Starting phenix.real_space_refine on Fri Jul 25 10:40:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f6i_31481/07_2025/7f6i_31481.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f6i_31481/07_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_31481/07_2025/7f6i_31481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f6i_31481/07_2025/7f6i_31481.map" model { file = "/net/cci-nas-00/data/ceres_data/7f6i_31481/07_2025/7f6i_31481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f6i_31481/07_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-5711/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: 4.59, per 1000 atoms: 0.62 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: 1.78 Conformation dependent library (CDL) restraints added in 963.6 milliseconds 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: 0.81 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: 1.95 Time building geometry restraints manager: 2.12 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: 1.200 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.950 Find NCS groups from input model: 0.080 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:11.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.210 ------------------------------------------------------------------------------- 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 7520 Z= 0.437 Angle : 0.922 9.110 10209 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 Details of bonding type rmsd hydrogen bonds : bond 0.11764 ( 358) hydrogen bonds : angle 5.07715 ( 1041) SS BOND : bond 0.00259 ( 2) SS BOND : angle 0.88931 ( 4) covalent geometry : bond 0.00794 ( 7518) covalent geometry : angle 0.92192 (10205) *********************** 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 : 1.081 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: 1.4380 time to fit residues: 185.6596 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 : 0.766 ------------------------------------------------------------------------------- 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 = 0.121412 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 7520 Z= 0.150 Angle : 0.585 7.291 10209 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 Details of bonding type rmsd hydrogen bonds : bond 0.04766 ( 358) hydrogen bonds : angle 4.13744 ( 1041) SS BOND : bond 0.00208 ( 2) SS BOND : angle 0.60014 ( 4) covalent geometry : bond 0.00339 ( 7518) covalent geometry : angle 0.58465 (10205) *********************** 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 : 0.812 Fit side-chains REVERT: A 249 GLN cc_start: 0.8469 (tt0) cc_final: 0.8263 (tt0) REVERT: B 19 ARG cc_start: 0.7348 (mmm-85) cc_final: 0.6791 (mmm160) REVERT: D 21 MET cc_start: 0.5923 (tmm) cc_final: 0.5665 (tmm) outliers start: 14 outliers final: 5 residues processed: 113 average time/residue: 1.1229 time to fit residues: 134.8150 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 : 0.833 ------------------------------------------------------------------------------- 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: 1.9990 chunk 76 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 73 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN 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 = 0.3775 r_free = 0.3775 target = 0.155854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.120168 restraints weight = 8247.558| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.92 r_work: 0.3144 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7520 Z= 0.164 Angle : 0.594 8.635 10209 Z= 0.307 Chirality : 0.044 0.187 1176 Planarity : 0.004 0.049 1270 Dihedral : 7.399 59.865 1190 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.98 % Allowed : 12.05 % Favored : 84.97 % 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: 0.75 (0.27), residues: 903 helix: 2.17 (0.26), residues: 382 sheet: 0.18 (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 0.004 0.001 HIS C 54 PHE 0.026 0.002 PHE B 55 TYR 0.016 0.002 TYR A 177 ARG 0.007 0.001 ARG C 197 Details of bonding type rmsd hydrogen bonds : bond 0.04925 ( 358) hydrogen bonds : angle 4.08128 ( 1041) SS BOND : bond 0.00268 ( 2) SS BOND : angle 0.67788 ( 4) covalent geometry : bond 0.00382 ( 7518) covalent geometry : angle 0.59356 (10205) *********************** 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 123 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.742 Fit side-chains REVERT: A 262 ILE cc_start: 0.7886 (mp) cc_final: 0.7458 (pp) REVERT: B 19 ARG cc_start: 0.7155 (mmm-85) cc_final: 0.6634 (mmm160) REVERT: C 217 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.7893 (pp-130) outliers start: 24 outliers final: 11 residues processed: 111 average time/residue: 1.3924 time to fit residues: 163.1606 Evaluate side-chains 105 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 229 ASN 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: 0.4980 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.155978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.120697 restraints weight = 8218.838| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.89 r_work: 0.3152 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7520 Z= 0.171 Angle : 0.581 7.502 10209 Z= 0.304 Chirality : 0.044 0.190 1176 Planarity : 0.005 0.046 1270 Dihedral : 6.586 59.067 1190 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.61 % Allowed : 13.04 % 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: 0.73 (0.27), residues: 903 helix: 2.18 (0.26), residues: 382 sheet: 0.10 (0.37), residues: 184 loop : -1.32 (0.29), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.004 0.001 HIS C 311 PHE 0.021 0.002 PHE B 55 TYR 0.018 0.002 TYR A 177 ARG 0.008 0.001 ARG C 197 Details of bonding type rmsd hydrogen bonds : bond 0.04891 ( 358) hydrogen bonds : angle 4.07997 ( 1041) SS BOND : bond 0.00287 ( 2) SS BOND : angle 0.73331 ( 4) covalent geometry : bond 0.00402 ( 7518) covalent geometry : angle 0.58053 (10205) *********************** 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 117 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.815 Fit side-chains REVERT: A 262 ILE cc_start: 0.7820 (mp) cc_final: 0.7454 (pp) REVERT: B 19 ARG cc_start: 0.7257 (mmm-85) cc_final: 0.6602 (mmm160) REVERT: C 217 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8173 (ppp) outliers start: 21 outliers final: 10 residues processed: 106 average time/residue: 1.1284 time to fit residues: 126.9918 Evaluate side-chains 105 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 54 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.156873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.122378 restraints weight = 8162.699| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.88 r_work: 0.3162 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7520 Z= 0.141 Angle : 0.541 6.533 10209 Z= 0.284 Chirality : 0.043 0.191 1176 Planarity : 0.004 0.042 1270 Dihedral : 6.433 58.526 1190 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.86 % Allowed : 13.91 % Favored : 83.23 % 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: 0.85 (0.28), residues: 903 helix: 2.37 (0.27), residues: 382 sheet: -0.07 (0.36), residues: 191 loop : -1.24 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 82 HIS 0.003 0.001 HIS C 311 PHE 0.024 0.001 PHE B 55 TYR 0.018 0.001 TYR A 177 ARG 0.009 0.000 ARG B 31 Details of bonding type rmsd hydrogen bonds : bond 0.04439 ( 358) hydrogen bonds : angle 3.94893 ( 1041) SS BOND : bond 0.00246 ( 2) SS BOND : angle 0.56218 ( 4) covalent geometry : bond 0.00325 ( 7518) covalent geometry : angle 0.54079 (10205) *********************** 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 119 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.812 Fit side-chains REVERT: A 200 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7120 (tm-30) REVERT: B 19 ARG cc_start: 0.7123 (mmm-85) cc_final: 0.6444 (mmm160) REVERT: C 217 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7915 (pp-130) outliers start: 23 outliers final: 12 residues processed: 108 average time/residue: 1.1085 time to fit residues: 127.0890 Evaluate side-chains 105 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 74 optimal weight: 0.0050 chunk 54 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN A 287 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 = 0.3790 r_free = 0.3790 target = 0.157230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.122439 restraints weight = 8166.746| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.89 r_work: 0.3190 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7520 Z= 0.128 Angle : 0.530 6.064 10209 Z= 0.279 Chirality : 0.042 0.192 1176 Planarity : 0.004 0.041 1270 Dihedral : 6.318 58.567 1190 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.35 % Allowed : 14.04 % Favored : 82.61 % 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: 0.97 (0.28), residues: 903 helix: 2.49 (0.27), residues: 382 sheet: -0.07 (0.36), residues: 191 loop : -1.17 (0.30), residues: 330 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 0.024 0.001 PHE B 55 TYR 0.021 0.001 TYR A 177 ARG 0.010 0.000 ARG B 31 Details of bonding type rmsd hydrogen bonds : bond 0.04215 ( 358) hydrogen bonds : angle 3.86916 ( 1041) SS BOND : bond 0.00209 ( 2) SS BOND : angle 0.54326 ( 4) covalent geometry : bond 0.00289 ( 7518) covalent geometry : angle 0.52978 (10205) *********************** 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 126 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.808 Fit side-chains REVERT: A 200 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7108 (tm-30) REVERT: A 322 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.7915 (m-80) REVERT: B 19 ARG cc_start: 0.7032 (mmm-85) cc_final: 0.6439 (mmm160) REVERT: B 197 GLN cc_start: 0.6643 (mt0) cc_final: 0.6124 (tt0) REVERT: B 356 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.7766 (m-80) REVERT: C 217 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.7884 (pp-130) REVERT: D 47 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7264 (mp0) outliers start: 27 outliers final: 12 residues processed: 112 average time/residue: 1.0868 time to fit residues: 129.5285 Evaluate side-chains 106 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 263 GLN 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 217 MET 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: 0.0050 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 39 optimal weight: 0.0870 chunk 70 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.4772 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.159000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.121297 restraints weight = 8078.187| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.95 r_work: 0.3224 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7520 Z= 0.109 Angle : 0.507 5.907 10209 Z= 0.267 Chirality : 0.041 0.196 1176 Planarity : 0.004 0.045 1270 Dihedral : 6.160 58.461 1190 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.73 % Allowed : 15.03 % 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: 1.15 (0.28), residues: 903 helix: 2.75 (0.27), residues: 379 sheet: -0.01 (0.36), residues: 184 loop : -1.16 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 123 HIS 0.002 0.001 HIS B 287 PHE 0.022 0.001 PHE B 55 TYR 0.021 0.001 TYR A 177 ARG 0.012 0.000 ARG C 197 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 358) hydrogen bonds : angle 3.74181 ( 1041) SS BOND : bond 0.00116 ( 2) SS BOND : angle 0.41156 ( 4) covalent geometry : bond 0.00236 ( 7518) covalent geometry : angle 0.50701 (10205) *********************** 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 120 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.816 Fit side-chains REVERT: A 322 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.7723 (m-80) REVERT: B 19 ARG cc_start: 0.6943 (mmm-85) cc_final: 0.6372 (mmm160) REVERT: B 197 GLN cc_start: 0.6544 (mt0) cc_final: 0.6055 (tt0) REVERT: B 249 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8063 (mm-30) REVERT: B 356 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.7721 (m-80) REVERT: C 217 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7827 (pp-130) REVERT: D 47 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7191 (mp0) outliers start: 22 outliers final: 14 residues processed: 110 average time/residue: 1.0804 time to fit residues: 126.5127 Evaluate side-chains 107 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 263 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 8 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 83 optimal weight: 0.0980 chunk 65 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN C 237 ASN ** 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 = 0.3797 r_free = 0.3797 target = 0.157801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.122444 restraints weight = 8198.222| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.90 r_work: 0.3213 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7520 Z= 0.120 Angle : 0.523 6.015 10209 Z= 0.275 Chirality : 0.042 0.193 1176 Planarity : 0.004 0.050 1270 Dihedral : 6.156 59.142 1190 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.86 % Allowed : 15.65 % 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: 1.13 (0.28), residues: 903 helix: 2.72 (0.27), residues: 379 sheet: -0.04 (0.37), residues: 184 loop : -1.13 (0.30), residues: 340 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 0.032 0.001 PHE B 55 TYR 0.024 0.001 TYR A 177 ARG 0.012 0.001 ARG C 197 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 358) hydrogen bonds : angle 3.77623 ( 1041) SS BOND : bond 0.00159 ( 2) SS BOND : angle 0.46299 ( 4) covalent geometry : bond 0.00269 ( 7518) covalent geometry : angle 0.52257 (10205) *********************** 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 118 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.762 Fit side-chains REVERT: A 263 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7237 (mm-40) REVERT: A 322 TYR cc_start: 0.8657 (OUTLIER) cc_final: 0.7758 (m-80) REVERT: B 19 ARG cc_start: 0.6901 (mmm-85) cc_final: 0.6347 (mmm160) REVERT: B 197 GLN cc_start: 0.6645 (mt0) cc_final: 0.6106 (tt0) REVERT: B 356 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.7752 (m-80) REVERT: C 217 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.7892 (pp-130) REVERT: D 47 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7230 (mp0) outliers start: 23 outliers final: 14 residues processed: 110 average time/residue: 1.0422 time to fit residues: 122.1604 Evaluate side-chains 108 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 263 GLN 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 123 ILE 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: 0.9990 chunk 74 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.158115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.122469 restraints weight = 8275.385| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.93 r_work: 0.3198 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7520 Z= 0.132 Angle : 0.550 6.274 10209 Z= 0.288 Chirality : 0.042 0.191 1176 Planarity : 0.004 0.052 1270 Dihedral : 6.202 59.571 1190 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.11 % Allowed : 16.40 % Favored : 80.50 % 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: 1.09 (0.28), residues: 903 helix: 2.62 (0.27), residues: 382 sheet: -0.03 (0.37), residues: 183 loop : -1.11 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 123 HIS 0.003 0.001 HIS B 287 PHE 0.023 0.002 PHE B 55 TYR 0.027 0.001 TYR A 177 ARG 0.013 0.001 ARG B 31 Details of bonding type rmsd hydrogen bonds : bond 0.04208 ( 358) hydrogen bonds : angle 3.83031 ( 1041) SS BOND : bond 0.00099 ( 2) SS BOND : angle 0.71036 ( 4) covalent geometry : bond 0.00301 ( 7518) covalent geometry : angle 0.55006 (10205) *********************** 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 114 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.931 Fit side-chains REVERT: A 200 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: A 322 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.7664 (m-80) REVERT: B 19 ARG cc_start: 0.6824 (mmm-85) cc_final: 0.6264 (mmm160) REVERT: B 197 GLN cc_start: 0.6722 (mt0) cc_final: 0.6114 (tt0) REVERT: B 356 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.7767 (m-80) REVERT: C 217 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7850 (pp-130) REVERT: C 256 ARG cc_start: 0.7728 (mtm110) cc_final: 0.7474 (mtm110) REVERT: D 47 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7233 (mp0) outliers start: 25 outliers final: 15 residues processed: 104 average time/residue: 1.0347 time to fit residues: 114.8675 Evaluate side-chains 111 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR 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 263 GLN 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 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: 6.9990 chunk 83 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 79 optimal weight: 0.0970 chunk 45 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.159333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.124523 restraints weight = 8240.736| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.89 r_work: 0.3190 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7520 Z= 0.121 Angle : 0.533 5.941 10209 Z= 0.281 Chirality : 0.042 0.193 1176 Planarity : 0.004 0.056 1270 Dihedral : 6.164 59.818 1190 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.86 % Allowed : 16.65 % Favored : 80.50 % 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: 1.13 (0.28), residues: 903 helix: 2.64 (0.27), residues: 382 sheet: -0.02 (0.37), residues: 183 loop : -1.08 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 123 HIS 0.003 0.001 HIS B 287 PHE 0.033 0.001 PHE B 55 TYR 0.028 0.001 TYR A 177 ARG 0.014 0.001 ARG B 31 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 358) hydrogen bonds : angle 3.80431 ( 1041) SS BOND : bond 0.00102 ( 2) SS BOND : angle 0.52280 ( 4) covalent geometry : bond 0.00274 ( 7518) covalent geometry : angle 0.53343 (10205) ********************** 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 119 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.749 Fit side-chains REVERT: A 200 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: A 263 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7255 (mm-40) REVERT: A 322 TYR cc_start: 0.8697 (OUTLIER) cc_final: 0.7653 (m-80) REVERT: B 19 ARG cc_start: 0.6808 (mmm-85) cc_final: 0.6308 (mmm160) REVERT: B 197 GLN cc_start: 0.6724 (mt0) cc_final: 0.6117 (tt0) REVERT: B 356 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.7775 (m-80) REVERT: C 217 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.7876 (pp-130) REVERT: D 47 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7203 (mp0) outliers start: 23 outliers final: 14 residues processed: 110 average time/residue: 1.1114 time to fit residues: 130.0452 Evaluate side-chains 108 residues out of total 805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR 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 263 GLN 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 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 28 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 26 optimal weight: 0.0270 chunk 47 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 39 optimal weight: 0.0770 chunk 15 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.158071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.122474 restraints weight = 8222.434| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.95 r_work: 0.3192 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7520 Z= 0.116 Angle : 0.537 6.404 10209 Z= 0.281 Chirality : 0.042 0.195 1176 Planarity : 0.004 0.057 1270 Dihedral : 6.119 59.727 1190 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.61 % Allowed : 17.14 % Favored : 80.25 % 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: 1.18 (0.28), residues: 903 helix: 2.74 (0.27), residues: 380 sheet: -0.05 (0.37), residues: 183 loop : -1.07 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 123 HIS 0.003 0.001 HIS B 287 PHE 0.033 0.001 PHE B 55 TYR 0.029 0.001 TYR A 177 ARG 0.014 0.001 ARG B 31 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 358) hydrogen bonds : angle 3.79085 ( 1041) SS BOND : bond 0.00062 ( 2) SS BOND : angle 0.58991 ( 4) covalent geometry : bond 0.00256 ( 7518) covalent geometry : angle 0.53676 (10205) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6203.15 seconds wall clock time: 107 minutes 0.36 seconds (6420.36 seconds total)