.018 Fit side-chains REVERT: A 21 ARG cc_start: 0.7855 (ttm110) cc_final: 0.7362 (mtm-85) REVERT: A 198 MET cc_start: 0.8061 (ttp) cc_final: 0.7802 (ttp) REVERT: A 275 GLU cc_start: 0.7671 (pp20) cc_final: 0.7268 (pp20) REVERT: A 330 LYS cc_start: 0.7189 (mttt) cc_final: 0.6671 (mtpp) REVERT: B 42 ARG cc_start: 0.7163 (tpt170) cc_final: 0.6740 (tpt170) REVERT: B 101 MET cc_start: 0.8257 (mtp) cc_final: 0.8050 (mtp) REVERT: S 93 MET cc_start: 0.7844 (tpp) cc_final: 0.7615 (ttt) REVERT: S 238 THR cc_start: 0.8616 (m) cc_final: 0.8265 (p) REVERT: R 101 ARG cc_start: 0.7693 (mtm-85) cc_final: 0.7415 (mtm-85) outliers start: 17 outliers final: 6 residues processed: 141 average time/residue: 1.3991 time to fit residues: 209.7967 Evaluate side-chains 125 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain R residue 216 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 259 GLN B 340 ASN S 142 GLN S 167 HIS S 186 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9395 Z= 0.294 Angle : 0.587 6.799 12723 Z= 0.312 Chirality : 0.044 0.220 1429 Planarity : 0.005 0.068 1596 Dihedral : 6.287 69.060 1413 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.81 % Allowed : 11.16 % Favored : 86.03 % 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: 1.61 (0.26), residues: 392 sheet: 0.08 (0.29), residues: 287 loop : -0.24 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.005 0.001 HIS S 232 PHE 0.018 0.002 PHE R 277 TYR 0.034 0.002 TYR S 190 ARG 0.006 0.001 ARG S 72 *********************** 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 169 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 1.166 Fit side-chains REVERT: A 21 ARG cc_start: 0.7873 (ttm110) cc_final: 0.7440 (mtm-85) REVERT: A 22 ASN cc_start: 0.8403 (m-40) cc_final: 0.8201 (m110) REVERT: A 46 LYS cc_start: 0.6694 (mttp) cc_final: 0.6361 (mttt) REVERT: A 275 GLU cc_start: 0.7688 (pp20) cc_final: 0.7286 (pp20) REVERT: A 305 CYS cc_start: 0.7339 (m) cc_final: 0.7045 (m) REVERT: A 330 LYS cc_start: 0.7362 (mttt) cc_final: 0.6654 (mtpp) REVERT: B 44 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: B 325 MET cc_start: 0.8333 (tpp) cc_final: 0.8129 (mmt) REVERT: S 238 THR cc_start: 0.8656 (m) cc_final: 0.8393 (p) REVERT: R 60 LYS cc_start: 0.7662 (mttp) cc_final: 0.7424 (mtpt) REVERT: R 101 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.7564 (mtm-85) REVERT: R 150 LEU cc_start: 0.8230 (mp) cc_final: 0.8005 (mm) REVERT: R 164 LYS cc_start: 0.7201 (mppt) cc_final: 0.6833 (mtmm) REVERT: R 186 PHE cc_start: 0.7276 (m-80) cc_final: 0.6426 (t80) outliers start: 28 outliers final: 11 residues processed: 155 average time/residue: 1.5258 time to fit residues: 250.1548 Evaluate side-chains 141 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 142 GLN Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain R residue 216 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 108 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 ASN S 179 GLN S 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9395 Z= 0.188 Angle : 0.512 6.343 12723 Z= 0.274 Chirality : 0.042 0.189 1429 Planarity : 0.004 0.068 1596 Dihedral : 6.099 76.315 1413 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.41 % Allowed : 13.77 % Favored : 83.82 % 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 (0.26), residues: 1137 helix: 1.90 (0.27), residues: 390 sheet: 0.15 (0.29), residues: 293 loop : -0.20 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.002 0.001 HIS S 35 PHE 0.011 0.001 PHE R 277 TYR 0.030 0.001 TYR S 190 ARG 0.003 0.000 ARG S 180 *********************** 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 161 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 1.129 Fit side-chains REVERT: A 21 ARG cc_start: 0.7861 (ttm110) cc_final: 0.7492 (mtm-85) REVERT: A 46 LYS cc_start: 0.6663 (mttp) cc_final: 0.6293 (mttt) REVERT: A 275 GLU cc_start: 0.7699 (pp20) cc_final: 0.7402 (pp20) REVERT: A 330 LYS cc_start: 0.7382 (mttt) cc_final: 0.6648 (mtpp) REVERT: S 77 ASN cc_start: 0.8379 (m-40) cc_final: 0.8035 (m-40) REVERT: S 142 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7195 (mt0) REVERT: S 238 THR cc_start: 0.8617 (m) cc_final: 0.8361 (p) REVERT: R 60 LYS cc_start: 0.7581 (mttp) cc_final: 0.7332 (mtpt) REVERT: R 150 LEU cc_start: 0.8257 (mp) cc_final: 0.8037 (mm) REVERT: R 164 LYS cc_start: 0.7150 (mppt) cc_final: 0.6815 (mtmm) REVERT: R 186 PHE cc_start: 0.7205 (m-80) cc_final: 0.6391 (t80) REVERT: R 225 LYS cc_start: 0.7974 (mtpt) cc_final: 0.7757 (mtpt) outliers start: 24 outliers final: 8 residues processed: 148 average time/residue: 1.5276 time to fit residues: 238.7998 Evaluate side-chains 137 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 142 GLN Chi-restraints excluded: chain S residue 195 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN S 171 ASN S 179 GLN S 186 GLN R 189 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9395 Z= 0.347 Angle : 0.604 7.044 12723 Z= 0.321 Chirality : 0.045 0.225 1429 Planarity : 0.005 0.071 1596 Dihedral : 6.561 89.362 1413 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.52 % Allowed : 14.07 % Favored : 82.41 % 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: 0.77 (0.25), residues: 1137 helix: 1.90 (0.26), residues: 385 sheet: 0.00 (0.30), residues: 287 loop : -0.25 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 169 HIS 0.004 0.001 HIS S 35 PHE 0.020 0.002 PHE R 277 TYR 0.034 0.002 TYR S 190 ARG 0.004 0.001 ARG S 72 *********************** 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 161 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 1.214 Fit side-chains REVERT: A 21 ARG cc_start: 0.7857 (ttm110) cc_final: 0.7496 (mtm-85) REVERT: A 46 LYS cc_start: 0.6988 (mttp) cc_final: 0.6514 (mttt) REVERT: A 275 GLU cc_start: 0.7633 (pp20) cc_final: 0.7248 (pp20) REVERT: A 330 LYS cc_start: 0.7420 (mttt) cc_final: 0.6691 (mtpp) REVERT: B 44 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: B 197 ARG cc_start: 0.8160 (mmt-90) cc_final: 0.7712 (mmm160) REVERT: S 19 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7930 (tttt) REVERT: S 190 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.6265 (p90) REVERT: S 238 THR cc_start: 0.8630 (m) cc_final: 0.8398 (p) REVERT: R 60 LYS cc_start: 0.7691 (mttp) cc_final: 0.7479 (mtpt) REVERT: R 150 LEU cc_start: 0.8243 (mp) cc_final: 0.8005 (mm) REVERT: R 164 LYS cc_start: 0.7299 (mppt) cc_final: 0.6991 (mtmm) REVERT: R 186 PHE cc_start: 0.7314 (m-80) cc_final: 0.6460 (t80) REVERT: R 225 LYS cc_start: 0.7977 (mtpt) cc_final: 0.7722 (mtpt) outliers start: 35 outliers final: 12 residues processed: 146 average time/residue: 1.5486 time to fit residues: 239.1125 Evaluate side-chains 133 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 190 TYR Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain R residue 216 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 0.1980 chunk 104 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 294 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9395 Z= 0.174 Angle : 0.505 6.297 12723 Z= 0.271 Chirality : 0.041 0.186 1429 Planarity : 0.004 0.067 1596 Dihedral : 5.978 76.255 1413 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.51 % Allowed : 16.08 % Favored : 81.41 % 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: 2.08 (0.27), residues: 386 sheet: 0.15 (0.30), residues: 291 loop : -0.27 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.002 0.000 HIS S 35 PHE 0.010 0.001 PHE R 276 TYR 0.029 0.001 TYR S 190 ARG 0.006 0.000 ARG S 180 *********************** 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 160 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 1.006 Fit side-chains REVERT: A 21 ARG cc_start: 0.7849 (ttm110) cc_final: 0.7439 (mtm110) REVERT: A 46 LYS cc_start: 0.6991 (mttp) cc_final: 0.6417 (mttt) REVERT: A 275 GLU cc_start: 0.7618 (pp20) cc_final: 0.7301 (pp20) REVERT: A 305 CYS cc_start: 0.7380 (m) cc_final: 0.7065 (m) REVERT: A 330 LYS cc_start: 0.7416 (mttt) cc_final: 0.6708 (mtpp) REVERT: B 259 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7502 (mt0) REVERT: S 19 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7894 (tttt) REVERT: S 190 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.6074 (p90) REVERT: S 238 THR cc_start: 0.8588 (m) cc_final: 0.8387 (p) REVERT: R 60 LYS cc_start: 0.7657 (mttp) cc_final: 0.7424 (mtpt) REVERT: R 150 LEU cc_start: 0.8263 (mp) cc_final: 0.8050 (mm) REVERT: R 164 LYS cc_start: 0.7241 (mppt) cc_final: 0.6904 (mtmm) REVERT: R 186 PHE cc_start: 0.7240 (m-80) cc_final: 0.6402 (t80) REVERT: R 225 LYS cc_start: 0.7966 (mtpt) cc_final: 0.7709 (mtpt) outliers start: 25 outliers final: 11 residues processed: 145 average time/residue: 1.4916 time to fit residues: 229.1218 Evaluate side-chains 144 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 190 TYR Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 204 SER 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: 8.9990 chunk 79 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 0.0040 chunk 66 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9395 Z= 0.218 Angle : 0.531 6.395 12723 Z= 0.283 Chirality : 0.042 0.198 1429 Planarity : 0.004 0.067 1596 Dihedral : 5.865 69.901 1413 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.61 % Allowed : 16.38 % Favored : 81.01 % 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: 2.06 (0.26), residues: 387 sheet: 0.08 (0.30), residues: 294 loop : -0.22 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE R 277 TYR 0.031 0.001 TYR S 190 ARG 0.005 0.000 ARG B 219 *********************** 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 157 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 1.031 Fit side-chains REVERT: A 21 ARG cc_start: 0.7781 (ttm110) cc_final: 0.7389 (mtm110) REVERT: A 46 LYS cc_start: 0.7029 (mttp) cc_final: 0.6672 (mtmt) REVERT: A 275 GLU cc_start: 0.7604 (pp20) cc_final: 0.7270 (pp20) REVERT: A 305 CYS cc_start: 0.7339 (m) cc_final: 0.7019 (m) REVERT: A 330 LYS cc_start: 0.7455 (mttt) cc_final: 0.6761 (mtpp) REVERT: B 259 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7503 (mt0) REVERT: S 19 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7940 (tttt) REVERT: S 190 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.6154 (p90) REVERT: S 238 THR cc_start: 0.8604 (m) cc_final: 0.8395 (p) REVERT: R 60 LYS cc_start: 0.7664 (mttp) cc_final: 0.7436 (mtpt) REVERT: R 150 LEU cc_start: 0.8243 (mp) cc_final: 0.8039 (mm) REVERT: R 164 LYS cc_start: 0.7249 (mppt) cc_final: 0.6894 (mtmm) REVERT: R 186 PHE cc_start: 0.7405 (m-80) cc_final: 0.6557 (t80) REVERT: R 225 LYS cc_start: 0.7952 (mtpt) cc_final: 0.7677 (mtpt) outliers start: 26 outliers final: 11 residues processed: 142 average time/residue: 1.6098 time to fit residues: 241.1101 Evaluate side-chains 141 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 190 TYR Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS B 340 ASN S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9395 Z= 0.247 Angle : 0.553 7.102 12723 Z= 0.293 Chirality : 0.043 0.205 1429 Planarity : 0.004 0.067 1596 Dihedral : 5.820 64.929 1413 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.31 % Allowed : 16.78 % 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: 0.89 (0.26), residues: 1137 helix: 2.05 (0.26), residues: 386 sheet: 0.05 (0.30), residues: 294 loop : -0.22 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 PHE 0.014 0.001 PHE R 277 TYR 0.032 0.002 TYR S 190 ARG 0.004 0.000 ARG B 219 *********************** 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 153 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 1.086 Fit side-chains REVERT: A 21 ARG cc_start: 0.7756 (ttm110) cc_final: 0.7377 (mtm110) REVERT: A 46 LYS cc_start: 0.7041 (mttp) cc_final: 0.6668 (mtmt) REVERT: A 275 GLU cc_start: 0.7605 (pp20) cc_final: 0.7269 (pp20) REVERT: A 305 CYS cc_start: 0.7345 (m) cc_final: 0.7042 (m) REVERT: A 330 LYS cc_start: 0.7494 (mttt) cc_final: 0.6882 (mtpp) REVERT: B 259 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7529 (mt0) REVERT: S 19 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7948 (tttt) REVERT: S 190 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.6153 (p90) REVERT: S 238 THR cc_start: 0.8614 (m) cc_final: 0.8396 (p) REVERT: R 150 LEU cc_start: 0.8243 (mp) cc_final: 0.8036 (mm) REVERT: R 164 LYS cc_start: 0.7284 (mppt) cc_final: 0.6943 (mtmm) REVERT: R 186 PHE cc_start: 0.7434 (m-80) cc_final: 0.6564 (t80) REVERT: R 225 LYS cc_start: 0.7959 (mtpt) cc_final: 0.7672 (mtpt) outliers start: 23 outliers final: 11 residues processed: 139 average time/residue: 1.4910 time to fit residues: 219.4238 Evaluate side-chains 140 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 190 TYR Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain R residue 216 ARG 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: 1.9990 chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 0.0970 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 0.0010 chunk 95 optimal weight: 0.0670 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9395 Z= 0.140 Angle : 0.491 7.508 12723 Z= 0.261 Chirality : 0.041 0.164 1429 Planarity : 0.004 0.064 1596 Dihedral : 5.366 56.249 1413 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.11 % Allowed : 17.19 % Favored : 80.70 % 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: 1.08 (0.26), residues: 1137 helix: 2.25 (0.27), residues: 386 sheet: 0.16 (0.30), residues: 289 loop : -0.16 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 HIS 0.002 0.000 HIS S 35 PHE 0.010 0.001 PHE R 276 TYR 0.026 0.001 TYR S 190 ARG 0.005 0.000 ARG B 219 *********************** 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 164 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 1.060 Fit side-chains REVERT: A 21 ARG cc_start: 0.7793 (ttm110) cc_final: 0.7298 (mtm110) REVERT: A 46 LYS cc_start: 0.6997 (mttp) cc_final: 0.6590 (mtmt) REVERT: A 252 SER cc_start: 0.8689 (p) cc_final: 0.8463 (p) REVERT: A 275 GLU cc_start: 0.7588 (pp20) cc_final: 0.7236 (pp20) REVERT: A 330 LYS cc_start: 0.7457 (mttt) cc_final: 0.6853 (mtpp) REVERT: B 42 ARG cc_start: 0.7157 (tpt170) cc_final: 0.6801 (tpt170) REVERT: S 19 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7932 (tttt) REVERT: S 190 TYR cc_start: 0.7770 (OUTLIER) cc_final: 0.6005 (p90) REVERT: R 164 LYS cc_start: 0.7329 (mppt) cc_final: 0.6947 (mtmm) REVERT: R 225 LYS cc_start: 0.7949 (mtpt) cc_final: 0.7650 (mtpt) outliers start: 21 outliers final: 9 residues processed: 151 average time/residue: 1.3854 time to fit residues: 222.4360 Evaluate side-chains 141 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 190 TYR Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9395 Z= 0.195 Angle : 0.525 7.612 12723 Z= 0.278 Chirality : 0.042 0.192 1429 Planarity : 0.004 0.065 1596 Dihedral : 5.442 58.411 1413 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.41 % Allowed : 18.09 % Favored : 80.50 % 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: 1.08 (0.26), residues: 1137 helix: 2.22 (0.27), residues: 388 sheet: 0.18 (0.30), residues: 292 loop : -0.14 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.000 HIS S 35 PHE 0.011 0.001 PHE A 196 TYR 0.030 0.001 TYR S 190 ARG 0.008 0.000 ARG S 202 ********************** 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 149 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 1.009 Fit side-chains REVERT: A 21 ARG cc_start: 0.7741 (ttm110) cc_final: 0.7370 (mtm110) REVERT: A 46 LYS cc_start: 0.7050 (mttp) cc_final: 0.6642 (mtmt) REVERT: A 275 GLU cc_start: 0.7596 (pp20) cc_final: 0.7239 (pp20) REVERT: A 330 LYS cc_start: 0.7481 (mttt) cc_final: 0.6861 (mtpp) REVERT: B 42 ARG cc_start: 0.7139 (tpt170) cc_final: 0.6789 (tpt170) REVERT: S 19 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7947 (tttt) REVERT: S 190 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.6115 (p90) REVERT: R 85 ASP cc_start: 0.8001 (t0) cc_final: 0.7732 (t0) REVERT: R 164 LYS cc_start: 0.7238 (mppt) cc_final: 0.6875 (mtmm) REVERT: R 225 LYS cc_start: 0.7935 (mtpt) cc_final: 0.7648 (mtpt) outliers start: 14 outliers final: 8 residues processed: 143 average time/residue: 1.4520 time to fit residues: 220.1122 Evaluate side-chains 141 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 190 TYR Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 0.0570 chunk 91 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.160767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.119725 restraints weight = 8951.630| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.01 r_work: 0.3117 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9395 Z= 0.214 Angle : 0.539 9.184 12723 Z= 0.285 Chirality : 0.043 0.197 1429 Planarity : 0.004 0.067 1596 Dihedral : 5.484 57.489 1413 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.21 % Allowed : 18.19 % Favored : 80.60 % 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: 2.16 (0.27), residues: 388 sheet: 0.12 (0.30), residues: 295 loop : -0.14 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE R 277 TYR 0.031 0.001 TYR S 190 ARG 0.008 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4257.44 seconds wall clock time: 77 minutes 9.53 seconds (4629.53 seconds total)