Starting phenix.real_space_refine on Thu Mar 14 16:07:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6p_36010/03_2024/8j6p_36010_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6p_36010/03_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_36010/03_2024/8j6p_36010.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6p_36010/03_2024/8j6p_36010.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6p_36010/03_2024/8j6p_36010_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6p_36010/03_2024/8j6p_36010_updated.pdb" } 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 Residue "S PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.58, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG R 405 " - " ASN R 17 " Time building additional restraints: 3.48 Conformation dependent library (CDL) restraints added in 1.7 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... running ksdssp... Secondary structure from input PDB file: 30 helices and 13 sheets defined 34.4% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.796A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 350 removed outlier: 4.229A pdb=" N VAL A 332 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.667A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 removed outlier: 3.511A pdb=" N ILE G 9 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA G 23 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing helix chain 'R' and resid 24 through 53 Proline residue: R 31 - end of helix Processing helix chain 'R' and resid 61 through 77 Processing helix chain 'R' and resid 80 through 88 Processing helix chain 'R' and resid 98 through 129 Processing helix chain 'R' and resid 135 through 138 Processing helix chain 'R' and resid 141 through 162 removed outlier: 5.104A pdb=" N HIS R 161 " --> pdb=" O GLY R 157 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU R 162 " --> pdb=" O LEU R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 173 No H-bonds generated for 'chain 'R' and resid 171 through 173' Processing helix chain 'R' and resid 188 through 217 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 220 through 222 No H-bonds generated for 'chain 'R' and resid 220 through 222' Processing helix chain 'R' and resid 224 through 260 Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 266 through 294 removed outlier: 4.072A pdb=" N ARG R 270 " --> pdb=" O GLU R 267 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER R 271 " --> pdb=" O VAL R 268 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL R 272 " --> pdb=" O TYR R 269 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA R 275 " --> pdb=" O VAL R 272 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN R 286 " --> pdb=" O THR R 283 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP R 290 " --> pdb=" O SER R 287 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 319 through 324 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= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.766A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) 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: 6.279A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.730A 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= D, 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= E, first strand: chain 'B' and resid 198 through 202 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= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.578A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) 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= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.529A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) 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= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.469A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 115 through 117 removed outlier: 5.994A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.250A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'S' and resid 155 through 160 Processing sheet with id= M, first strand: chain 'S' and resid 226 through 231 removed outlier: 3.593A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1017 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: 2.41 Time building geometry restraints manager: 3.81 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: 95.49 - 103.39: 73 103.39 - 111.29: 3866 111.29 - 119.19: 3855 119.19 - 127.09: 4818 127.09 - 134.99: 111 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: 8290 3.23 - 3.79: 15187 3.79 - 4.34: 21030 4.34 - 4.90: 34518 Nonbonded interactions: 79200 Sorted by model distance: nonbonded pdb=" OE1 GLN A 52 " pdb=" ND2 ASN A 331 " model vdw 2.120 2.520 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 175 " model vdw 2.230 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.243 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.255 2.440 nonbonded pdb=" OH TYR R 284 " pdb=" O1 NIO R 403 " model vdw 2.283 2.440 ... (remaining 79195 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 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: 2.870 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.190 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.340 ------------------------------------------------------------------------------- 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= 0.341 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 fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.000 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: 1.1679 time to fit residues: 214.7054 Evaluate side-chains 127 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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: 4.9990 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.0570 chunk 101 optimal weight: 6.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN B 340 ASN S 142 GLN S 186 GLN R 112 GLN R 141 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9395 Z= 0.196 Angle : 0.531 6.680 12723 Z= 0.285 Chirality : 0.042 0.177 1429 Planarity : 0.005 0.076 1596 Dihedral : 5.816 51.763 1413 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.81 % Allowed : 8.24 % Favored : 89.95 % 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: 1.20 (0.26), residues: 385 sheet: 0.30 (0.29), residues: 292 loop : -0.24 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.004 0.001 HIS S 232 PHE 0.012 0.001 PHE A 196 TYR 0.028 0.001 TYR S 190 ARG 0.006 0.000 ARG B 197 *********************** 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 166 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 0.905 Fit side-chains REVERT: A 8 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7191 (mt-10) REVERT: A 21 ARG cc_start: 0.7772 (ttm110) cc_final: 0.7247 (mtm-85) REVERT: A 198 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7709 (ttp) REVERT: A 275 GLU cc_start: 0.7647 (pp20) cc_final: 0.7319 (pp20) REVERT: A 330 LYS cc_start: 0.6794 (mttt) cc_final: 0.6179 (mtpp) REVERT: B 42 ARG cc_start: 0.7151 (tpt170) cc_final: 0.6781 (tpt170) REVERT: S 142 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.6994 (mt0) REVERT: S 238 THR cc_start: 0.8555 (m) cc_final: 0.8179 (p) outliers start: 18 outliers final: 5 residues processed: 155 average time/residue: 1.3237 time to fit residues: 218.2051 Evaluate side-chains 134 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 127 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET 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 142 GLN 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: 6.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN R 141 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9395 Z= 0.183 Angle : 0.497 6.416 12723 Z= 0.266 Chirality : 0.041 0.177 1429 Planarity : 0.004 0.068 1596 Dihedral : 5.749 62.833 1413 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.01 % Allowed : 10.75 % Favored : 87.24 % 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: 0.63 (0.25), residues: 1137 helix: 1.24 (0.27), residues: 386 sheet: 0.39 (0.29), residues: 293 loop : -0.15 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.013 0.001 PHE R 277 TYR 0.027 0.001 TYR S 190 ARG 0.004 0.000 ARG B 129 *********************** 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 161 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 1.033 Fit side-chains REVERT: A 21 ARG cc_start: 0.7833 (ttm110) cc_final: 0.7333 (mtm-85) REVERT: A 198 MET cc_start: 0.8047 (ttp) cc_final: 0.7844 (ttp) REVERT: A 275 GLU cc_start: 0.7627 (pp20) cc_final: 0.7208 (pp20) REVERT: A 330 LYS cc_start: 0.6864 (mttt) cc_final: 0.6353 (mtpp) REVERT: B 42 ARG cc_start: 0.7116 (tpt170) cc_final: 0.6711 (tpt170) REVERT: B 197 ARG cc_start: 0.7964 (mmm160) cc_final: 0.7750 (mmt-90) REVERT: S 77 ASN cc_start: 0.8105 (m-40) cc_final: 0.7825 (m110) REVERT: S 238 THR cc_start: 0.8621 (m) cc_final: 0.8267 (p) REVERT: R 150 LEU cc_start: 0.8251 (mp) cc_final: 0.8030 (mm) outliers start: 20 outliers final: 8 residues processed: 149 average time/residue: 1.1982 time to fit residues: 190.7176 Evaluate side-chains 145 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 B residue 270 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain R residue 112 GLN 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: 4.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 108 optimal weight: 0.0870 chunk 53 optimal weight: 0.0870 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.3540 ------------------------------------------------------------------------------- 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** A 331 ASN B 75 GLN B 340 ASN S 142 GLN S 167 HIS S 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9395 Z= 0.267 Angle : 0.556 6.522 12723 Z= 0.294 Chirality : 0.043 0.208 1429 Planarity : 0.005 0.067 1596 Dihedral : 6.056 72.040 1413 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.51 % Allowed : 12.46 % Favored : 85.03 % 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: 0.59 (0.25), residues: 1137 helix: 1.25 (0.27), residues: 385 sheet: 0.26 (0.29), residues: 296 loop : -0.14 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.018 0.002 PHE R 277 TYR 0.031 0.002 TYR S 190 ARG 0.005 0.001 ARG B 129 *********************** 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 171 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 146 time to evaluate : 0.974 Fit side-chains REVERT: A 21 ARG cc_start: 0.7819 (ttm110) cc_final: 0.7423 (mtm-85) REVERT: A 46 LYS cc_start: 0.6901 (mttp) cc_final: 0.6532 (mttt) REVERT: A 198 MET cc_start: 0.8152 (ttp) cc_final: 0.7930 (ttp) REVERT: A 275 GLU cc_start: 0.7688 (pp20) cc_final: 0.7381 (pp20) REVERT: A 305 CYS cc_start: 0.7296 (m) cc_final: 0.7037 (m) REVERT: A 330 LYS cc_start: 0.6965 (mttt) cc_final: 0.6341 (mtpp) REVERT: B 42 ARG cc_start: 0.7166 (tpt170) cc_final: 0.6707 (tpt170) REVERT: B 44 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7908 (tt0) REVERT: B 61 MET cc_start: 0.8188 (ptm) cc_final: 0.7704 (ptm) REVERT: B 196 THR cc_start: 0.7846 (p) cc_final: 0.7628 (p) REVERT: S 238 THR cc_start: 0.8618 (m) cc_final: 0.8367 (p) REVERT: R 85 ASP cc_start: 0.7945 (t0) cc_final: 0.7706 (t0) REVERT: R 150 LEU cc_start: 0.8235 (mp) cc_final: 0.8008 (mm) REVERT: R 164 LYS cc_start: 0.7145 (mppt) cc_final: 0.6809 (mtmm) outliers start: 25 outliers final: 13 residues processed: 159 average time/residue: 1.3570 time to fit residues: 228.6244 Evaluate side-chains 146 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 44 GLN 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 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 216 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 7.9990 chunk 1 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN S 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9395 Z= 0.269 Angle : 0.544 6.325 12723 Z= 0.290 Chirality : 0.043 0.204 1429 Planarity : 0.005 0.066 1596 Dihedral : 6.248 86.499 1413 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.51 % Allowed : 14.57 % Favored : 82.91 % 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: 0.57 (0.26), residues: 1137 helix: 1.19 (0.27), residues: 386 sheet: 0.25 (0.29), residues: 305 loop : -0.10 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.016 0.002 PHE R 277 TYR 0.030 0.002 TYR S 190 ARG 0.003 0.000 ARG S 202 *********************** 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 165 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 0.963 Fit side-chains REVERT: A 21 ARG cc_start: 0.7863 (ttm110) cc_final: 0.7463 (mtm-85) REVERT: A 46 LYS cc_start: 0.7043 (mttp) cc_final: 0.6707 (mttt) REVERT: A 198 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7943 (ttp) REVERT: A 275 GLU cc_start: 0.7682 (pp20) cc_final: 0.7404 (pp20) REVERT: A 305 CYS cc_start: 0.7303 (m) cc_final: 0.7045 (m) REVERT: A 330 LYS cc_start: 0.7020 (mttt) cc_final: 0.6364 (mtpp) REVERT: B 61 MET cc_start: 0.8241 (ptm) cc_final: 0.7607 (ptm) REVERT: B 196 THR cc_start: 0.7832 (p) cc_final: 0.7628 (p) REVERT: S 18 ARG cc_start: 0.8227 (tpp80) cc_final: 0.8024 (tpp-160) REVERT: S 76 LYS cc_start: 0.7079 (OUTLIER) cc_final: 0.6626 (mttp) REVERT: S 142 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7854 (mt0) REVERT: S 238 THR cc_start: 0.8588 (m) cc_final: 0.8354 (p) REVERT: R 150 LEU cc_start: 0.8240 (mp) cc_final: 0.8002 (mm) REVERT: R 164 LYS cc_start: 0.7204 (mppt) cc_final: 0.6876 (mtmm) REVERT: R 225 LYS cc_start: 0.7960 (mtpt) cc_final: 0.7743 (mtpt) outliers start: 25 outliers final: 13 residues processed: 153 average time/residue: 1.3439 time to fit residues: 218.2003 Evaluate side-chains 147 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 329 THR 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 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 141 THR 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 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: 3.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 108 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN R 112 GLN R 141 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9395 Z= 0.195 Angle : 0.504 6.848 12723 Z= 0.269 Chirality : 0.042 0.186 1429 Planarity : 0.004 0.065 1596 Dihedral : 6.081 85.029 1413 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.41 % Allowed : 15.48 % Favored : 82.11 % 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: 0.63 (0.26), residues: 1137 helix: 1.28 (0.27), residues: 384 sheet: 0.21 (0.30), residues: 295 loop : -0.03 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE R 277 TYR 0.029 0.001 TYR S 190 ARG 0.004 0.000 ARG S 202 *********************** 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 163 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 139 time to evaluate : 1.068 Fit side-chains REVERT: A 21 ARG cc_start: 0.7827 (ttm110) cc_final: 0.7441 (mtm-85) REVERT: A 46 LYS cc_start: 0.7019 (mttp) cc_final: 0.6693 (mttt) REVERT: A 198 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7921 (ttp) REVERT: A 243 MET cc_start: 0.7948 (tpp) cc_final: 0.7660 (tpp) REVERT: A 275 GLU cc_start: 0.7701 (pp20) cc_final: 0.7419 (pp20) REVERT: A 330 LYS cc_start: 0.7036 (mttt) cc_final: 0.6376 (mtpp) REVERT: B 61 MET cc_start: 0.8092 (ptm) cc_final: 0.7734 (ptm) REVERT: B 196 THR cc_start: 0.7758 (p) cc_final: 0.7540 (p) REVERT: B 197 ARG cc_start: 0.8090 (mmt-90) cc_final: 0.7663 (mmm160) REVERT: B 223 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.8466 (p) REVERT: S 113 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7904 (mm-40) REVERT: S 190 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.6167 (p90) REVERT: S 238 THR cc_start: 0.8576 (m) cc_final: 0.8362 (p) REVERT: R 150 LEU cc_start: 0.8246 (mp) cc_final: 0.8020 (mm) REVERT: R 164 LYS cc_start: 0.7202 (mppt) cc_final: 0.6870 (mtmm) outliers start: 24 outliers final: 13 residues processed: 150 average time/residue: 1.3837 time to fit residues: 219.9276 Evaluate side-chains 151 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 198 MET 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 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 190 TYR Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain R residue 216 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 0.0870 chunk 43 optimal weight: 0.8980 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN S 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9395 Z= 0.177 Angle : 0.489 6.915 12723 Z= 0.262 Chirality : 0.041 0.180 1429 Planarity : 0.004 0.067 1596 Dihedral : 5.720 73.731 1413 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.91 % Allowed : 16.68 % 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: 0.72 (0.26), residues: 1137 helix: 1.34 (0.27), residues: 384 sheet: 0.27 (0.30), residues: 298 loop : 0.02 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.011 0.001 PHE R 277 TYR 0.028 0.001 TYR S 190 ARG 0.004 0.000 ARG S 202 *********************** 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 159 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 140 time to evaluate : 1.053 Fit side-chains REVERT: A 21 ARG cc_start: 0.7794 (ttm110) cc_final: 0.7372 (mtm110) REVERT: A 46 LYS cc_start: 0.7006 (mttp) cc_final: 0.6713 (mtmt) REVERT: A 198 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7917 (ttp) REVERT: A 243 MET cc_start: 0.7947 (tpp) cc_final: 0.7661 (tpp) REVERT: A 275 GLU cc_start: 0.7696 (pp20) cc_final: 0.7410 (pp20) REVERT: A 330 LYS cc_start: 0.7063 (mttt) cc_final: 0.6399 (mtpp) REVERT: B 61 MET cc_start: 0.8162 (ptm) cc_final: 0.7613 (ptm) REVERT: B 196 THR cc_start: 0.7696 (p) cc_final: 0.7474 (p) REVERT: B 223 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8451 (p) REVERT: S 113 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7928 (mm-40) REVERT: S 190 TYR cc_start: 0.7973 (OUTLIER) cc_final: 0.6171 (p90) REVERT: S 192 MET cc_start: 0.7865 (ttp) cc_final: 0.7620 (tmm) REVERT: S 238 THR cc_start: 0.8578 (m) cc_final: 0.8345 (p) REVERT: R 16 LYS cc_start: 0.7075 (pttp) cc_final: 0.6684 (ptpt) REVERT: R 150 LEU cc_start: 0.8255 (mp) cc_final: 0.8044 (mm) REVERT: R 164 LYS cc_start: 0.7166 (mppt) cc_final: 0.6819 (mtmm) REVERT: R 225 LYS cc_start: 0.7898 (mtpt) cc_final: 0.7649 (mtpt) REVERT: R 238 ILE cc_start: 0.8144 (mt) cc_final: 0.7918 (mp) outliers start: 19 outliers final: 15 residues processed: 151 average time/residue: 1.3958 time to fit residues: 223.6578 Evaluate side-chains 154 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 198 MET 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 78 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN 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 190 TYR Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain R residue 216 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 84 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9395 Z= 0.159 Angle : 0.478 7.721 12723 Z= 0.256 Chirality : 0.041 0.173 1429 Planarity : 0.004 0.064 1596 Dihedral : 5.481 67.145 1413 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.01 % Allowed : 16.98 % 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: 0.79 (0.26), residues: 1137 helix: 1.46 (0.27), residues: 379 sheet: 0.33 (0.29), residues: 306 loop : -0.01 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 PHE 0.009 0.001 PHE R 277 TYR 0.027 0.001 TYR S 190 ARG 0.002 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 166 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 0.936 Fit side-chains REVERT: A 21 ARG cc_start: 0.7795 (ttm110) cc_final: 0.7369 (mtm110) REVERT: A 46 LYS cc_start: 0.6932 (mttp) cc_final: 0.6625 (mttt) REVERT: A 198 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7908 (ttp) REVERT: A 243 MET cc_start: 0.7950 (tpp) cc_final: 0.7664 (tpp) REVERT: A 275 GLU cc_start: 0.7664 (pp20) cc_final: 0.7408 (pp20) REVERT: A 330 LYS cc_start: 0.7085 (mttt) cc_final: 0.6394 (mtpp) REVERT: B 61 MET cc_start: 0.8145 (ptm) cc_final: 0.7709 (ptm) REVERT: B 78 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8356 (tppt) REVERT: B 196 THR cc_start: 0.7659 (p) cc_final: 0.7422 (p) REVERT: B 197 ARG cc_start: 0.8070 (mmt-90) cc_final: 0.7637 (mmm160) REVERT: B 223 THR cc_start: 0.8747 (OUTLIER) cc_final: 0.8434 (p) REVERT: B 258 ASP cc_start: 0.7706 (t0) cc_final: 0.7455 (t70) REVERT: S 83 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8341 (mtm) REVERT: S 93 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7764 (ttp) REVERT: S 113 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7881 (mm-40) REVERT: S 190 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.6132 (p90) REVERT: S 238 THR cc_start: 0.8578 (m) cc_final: 0.8343 (p) REVERT: R 60 LYS cc_start: 0.7627 (mttp) cc_final: 0.7355 (mtpt) REVERT: R 164 LYS cc_start: 0.7103 (mppt) cc_final: 0.6788 (mtmm) REVERT: R 187 GLN cc_start: 0.7600 (mm-40) cc_final: 0.7322 (tp-100) REVERT: R 238 ILE cc_start: 0.8122 (mt) cc_final: 0.7904 (mp) outliers start: 20 outliers final: 11 residues processed: 155 average time/residue: 1.3578 time to fit residues: 223.3707 Evaluate side-chains 156 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 190 TYR Chi-restraints excluded: chain S residue 195 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 43 optimal weight: 0.4980 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 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 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN B 175 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** S 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9395 Z= 0.173 Angle : 0.485 7.320 12723 Z= 0.259 Chirality : 0.041 0.179 1429 Planarity : 0.004 0.065 1596 Dihedral : 5.349 62.948 1413 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.71 % Allowed : 16.28 % 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: 0.73 (0.26), residues: 1137 helix: 1.45 (0.27), residues: 379 sheet: 0.19 (0.30), residues: 294 loop : 0.01 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.000 HIS S 35 PHE 0.010 0.001 PHE R 277 TYR 0.028 0.001 TYR S 190 ARG 0.002 0.000 ARG S 72 *********************** 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 166 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.036 Fit side-chains REVERT: A 21 ARG cc_start: 0.7779 (ttm110) cc_final: 0.7364 (mtm110) REVERT: A 46 LYS cc_start: 0.6999 (mttp) cc_final: 0.6632 (mttt) REVERT: A 198 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7893 (ttp) REVERT: A 243 MET cc_start: 0.7954 (tpp) cc_final: 0.7670 (tpp) REVERT: A 275 GLU cc_start: 0.7653 (pp20) cc_final: 0.7341 (pp20) REVERT: A 330 LYS cc_start: 0.7075 (mttt) cc_final: 0.6406 (mtpp) REVERT: B 61 MET cc_start: 0.8165 (ptm) cc_final: 0.7780 (ptm) REVERT: B 196 THR cc_start: 0.7652 (p) cc_final: 0.7406 (p) REVERT: B 197 ARG cc_start: 0.8079 (mmt-90) cc_final: 0.7658 (mmm160) REVERT: B 223 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8432 (p) REVERT: B 258 ASP cc_start: 0.7703 (t0) cc_final: 0.7469 (t70) REVERT: S 83 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8373 (mtm) REVERT: S 113 GLN cc_start: 0.8232 (mm-40) cc_final: 0.7914 (mm-40) REVERT: S 190 TYR cc_start: 0.7973 (OUTLIER) cc_final: 0.6183 (p90) REVERT: S 238 THR cc_start: 0.8584 (m) cc_final: 0.8350 (p) REVERT: R 164 LYS cc_start: 0.7126 (mppt) cc_final: 0.6806 (mtmm) REVERT: R 187 GLN cc_start: 0.7612 (mm-40) cc_final: 0.7328 (tp-100) REVERT: R 238 ILE cc_start: 0.8124 (mt) cc_final: 0.7907 (mp) outliers start: 27 outliers final: 13 residues processed: 150 average time/residue: 1.3324 time to fit residues: 212.1325 Evaluate side-chains 153 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 136 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 83 MET 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 159 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 0.3980 chunk 94 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 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 GLN ** 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: 0.7721 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9395 Z= 0.164 Angle : 0.481 7.497 12723 Z= 0.257 Chirality : 0.041 0.174 1429 Planarity : 0.004 0.064 1596 Dihedral : 5.217 59.819 1413 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.91 % Allowed : 17.49 % 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: 0.75 (0.26), residues: 1137 helix: 1.46 (0.27), residues: 379 sheet: 0.22 (0.30), residues: 293 loop : 0.00 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 PHE 0.010 0.001 PHE R 277 TYR 0.027 0.001 TYR S 190 ARG 0.003 0.000 ARG B 219 ********************** 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 157 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 1.068 Fit side-chains REVERT: A 21 ARG cc_start: 0.7768 (ttm110) cc_final: 0.7363 (mtm110) REVERT: A 46 LYS cc_start: 0.6982 (mttp) cc_final: 0.6652 (mttt) REVERT: A 198 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7840 (ttp) REVERT: A 243 MET cc_start: 0.7956 (tpp) cc_final: 0.7675 (tpp) REVERT: A 275 GLU cc_start: 0.7641 (pp20) cc_final: 0.7372 (pp20) REVERT: A 330 LYS cc_start: 0.7059 (mttt) cc_final: 0.6371 (mtpp) REVERT: B 61 MET cc_start: 0.8145 (ptm) cc_final: 0.7761 (ptm) REVERT: B 197 ARG cc_start: 0.8071 (mmt-90) cc_final: 0.7671 (mmm160) REVERT: B 223 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8432 (p) REVERT: B 258 ASP cc_start: 0.7741 (t0) cc_final: 0.7504 (t70) REVERT: S 83 MET cc_start: 0.8710 (mtp) cc_final: 0.8373 (mtm) REVERT: S 113 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7911 (mm-40) REVERT: S 190 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.6165 (p90) REVERT: S 238 THR cc_start: 0.8574 (m) cc_final: 0.8352 (p) REVERT: R 16 LYS cc_start: 0.7234 (pttt) cc_final: 0.6797 (ptpt) REVERT: R 164 LYS cc_start: 0.7152 (mppt) cc_final: 0.6824 (mtmm) REVERT: R 187 GLN cc_start: 0.7610 (mm-40) cc_final: 0.7340 (tp-100) REVERT: R 238 ILE cc_start: 0.8121 (mt) cc_final: 0.7908 (mp) outliers start: 19 outliers final: 15 residues processed: 149 average time/residue: 1.2530 time to fit residues: 199.3321 Evaluate side-chains 154 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 252 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 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain S residue 23 SER 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 159 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 0.0050 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 91 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.161855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.121607 restraints weight = 8976.730| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.06 r_work: 0.3123 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9395 Z= 0.155 Angle : 0.473 7.604 12723 Z= 0.253 Chirality : 0.041 0.171 1429 Planarity : 0.004 0.065 1596 Dihedral : 5.021 56.808 1413 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.61 % Allowed : 17.89 % 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: 0.78 (0.26), residues: 1137 helix: 1.50 (0.27), residues: 379 sheet: 0.22 (0.30), residues: 293 loop : 0.03 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.000 HIS S 35 PHE 0.009 0.001 PHE R 277 TYR 0.026 0.001 TYR S 190 ARG 0.004 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4077.51 seconds wall clock time: 72 minutes 29.50 seconds (4349.50 seconds total)