Starting phenix.real_space_refine on Wed Feb 12 07:01:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f6i_31481/02_2025/7f6i_31481.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f6i_31481/02_2025/7f6i_31481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f6i_31481/02_2025/7f6i_31481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f6i_31481/02_2025/7f6i_31481.map" model { file = "/net/cci-nas-00/data/ceres_data/7f6i_31481/02_2025/7f6i_31481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f6i_31481/02_2025/7f6i_31481.cif" } resolution = 2.8 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= 0.004 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 57 5.16 5 C 4724 2.51 5 N 1244 2.21 5 O 1336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7361 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2448 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 9, 'TRANS': 295} Chain: "L" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 84 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 3, 'TRANS': 6} Chain: "B" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1867 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain breaks: 1 Chain: "C" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2507 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 321} Chain: "D" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 371 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 4, 'TRANS': 43} Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.83, per 1000 atoms: 0.66 Number of scatterers: 7361 At special positions: 0 Unit cell: (104.442, 94.302, 120.666, 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 57 16.00 O 1336 8.00 N 1244 7.00 C 4724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 304 " distance=2.03 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 211 " 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 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 1.0 seconds 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1734 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 9 sheets defined 45.1% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 50 through 85 removed outlier: 3.756A pdb=" N GLY A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Proline residue: A 61 - end of helix removed outlier: 3.655A pdb=" N HIS A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 108 removed outlier: 3.663A pdb=" N TYR A 95 " --> pdb=" O VAL A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 119 removed outlier: 3.946A pdb=" N TRP A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 160 removed outlier: 4.091A pdb=" N LEU A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN A 134 " --> pdb=" O CYS A 130 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 169 removed outlier: 3.740A pdb=" N ARG A 169 " --> pdb=" O GLY A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 189 Processing helix chain 'A' and resid 189 through 195 removed outlier: 3.594A pdb=" N LEU A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 230 removed outlier: 3.892A pdb=" N GLU A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 Processing helix chain 'A' and resid 253 through 257 removed outlier: 3.804A pdb=" N MET A 256 " --> pdb=" O ASN A 253 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 257 " --> pdb=" O ASN A 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 257' Processing helix chain 'A' and resid 264 through 298 removed outlier: 3.973A pdb=" N ALA A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 303 through 321 removed outlier: 4.061A pdb=" N PHE A 319 " --> pdb=" O GLN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 333 removed outlier: 3.815A pdb=" N CYS A 326 " --> pdb=" O TYR A 322 " (cutoff:3.500A) Proline residue: A 329 - end of helix Processing helix chain 'A' and resid 336 through 351 Processing helix chain 'B' and resid 15 through 36 Processing helix chain 'B' and resid 51 through 63 Processing helix chain 'B' and resid 212 through 217 removed outlier: 4.061A pdb=" N TRP B 216 " --> pdb=" O GLU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 221 Processing helix chain 'B' and resid 246 through 261 removed outlier: 3.615A pdb=" N TYR B 261 " --> pdb=" O THR B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 265 removed outlier: 3.566A pdb=" N GLN B 265 " --> pdb=" O PRO B 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 276 through 283 Processing helix chain 'B' and resid 302 through 315 Processing helix chain 'B' and resid 335 through 356 Processing helix chain 'C' and resid 15 through 25 Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.695A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'D' and resid 16 through 24 removed outlier: 3.542A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 45 Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 201 Processing sheet with id=AA2, first strand: chain 'B' and resid 190 through 196 removed outlier: 6.444A pdb=" N LEU B 40 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL B 204 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU B 42 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 10.101A pdb=" N SER B 225 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LYS B 41 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N MET B 227 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU B 43 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU B 229 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU B 45 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N ALA B 231 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE B 226 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N PHE B 272 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE B 228 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN B 274 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL B 230 " --> pdb=" O ASN B 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.761A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.656A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN C 88 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.987A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 153 removed outlier: 3.852A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.646A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.621A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.931A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 1041 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: 2.20 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2361 1.34 - 1.46: 1415 1.46 - 1.58: 3658 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 7518 Sorted by residual: bond pdb=" C10 CLR A 503 " pdb=" C5 CLR A 503 " ideal model delta sigma weight residual 1.519 1.401 0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" C10 CLR A 501 " pdb=" C5 CLR A 501 " ideal model delta sigma weight residual 1.519 1.402 0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C4 CLR A 501 " pdb=" C5 CLR A 501 " ideal model delta sigma weight residual 1.506 1.392 0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C10 CLR A 502 " pdb=" C5 CLR A 502 " ideal model delta sigma weight residual 1.519 1.405 0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C4 CLR A 502 " pdb=" C5 CLR A 502 " ideal model delta sigma weight residual 1.506 1.395 0.111 2.00e-02 2.50e+03 3.09e+01 ... (remaining 7513 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 9606 1.82 - 3.64: 511 3.64 - 5.47: 63 5.47 - 7.29: 21 7.29 - 9.11: 4 Bond angle restraints: 10205 Sorted by residual: angle pdb=" N PHE A 259 " pdb=" CA PHE A 259 " pdb=" C PHE A 259 " ideal model delta sigma weight residual 113.20 106.01 7.19 1.21e+00 6.83e-01 3.53e+01 angle pdb=" CA GLN B 197 " pdb=" C GLN B 197 " pdb=" O GLN B 197 " ideal model delta sigma weight residual 122.27 117.41 4.86 1.16e+00 7.43e-01 1.75e+01 angle pdb=" N ASN A 254 " pdb=" CA ASN A 254 " pdb=" C ASN A 254 " ideal model delta sigma weight residual 113.02 108.55 4.47 1.20e+00 6.94e-01 1.39e+01 angle pdb=" N GLU A 255 " pdb=" CA GLU A 255 " pdb=" C GLU A 255 " ideal model delta sigma weight residual 113.19 108.77 4.42 1.19e+00 7.06e-01 1.38e+01 angle pdb=" N VAL C 90 " pdb=" CA VAL C 90 " pdb=" C VAL C 90 " ideal model delta sigma weight residual 111.67 108.14 3.53 9.50e-01 1.11e+00 1.38e+01 ... (remaining 10200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.42: 4426 24.42 - 48.83: 175 48.83 - 73.25: 26 73.25 - 97.67: 4 97.67 - 122.08: 3 Dihedral angle restraints: 4634 sinusoidal: 1965 harmonic: 2669 Sorted by residual: dihedral pdb=" CB CYS A 130 " pdb=" SG CYS A 130 " pdb=" SG CYS A 211 " pdb=" CB CYS A 211 " ideal model delta sinusoidal sigma weight residual -86.00 -170.09 84.09 1 1.00e+01 1.00e-02 8.61e+01 dihedral pdb=" CB CYS A 47 " pdb=" SG CYS A 47 " pdb=" SG CYS A 304 " pdb=" CB CYS A 304 " ideal model delta sinusoidal sigma weight residual 93.00 151.56 -58.56 1 1.00e+01 1.00e-02 4.59e+01 dihedral pdb=" CA ASP B 290 " pdb=" C ASP B 290 " pdb=" N TYR B 291 " pdb=" CA TYR B 291 " ideal model delta harmonic sigma weight residual 180.00 155.61 24.39 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 4631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1053 0.094 - 0.189: 105 0.189 - 0.283: 8 0.283 - 0.377: 4 0.377 - 0.472: 6 Chirality restraints: 1176 Sorted by residual: chirality pdb=" C14 CLR A 503 " pdb=" C13 CLR A 503 " pdb=" C15 CLR A 503 " pdb=" C8 CLR A 503 " both_signs ideal model delta sigma weight residual False -2.32 -2.79 0.47 2.00e-01 2.50e+01 5.57e+00 chirality pdb=" C14 CLR A 502 " pdb=" C13 CLR A 502 " pdb=" C15 CLR A 502 " pdb=" C8 CLR A 502 " both_signs ideal model delta sigma weight residual False -2.32 -2.79 0.47 2.00e-01 2.50e+01 5.52e+00 chirality pdb=" C14 CLR A 501 " pdb=" C13 CLR A 501 " pdb=" C15 CLR A 501 " pdb=" C8 CLR A 501 " both_signs ideal model delta sigma weight residual False -2.32 -2.76 0.44 2.00e-01 2.50e+01 4.84e+00 ... (remaining 1173 not shown) Planarity restraints: 1270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 38 " 0.043 5.00e-02 4.00e+02 6.60e-02 6.98e+00 pdb=" N PRO C 39 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 39 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 39 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 55 " -0.023 2.00e-02 2.50e+03 1.67e-02 4.90e+00 pdb=" CG PHE B 55 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE B 55 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 55 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 55 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 55 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 55 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 42 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.07e+00 pdb=" C ARG C 42 " -0.035 2.00e-02 2.50e+03 pdb=" O ARG C 42 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE C 43 " 0.012 2.00e-02 2.50e+03 ... (remaining 1267 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1209 2.76 - 3.30: 6925 3.30 - 3.83: 12054 3.83 - 4.37: 14786 4.37 - 4.90: 25270 Nonbonded interactions: 60244 Sorted by model distance: nonbonded pdb=" OG1 THR A 314 " pdb=" NH2 ARG L 10 " model vdw 2.227 3.120 nonbonded pdb=" NE ARG C 251 " pdb=" OE2 GLU C 260 " model vdw 2.257 3.120 nonbonded pdb=" OG SER A 318 " pdb=" OG SER L 7 " model vdw 2.331 3.040 nonbonded pdb=" OG SER C 108 " pdb=" OD1 ASP C 154 " model vdw 2.368 3.040 nonbonded pdb=" OG SER C 147 " pdb=" O VAL C 187 " model vdw 2.400 3.040 ... (remaining 60239 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: 0.580 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.360 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 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 : 0.008 0.118 7518 Z= 0.504 Angle : 0.922 9.110 10205 Z= 0.554 Chirality : 0.067 0.472 1176 Planarity : 0.005 0.066 1270 Dihedral : 13.558 122.083 2894 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.50 % Allowed : 0.99 % Favored : 98.51 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % 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: 0.20 (0.27), residues: 903 helix: 1.40 (0.26), residues: 387 sheet: -0.03 (0.39), residues: 184 loop : -1.26 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 283 HIS 0.008 0.001 HIS C 54 PHE 0.035 0.002 PHE B 55 TYR 0.014 0.002 TYR A 347 ARG 0.020 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.780 Fit side-chains REVERT: C 340 ASN cc_start: 0.8017 (t0) cc_final: 0.7806 (t0) outliers start: 4 outliers final: 1 residues processed: 123 average time/residue: 1.4269 time to fit residues: 184.1547 Evaluate side-chains 86 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 254 ASN A 324 ASN B 265 GLN C 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.157780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.121413 restraints weight = 8118.437| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.12 r_work: 0.3222 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7518 Z= 0.223 Angle : 0.585 7.291 10205 Z= 0.305 Chirality : 0.044 0.207 1176 Planarity : 0.004 0.055 1270 Dihedral : 8.750 90.800 1190 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.74 % Allowed : 10.19 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.66 (0.27), residues: 903 helix: 2.03 (0.26), residues: 383 sheet: 0.16 (0.38), residues: 179 loop : -1.29 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.004 0.001 HIS C 54 PHE 0.025 0.002 PHE B 55 TYR 0.010 0.001 TYR B 291 ARG 0.008 0.001 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.789 Fit side-chains REVERT: A 249 GLN cc_start: 0.8468 (tt0) cc_final: 0.8264 (tt0) REVERT: B 19 ARG cc_start: 0.7346 (mmm-85) cc_final: 0.6788 (mmm160) REVERT: D 21 MET cc_start: 0.5915 (tmm) cc_final: 0.5656 (tmm) outliers start: 14 outliers final: 5 residues processed: 113 average time/residue: 1.2442 time to fit residues: 149.1604 Evaluate side-chains 103 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain C residue 277 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 GLN A 324 ASN C 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.155312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.119735 restraints weight = 8245.579| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.91 r_work: 0.3141 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7518 Z= 0.256 Angle : 0.596 8.441 10205 Z= 0.308 Chirality : 0.044 0.184 1176 Planarity : 0.004 0.049 1270 Dihedral : 7.330 59.067 1190 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.98 % Allowed : 12.17 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.74 (0.27), residues: 903 helix: 2.16 (0.26), residues: 382 sheet: 0.17 (0.37), residues: 184 loop : -1.33 (0.29), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS C 311 PHE 0.027 0.002 PHE B 55 TYR 0.016 0.002 TYR A 177 ARG 0.008 0.001 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.821 Fit side-chains REVERT: A 262 ILE cc_start: 0.7882 (mp) cc_final: 0.7453 (pp) REVERT: B 19 ARG cc_start: 0.7161 (mmm-85) cc_final: 0.6633 (mmm160) REVERT: C 217 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7916 (pp-130) outliers start: 24 outliers final: 10 residues processed: 110 average time/residue: 1.2616 time to fit residues: 146.7518 Evaluate side-chains 103 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 277 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 45 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 80 optimal weight: 0.0770 chunk 34 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.156909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122200 restraints weight = 8197.408| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.89 r_work: 0.3163 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7518 Z= 0.216 Angle : 0.547 6.730 10205 Z= 0.287 Chirality : 0.043 0.195 1176 Planarity : 0.004 0.044 1270 Dihedral : 6.425 59.123 1190 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.48 % Allowed : 13.17 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.27), residues: 903 helix: 2.34 (0.26), residues: 382 sheet: 0.13 (0.37), residues: 184 loop : -1.31 (0.29), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS C 311 PHE 0.020 0.002 PHE B 55 TYR 0.017 0.001 TYR A 177 ARG 0.009 0.001 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 1.136 Fit side-chains REVERT: A 262 ILE cc_start: 0.7864 (mp) cc_final: 0.7504 (pp) REVERT: B 19 ARG cc_start: 0.7247 (mmm-85) cc_final: 0.6575 (mmm160) REVERT: C 217 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8184 (ppp) outliers start: 20 outliers final: 9 residues processed: 107 average time/residue: 1.1788 time to fit residues: 133.8549 Evaluate side-chains 104 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 277 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 39 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN A 315 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.157854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.122356 restraints weight = 8145.002| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.93 r_work: 0.3212 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7518 Z= 0.180 Angle : 0.522 5.872 10205 Z= 0.275 Chirality : 0.042 0.195 1176 Planarity : 0.004 0.042 1270 Dihedral : 6.280 58.903 1190 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.48 % Allowed : 14.16 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.28), residues: 903 helix: 2.52 (0.27), residues: 382 sheet: 0.05 (0.36), residues: 189 loop : -1.24 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 82 HIS 0.002 0.001 HIS B 287 PHE 0.026 0.001 PHE B 55 TYR 0.020 0.001 TYR A 177 ARG 0.008 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7155 (mmm-85) cc_final: 0.6508 (mmm160) REVERT: C 217 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.7920 (pp-130) REVERT: D 47 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7136 (mp0) outliers start: 20 outliers final: 13 residues processed: 102 average time/residue: 1.2196 time to fit residues: 131.7547 Evaluate side-chains 102 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 322 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 27 optimal weight: 0.9980 chunk 74 optimal weight: 0.0970 chunk 54 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.159068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.121382 restraints weight = 8166.065| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.96 r_work: 0.3215 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7518 Z= 0.171 Angle : 0.511 6.330 10205 Z= 0.269 Chirality : 0.042 0.196 1176 Planarity : 0.004 0.040 1270 Dihedral : 6.175 59.266 1190 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.98 % Allowed : 13.66 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.12 (0.28), residues: 903 helix: 2.67 (0.26), residues: 379 sheet: 0.06 (0.36), residues: 189 loop : -1.17 (0.30), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 123 HIS 0.003 0.001 HIS B 287 PHE 0.029 0.001 PHE B 55 TYR 0.022 0.001 TYR A 177 ARG 0.009 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.792 Fit side-chains REVERT: B 19 ARG cc_start: 0.7031 (mmm-85) cc_final: 0.6408 (mmm160) REVERT: B 249 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8096 (mm-30) REVERT: C 217 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7842 (pp-130) REVERT: D 47 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7188 (mp0) outliers start: 24 outliers final: 13 residues processed: 107 average time/residue: 1.1778 time to fit residues: 133.6940 Evaluate side-chains 102 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 263 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 277 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 0.0770 chunk 3 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN A 315 GLN C 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.158876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124337 restraints weight = 8115.728| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.88 r_work: 0.3191 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7518 Z= 0.171 Angle : 0.516 5.886 10205 Z= 0.272 Chirality : 0.042 0.195 1176 Planarity : 0.004 0.047 1270 Dihedral : 6.122 59.613 1190 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.61 % Allowed : 14.91 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.17 (0.28), residues: 903 helix: 2.76 (0.26), residues: 379 sheet: 0.02 (0.36), residues: 183 loop : -1.14 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 123 HIS 0.002 0.001 HIS B 287 PHE 0.020 0.001 PHE B 55 TYR 0.024 0.001 TYR A 177 ARG 0.013 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.771 Fit side-chains REVERT: A 322 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.7783 (m-80) REVERT: B 19 ARG cc_start: 0.7002 (mmm-85) cc_final: 0.6433 (mmm160) REVERT: B 197 GLN cc_start: 0.6605 (mt0) cc_final: 0.6098 (tt0) REVERT: B 356 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.7999 (m-80) REVERT: C 217 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.7900 (pp-130) REVERT: D 47 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7177 (mp0) outliers start: 21 outliers final: 14 residues processed: 107 average time/residue: 1.0863 time to fit residues: 123.6073 Evaluate side-chains 106 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 277 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 8 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 27 optimal weight: 0.0970 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 29 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.159976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.125369 restraints weight = 8199.244| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.90 r_work: 0.3195 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7518 Z= 0.153 Angle : 0.498 5.671 10205 Z= 0.263 Chirality : 0.041 0.198 1176 Planarity : 0.004 0.049 1270 Dihedral : 6.019 59.937 1190 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.61 % Allowed : 15.16 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.25 (0.28), residues: 903 helix: 2.83 (0.26), residues: 379 sheet: 0.02 (0.36), residues: 183 loop : -1.08 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 123 HIS 0.002 0.001 HIS B 287 PHE 0.031 0.001 PHE B 55 TYR 0.025 0.001 TYR A 177 ARG 0.012 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 322 TYR cc_start: 0.8600 (OUTLIER) cc_final: 0.7722 (m-80) REVERT: B 19 ARG cc_start: 0.6793 (mmm-85) cc_final: 0.6268 (mmm160) REVERT: B 197 GLN cc_start: 0.6580 (mt0) cc_final: 0.6037 (tt0) REVERT: C 55 LEU cc_start: 0.8765 (mt) cc_final: 0.8564 (mm) REVERT: C 217 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7933 (pp-130) REVERT: C 246 ASP cc_start: 0.8404 (m-30) cc_final: 0.8176 (m-30) REVERT: D 47 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7126 (mp0) outliers start: 21 outliers final: 15 residues processed: 111 average time/residue: 1.0934 time to fit residues: 129.5269 Evaluate side-chains 109 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 322 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 32 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN A 315 GLN C 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.158412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.123696 restraints weight = 8284.638| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.90 r_work: 0.3176 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7518 Z= 0.191 Angle : 0.535 6.242 10205 Z= 0.281 Chirality : 0.042 0.193 1176 Planarity : 0.004 0.052 1270 Dihedral : 6.091 59.137 1190 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.48 % Allowed : 16.02 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.16 (0.28), residues: 903 helix: 2.72 (0.27), residues: 382 sheet: -0.01 (0.36), residues: 183 loop : -1.11 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 123 HIS 0.003 0.001 HIS B 287 PHE 0.023 0.001 PHE B 55 TYR 0.027 0.001 TYR A 177 ARG 0.013 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.881 Fit side-chains REVERT: A 322 TYR cc_start: 0.8687 (OUTLIER) cc_final: 0.7728 (m-80) REVERT: B 197 GLN cc_start: 0.6627 (mt0) cc_final: 0.6063 (tt0) REVERT: B 356 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.8019 (m-80) REVERT: C 217 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.7903 (pp-130) REVERT: D 47 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7203 (mp0) outliers start: 20 outliers final: 13 residues processed: 103 average time/residue: 1.0986 time to fit residues: 120.4565 Evaluate side-chains 102 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 322 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 54 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN C 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.156294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.121080 restraints weight = 8272.010| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.92 r_work: 0.3170 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7518 Z= 0.233 Angle : 0.569 6.985 10205 Z= 0.297 Chirality : 0.044 0.188 1176 Planarity : 0.004 0.056 1270 Dihedral : 6.269 58.472 1190 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.61 % Allowed : 15.90 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.02 (0.28), residues: 903 helix: 2.52 (0.27), residues: 383 sheet: -0.04 (0.37), residues: 183 loop : -1.13 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 123 HIS 0.003 0.001 HIS C 311 PHE 0.034 0.002 PHE B 55 TYR 0.030 0.002 TYR A 177 ARG 0.014 0.001 ARG B 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.915 Fit side-chains REVERT: A 200 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7062 (tm-30) REVERT: A 322 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.7748 (m-80) REVERT: B 19 ARG cc_start: 0.6867 (mmm-85) cc_final: 0.6315 (mmm160) REVERT: B 197 GLN cc_start: 0.6704 (mt0) cc_final: 0.6095 (tt0) REVERT: B 356 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.8043 (m-80) REVERT: C 34 THR cc_start: 0.7519 (p) cc_final: 0.7275 (p) REVERT: C 217 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8172 (ppp) REVERT: D 47 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7283 (mp0) outliers start: 21 outliers final: 12 residues processed: 108 average time/residue: 1.1816 time to fit residues: 135.6512 Evaluate side-chains 107 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 277 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 28 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 26 optimal weight: 0.0070 chunk 47 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 GLN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.155836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.121009 restraints weight = 8274.463| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.90 r_work: 0.3163 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7518 Z= 0.256 Angle : 0.589 7.421 10205 Z= 0.307 Chirality : 0.044 0.187 1176 Planarity : 0.004 0.056 1270 Dihedral : 6.392 58.616 1190 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.48 % Allowed : 16.65 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 903 helix: 2.41 (0.27), residues: 382 sheet: -0.10 (0.37), residues: 183 loop : -1.18 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 123 HIS 0.003 0.001 HIS C 311 PHE 0.036 0.002 PHE B 55 TYR 0.032 0.002 TYR A 177 ARG 0.014 0.001 ARG B 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5799.10 seconds wall clock time: 103 minutes 4.34 seconds (6184.34 seconds total)