Starting phenix.real_space_refine on Fri Mar 6 16:36:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6p7x_20272/03_2026/6p7x_20272.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p7x_20272/03_2026/6p7x_20272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6p7x_20272/03_2026/6p7x_20272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p7x_20272/03_2026/6p7x_20272.map" model { file = "/net/cci-nas-00/data/ceres_data/6p7x_20272/03_2026/6p7x_20272.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p7x_20272/03_2026/6p7x_20272.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2377 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 68 5.16 5 C 9925 2.51 5 N 2511 2.21 5 O 2745 1.98 5 H 15288 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30537 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 6326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 6326 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 26, 'TRANS': 358} Chain breaks: 2 Chain: "C" Number of atoms: 6464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 6464 Classifications: {'peptide': 387} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 373} Chain: "D" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2059 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain breaks: 1 Chain: "B" Number of atoms: 7977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 7977 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 14, 'TRANS': 461} Chain breaks: 6 Chain: "A" Number of atoms: 7711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 7711 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 14, 'TRANS': 444} Chain breaks: 6 Time building chain proxies: 5.56, per 1000 atoms: 0.18 Number of scatterers: 30537 At special positions: 0 Unit cell: (123.018, 164.378, 126.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 O 2745 8.00 N 2511 7.00 C 9925 6.00 H 15288 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 893.7 milliseconds 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3570 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 7 sheets defined 65.4% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'E' and resid 4 through 10 Processing helix chain 'E' and resid 12 through 32 removed outlier: 3.573A pdb=" N ALA E 16 " --> pdb=" O PRO E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 Processing helix chain 'E' and resid 59 through 63 Processing helix chain 'E' and resid 64 through 76 Processing helix chain 'E' and resid 81 through 101 removed outlier: 4.198A pdb=" N PHE E 101 " --> pdb=" O LYS E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 119 removed outlier: 3.989A pdb=" N ASN E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 150 removed outlier: 4.049A pdb=" N LYS E 136 " --> pdb=" O THR E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 159 Processing helix chain 'E' and resid 193 through 196 Processing helix chain 'E' and resid 197 through 211 Processing helix chain 'E' and resid 223 through 228 removed outlier: 4.126A pdb=" N GLN E 227 " --> pdb=" O GLN E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 260 Proline residue: E 253 - end of helix Processing helix chain 'E' and resid 264 through 270 removed outlier: 3.945A pdb=" N TRP E 268 " --> pdb=" O THR E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 311 removed outlier: 3.918A pdb=" N ILE E 307 " --> pdb=" O PRO E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 356 removed outlier: 4.049A pdb=" N ALA E 336 " --> pdb=" O PRO E 332 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL E 337 " --> pdb=" O ASP E 333 " (cutoff:3.500A) Proline residue: E 350 - end of helix Processing helix chain 'E' and resid 359 through 364 Processing helix chain 'E' and resid 365 through 368 Processing helix chain 'E' and resid 369 through 377 Processing helix chain 'E' and resid 383 through 386 Processing helix chain 'E' and resid 387 through 392 Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 11 through 22 removed outlier: 3.882A pdb=" N ARG C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 64 Processing helix chain 'C' and resid 72 through 83 Processing helix chain 'C' and resid 86 through 100 Processing helix chain 'C' and resid 132 through 140 Processing helix chain 'C' and resid 157 through 170 Processing helix chain 'C' and resid 189 through 195 Processing helix chain 'C' and resid 196 through 198 No H-bonds generated for 'chain 'C' and resid 196 through 198' Processing helix chain 'C' and resid 211 through 217 Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 303 through 309 Processing helix chain 'C' and resid 327 through 345 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'D' and resid 22 through 27 Processing helix chain 'D' and resid 29 through 35 Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 95 through 101 Processing helix chain 'D' and resid 105 through 112 Processing helix chain 'D' and resid 115 through 130 removed outlier: 3.716A pdb=" N LEU D 119 " --> pdb=" O ASP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 148 removed outlier: 3.825A pdb=" N LEU D 135 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 156 removed outlier: 4.019A pdb=" N ILE D 154 " --> pdb=" O THR D 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 81 Processing helix chain 'B' and resid 100 through 105 Processing helix chain 'B' and resid 118 through 133 Processing helix chain 'B' and resid 134 through 141 Processing helix chain 'B' and resid 145 through 162 Processing helix chain 'B' and resid 181 through 200 Processing helix chain 'B' and resid 202 through 210 removed outlier: 3.594A pdb=" N ILE B 206 " --> pdb=" O PRO B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 218 removed outlier: 3.764A pdb=" N GLU B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 256 Processing helix chain 'B' and resid 261 through 272 removed outlier: 3.659A pdb=" N GLN B 265 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'B' and resid 279 through 298 removed outlier: 3.674A pdb=" N GLY B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 333 Processing helix chain 'B' and resid 373 through 389 Processing helix chain 'B' and resid 394 through 413 Processing helix chain 'B' and resid 418 through 447 Processing helix chain 'B' and resid 451 through 473 Proline residue: B 459 - end of helix Processing helix chain 'B' and resid 475 through 480 removed outlier: 3.597A pdb=" N THR B 479 " --> pdb=" O TYR B 475 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR B 480 " --> pdb=" O PHE B 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 475 through 480' Processing helix chain 'B' and resid 481 through 502 removed outlier: 3.639A pdb=" N VAL B 485 " --> pdb=" O HIS B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 522 Processing helix chain 'B' and resid 525 through 548 Processing helix chain 'B' and resid 560 through 578 removed outlier: 4.545A pdb=" N GLU B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 618 Processing helix chain 'A' and resid 63 through 81 Processing helix chain 'A' and resid 118 through 133 Processing helix chain 'A' and resid 134 through 141 Processing helix chain 'A' and resid 145 through 162 Processing helix chain 'A' and resid 181 through 200 Processing helix chain 'A' and resid 202 through 210 removed outlier: 3.585A pdb=" N ILE A 206 " --> pdb=" O PRO A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 218 Processing helix chain 'A' and resid 232 through 256 removed outlier: 3.655A pdb=" N ARG A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 272 removed outlier: 3.599A pdb=" N GLN A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 297 Processing helix chain 'A' and resid 309 through 333 Processing helix chain 'A' and resid 373 through 389 Processing helix chain 'A' and resid 394 through 413 Processing helix chain 'A' and resid 418 through 447 Processing helix chain 'A' and resid 451 through 473 Proline residue: A 459 - end of helix Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.533A pdb=" N THR A 479 " --> pdb=" O TYR A 475 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR A 480 " --> pdb=" O PHE A 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 475 through 480' Processing helix chain 'A' and resid 481 through 502 removed outlier: 3.640A pdb=" N VAL A 485 " --> pdb=" O HIS A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 522 removed outlier: 3.601A pdb=" N PHE A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 548 Processing helix chain 'A' and resid 560 through 578 removed outlier: 4.307A pdb=" N GLU A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 618 Processing sheet with id=AA1, first strand: chain 'E' and resid 165 through 169 Processing sheet with id=AA2, first strand: chain 'E' and resid 212 through 213 Processing sheet with id=AA3, first strand: chain 'C' and resid 105 through 111 removed outlier: 3.601A pdb=" N VAL C 129 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 148 through 151 removed outlier: 4.242A pdb=" N LEU C 207 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 276 through 277 removed outlier: 7.108A pdb=" N ILE C 276 " --> pdb=" O ILE C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 363 through 366 Processing sheet with id=AA7, first strand: chain 'D' and resid 16 through 21 863 hydrogen bonds defined for protein. 2523 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: 7.88 Time building geometry restraints manager: 4.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15251 1.03 - 1.23: 151 1.23 - 1.43: 6506 1.43 - 1.62: 8897 1.62 - 1.82: 99 Bond restraints: 30904 Sorted by residual: bond pdb=" CA ILE E 300 " pdb=" CB ILE E 300 " ideal model delta sigma weight residual 1.540 1.586 -0.046 1.36e-02 5.41e+03 1.16e+01 bond pdb=" N ILE E 107 " pdb=" CA ILE E 107 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.12e+01 bond pdb=" N TYR E 103 " pdb=" CA TYR E 103 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.18e-02 7.18e+03 1.06e+01 bond pdb=" N VAL E 106 " pdb=" CA VAL E 106 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.67e+00 bond pdb=" N ASP E 102 " pdb=" CA ASP E 102 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.22e-02 6.72e+03 9.29e+00 ... (remaining 30899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 53351 2.09 - 4.18: 2299 4.18 - 6.26: 235 6.26 - 8.35: 25 8.35 - 10.44: 7 Bond angle restraints: 55917 Sorted by residual: angle pdb=" C TRP E 275 " pdb=" N PRO E 276 " pdb=" CA PRO E 276 " ideal model delta sigma weight residual 119.89 128.27 -8.38 1.02e+00 9.61e-01 6.75e+01 angle pdb=" N ILE E 302 " pdb=" CA ILE E 302 " pdb=" C ILE E 302 " ideal model delta sigma weight residual 107.89 116.60 -8.71 1.09e+00 8.42e-01 6.38e+01 angle pdb=" C CYS E 197 " pdb=" N PRO E 198 " pdb=" CA PRO E 198 " ideal model delta sigma weight residual 119.19 125.11 -5.92 1.06e+00 8.90e-01 3.12e+01 angle pdb=" N GLY E 219 " pdb=" CA GLY E 219 " pdb=" C GLY E 219 " ideal model delta sigma weight residual 112.54 105.72 6.82 1.28e+00 6.10e-01 2.84e+01 angle pdb=" N PHE E 185 " pdb=" CA PHE E 185 " pdb=" C PHE E 185 " ideal model delta sigma weight residual 108.60 116.12 -7.52 1.46e+00 4.69e-01 2.65e+01 ... (remaining 55912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 12568 17.85 - 35.70: 1513 35.70 - 53.55: 310 53.55 - 71.40: 80 71.40 - 89.25: 8 Dihedral angle restraints: 14479 sinusoidal: 7776 harmonic: 6703 Sorted by residual: dihedral pdb=" CA TYR C 246 " pdb=" C TYR C 246 " pdb=" N THR C 247 " pdb=" CA THR C 247 " ideal model delta harmonic sigma weight residual 180.00 144.33 35.67 0 5.00e+00 4.00e-02 5.09e+01 dihedral pdb=" CA PHE B 110 " pdb=" C PHE B 110 " pdb=" N TYR B 111 " pdb=" CA TYR B 111 " ideal model delta harmonic sigma weight residual -180.00 -148.60 -31.40 0 5.00e+00 4.00e-02 3.94e+01 dihedral pdb=" CA LEU A 220 " pdb=" C LEU A 220 " pdb=" N ASP A 221 " pdb=" CA ASP A 221 " ideal model delta harmonic sigma weight residual 180.00 148.78 31.22 0 5.00e+00 4.00e-02 3.90e+01 ... (remaining 14476 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1779 0.056 - 0.111: 456 0.111 - 0.167: 114 0.167 - 0.223: 19 0.223 - 0.278: 5 Chirality restraints: 2373 Sorted by residual: chirality pdb=" CA ILE E 107 " pdb=" N ILE E 107 " pdb=" C ILE E 107 " pdb=" CB ILE E 107 " both_signs ideal model delta sigma weight residual False 2.43 2.15 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA THR E 299 " pdb=" N THR E 299 " pdb=" C THR E 299 " pdb=" CB THR E 299 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA LEU E 161 " pdb=" N LEU E 161 " pdb=" C LEU E 161 " pdb=" CB LEU E 161 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 2370 not shown) Planarity restraints: 4381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 211 " 0.039 2.00e-02 2.50e+03 7.75e-02 6.00e+01 pdb=" C ASP A 211 " -0.134 2.00e-02 2.50e+03 pdb=" O ASP A 211 " 0.051 2.00e-02 2.50e+03 pdb=" N ILE A 212 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 105 " 0.024 2.00e-02 2.50e+03 4.71e-02 2.22e+01 pdb=" C ASN E 105 " -0.082 2.00e-02 2.50e+03 pdb=" O ASN E 105 " 0.030 2.00e-02 2.50e+03 pdb=" N VAL E 106 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 532 " -0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C PHE A 532 " 0.066 2.00e-02 2.50e+03 pdb=" O PHE A 532 " -0.025 2.00e-02 2.50e+03 pdb=" N PHE A 533 " -0.022 2.00e-02 2.50e+03 ... (remaining 4378 not shown) Histogram of nonbonded interaction distances: 0.97 - 1.70: 46 1.70 - 2.42: 15582 2.42 - 3.15: 96627 3.15 - 3.87: 119922 3.87 - 4.60: 191021 Warning: very small nonbonded interaction distances. Nonbonded interactions: 423198 Sorted by model distance: nonbonded pdb=" CZ ARG E 91 " pdb=" HB3 PRO E 279 " model vdw 0.970 2.336 nonbonded pdb="HD23 LEU E 98 " pdb=" HB3 PRO E 276 " model vdw 1.020 2.440 nonbonded pdb="HH22 ARG E 91 " pdb=" N ASP E 280 " model vdw 1.144 2.600 nonbonded pdb="HD21 LEU E 95 " pdb=" OH TYR E 306 " model vdw 1.304 2.620 nonbonded pdb="HH12 ARG E 91 " pdb=" HB2 PRO E 279 " model vdw 1.340 1.816 ... (remaining 423193 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 62 through 220 or resid 231 through 618)) selection = (chain 'B' and (resid 62 through 347 or (resid 372 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name HA or name H \ B2 or name HB3 or name HD21 or name HD22)) or resid 373 through 618)) } 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 group one per residue 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.100 Extract box with map and model: 0.330 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 31.330 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 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 : 0.007 0.200 15617 Z= 0.373 Angle : 1.007 10.439 21159 Z= 0.601 Chirality : 0.055 0.278 2373 Planarity : 0.006 0.077 2644 Dihedral : 15.452 89.251 5783 Min Nonbonded Distance : 1.495 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.32 % Favored : 89.40 % Rotamer: Outliers : 1.27 % Allowed : 5.54 % Favored : 93.19 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.84 (0.16), residues: 1793 helix: -1.96 (0.13), residues: 1093 sheet: -3.56 (0.50), residues: 80 loop : -3.28 (0.22), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 368 TYR 0.018 0.002 TYR C 338 PHE 0.040 0.003 PHE C 201 TRP 0.026 0.002 TRP E 268 HIS 0.011 0.002 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00693 (15616) covalent geometry : angle 1.00735 (21159) hydrogen bonds : bond 0.12459 ( 863) hydrogen bonds : angle 6.64202 ( 2523) Misc. bond : bond 0.19996 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 306 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 246 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8214 (mm) REVERT: E 359 HIS cc_start: 0.6406 (t-90) cc_final: 0.5725 (t70) REVERT: E 388 GLU cc_start: 0.5031 (OUTLIER) cc_final: 0.4760 (mp0) REVERT: C 13 ASP cc_start: 0.8454 (p0) cc_final: 0.8027 (p0) REVERT: B 400 MET cc_start: 0.8976 (mtp) cc_final: 0.8656 (mtp) REVERT: B 485 VAL cc_start: 0.9008 (t) cc_final: 0.8769 (p) REVERT: A 330 ASP cc_start: 0.8538 (t70) cc_final: 0.8024 (t0) outliers start: 22 outliers final: 4 residues processed: 199 average time/residue: 0.3178 time to fit residues: 92.0581 Evaluate side-chains 121 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 47 GLN E 150 ASN E 230 HIS ** E 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN C 160 ASN C 264 GLN C 336 ASN C 362 ASN D 116 GLN ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN A 454 GLN A 576 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.078455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.049537 restraints weight = 307353.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.048841 restraints weight = 192576.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.049443 restraints weight = 134930.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.049598 restraints weight = 107491.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.050003 restraints weight = 102429.477| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15617 Z= 0.151 Angle : 0.641 7.019 21159 Z= 0.347 Chirality : 0.040 0.180 2373 Planarity : 0.005 0.110 2644 Dihedral : 6.532 61.762 1982 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.86 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.18), residues: 1793 helix: -0.46 (0.14), residues: 1101 sheet: -3.36 (0.54), residues: 73 loop : -2.82 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG E 91 TYR 0.013 0.002 TYR C 177 PHE 0.020 0.001 PHE C 201 TRP 0.016 0.001 TRP E 251 HIS 0.009 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00308 (15616) covalent geometry : angle 0.64076 (21159) hydrogen bonds : bond 0.04934 ( 863) hydrogen bonds : angle 5.33388 ( 2523) Misc. bond : bond 0.01894 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 306 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 ASP cc_start: 0.9322 (p0) cc_final: 0.9098 (p0) REVERT: B 196 MET cc_start: 0.9398 (tpt) cc_final: 0.9058 (tpt) REVERT: B 295 LYS cc_start: 0.9762 (mttt) cc_final: 0.9551 (ptpp) REVERT: A 275 PHE cc_start: 0.9460 (t80) cc_final: 0.9229 (t80) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.3008 time to fit residues: 66.3980 Evaluate side-chains 122 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 11 optimal weight: 40.0000 chunk 162 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 ASN ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 272 ASN ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.074354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.046088 restraints weight = 306775.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.047091 restraints weight = 207712.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.047592 restraints weight = 139601.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.047143 restraints weight = 110858.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.046753 restraints weight = 97271.820| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15617 Z= 0.241 Angle : 0.667 6.274 21159 Z= 0.367 Chirality : 0.039 0.177 2373 Planarity : 0.005 0.106 2644 Dihedral : 6.178 62.702 1982 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.06 % Allowed : 2.54 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.19), residues: 1793 helix: -0.11 (0.15), residues: 1105 sheet: -3.14 (0.52), residues: 83 loop : -2.63 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG E 91 TYR 0.014 0.002 TYR C 338 PHE 0.029 0.002 PHE B 522 TRP 0.015 0.002 TRP C 314 HIS 0.009 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00470 (15616) covalent geometry : angle 0.66740 (21159) hydrogen bonds : bond 0.04766 ( 863) hydrogen bonds : angle 5.29537 ( 2523) Misc. bond : bond 0.01760 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 306 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 ASP cc_start: 0.9433 (p0) cc_final: 0.9202 (p0) REVERT: B 295 LYS cc_start: 0.9795 (mttt) cc_final: 0.9530 (ptpp) REVERT: B 319 MET cc_start: 0.9333 (mtm) cc_final: 0.8913 (mtp) outliers start: 1 outliers final: 1 residues processed: 126 average time/residue: 0.2983 time to fit residues: 54.7392 Evaluate side-chains 100 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 127 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 24 optimal weight: 30.0000 chunk 96 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 144 GLN ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 227 ASN C 235 ASN C 264 GLN ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 HIS B 245 HIS B 486 HIS A 156 ASN A 284 ASN A 337 ASN A 346 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.072184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.042969 restraints weight = 303819.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.043917 restraints weight = 194681.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.044485 restraints weight = 144275.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.045002 restraints weight = 121852.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.045011 restraints weight = 109313.524| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15617 Z= 0.283 Angle : 0.691 7.328 21159 Z= 0.384 Chirality : 0.040 0.231 2373 Planarity : 0.005 0.083 2644 Dihedral : 6.112 73.331 1982 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.19), residues: 1793 helix: -0.11 (0.15), residues: 1098 sheet: -3.19 (0.53), residues: 85 loop : -2.60 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG E 91 TYR 0.014 0.002 TYR C 177 PHE 0.027 0.002 PHE C 201 TRP 0.015 0.002 TRP C 314 HIS 0.009 0.002 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00533 (15616) covalent geometry : angle 0.69119 (21159) hydrogen bonds : bond 0.04926 ( 863) hydrogen bonds : angle 5.35045 ( 2523) Misc. bond : bond 0.01694 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 306 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 359 HIS cc_start: -0.0067 (t-90) cc_final: -0.0831 (t-90) REVERT: C 13 ASP cc_start: 0.9467 (p0) cc_final: 0.9246 (p0) REVERT: B 319 MET cc_start: 0.9394 (mtm) cc_final: 0.9105 (mtp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.3027 time to fit residues: 50.0175 Evaluate side-chains 99 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 141 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 157 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 19 optimal weight: 30.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 ASN ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 HIS ** 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 = 0.3830 r_free = 0.3830 target = 0.074703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.045890 restraints weight = 315075.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.045131 restraints weight = 198842.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.045711 restraints weight = 146519.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.045989 restraints weight = 120570.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.046051 restraints weight = 107917.390| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15617 Z= 0.182 Angle : 0.591 5.826 21159 Z= 0.323 Chirality : 0.039 0.165 2373 Planarity : 0.005 0.070 2644 Dihedral : 5.864 75.330 1982 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.19), residues: 1793 helix: 0.19 (0.15), residues: 1111 sheet: -3.22 (0.53), residues: 83 loop : -2.42 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG E 91 TYR 0.019 0.001 TYR E 206 PHE 0.027 0.002 PHE A 255 TRP 0.014 0.001 TRP A 378 HIS 0.008 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00359 (15616) covalent geometry : angle 0.59139 (21159) hydrogen bonds : bond 0.04470 ( 863) hydrogen bonds : angle 5.07408 ( 2523) Misc. bond : bond 0.01690 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 306 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 ASP cc_start: 0.9413 (p0) cc_final: 0.9181 (p0) REVERT: D 76 GLN cc_start: 0.9334 (tm-30) cc_final: 0.9091 (tm-30) REVERT: B 76 GLU cc_start: 0.9534 (pt0) cc_final: 0.9317 (pt0) REVERT: B 201 MET cc_start: 0.9185 (tpp) cc_final: 0.8433 (tpp) REVERT: B 295 LYS cc_start: 0.9821 (mttt) cc_final: 0.9571 (ptpp) REVERT: B 319 MET cc_start: 0.9397 (mtm) cc_final: 0.9101 (mtp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.3141 time to fit residues: 53.0659 Evaluate side-chains 101 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 89 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 15 optimal weight: 40.0000 chunk 21 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 164 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.074185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.045102 restraints weight = 309226.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.044376 restraints weight = 198739.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.045015 restraints weight = 145761.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.045351 restraints weight = 120687.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.045462 restraints weight = 109167.786| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15617 Z= 0.194 Angle : 0.590 5.766 21159 Z= 0.323 Chirality : 0.038 0.214 2373 Planarity : 0.005 0.060 2644 Dihedral : 5.706 79.095 1982 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.43 % Favored : 90.52 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.19), residues: 1793 helix: 0.28 (0.15), residues: 1112 sheet: -2.71 (0.58), residues: 73 loop : -2.43 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG E 91 TYR 0.014 0.001 TYR E 206 PHE 0.025 0.002 PHE A 255 TRP 0.015 0.001 TRP A 378 HIS 0.008 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00379 (15616) covalent geometry : angle 0.58973 (21159) hydrogen bonds : bond 0.04366 ( 863) hydrogen bonds : angle 4.99581 ( 2523) Misc. bond : bond 0.01660 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 306 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 359 HIS cc_start: -0.0045 (t-90) cc_final: -0.1974 (t70) REVERT: C 13 ASP cc_start: 0.9412 (p0) cc_final: 0.9195 (p0) REVERT: B 76 GLU cc_start: 0.9530 (pt0) cc_final: 0.9323 (pt0) REVERT: B 201 MET cc_start: 0.9212 (tpp) cc_final: 0.8714 (tpp) REVERT: B 295 LYS cc_start: 0.9819 (mttt) cc_final: 0.9602 (ptpt) REVERT: B 319 MET cc_start: 0.9418 (mtm) cc_final: 0.9110 (mtp) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.3077 time to fit residues: 51.5518 Evaluate side-chains 95 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 10 optimal weight: 9.9990 chunk 173 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 20 optimal weight: 50.0000 chunk 99 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 GLN C 128 GLN ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN D 69 ASN ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.070890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.042145 restraints weight = 299690.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.042194 restraints weight = 196654.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.042720 restraints weight = 146946.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.043101 restraints weight = 124008.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.043399 restraints weight = 107916.357| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 15617 Z= 0.313 Angle : 0.714 7.666 21159 Z= 0.399 Chirality : 0.040 0.200 2373 Planarity : 0.005 0.065 2644 Dihedral : 5.959 79.709 1982 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.19), residues: 1793 helix: -0.19 (0.14), residues: 1106 sheet: -2.63 (0.59), residues: 69 loop : -2.55 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG E 91 TYR 0.018 0.002 TYR E 206 PHE 0.032 0.002 PHE C 51 TRP 0.018 0.002 TRP A 378 HIS 0.010 0.002 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00594 (15616) covalent geometry : angle 0.71411 (21159) hydrogen bonds : bond 0.04926 ( 863) hydrogen bonds : angle 5.41774 ( 2523) Misc. bond : bond 0.01614 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 306 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 359 HIS cc_start: -0.0079 (t-90) cc_final: -0.1871 (t70) REVERT: D 132 LYS cc_start: 0.9629 (mmpt) cc_final: 0.9302 (mmmt) REVERT: B 201 MET cc_start: 0.9186 (tpp) cc_final: 0.8800 (tpp) REVERT: B 319 MET cc_start: 0.9504 (mtm) cc_final: 0.9143 (mtp) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.3390 time to fit residues: 51.9764 Evaluate side-chains 92 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 19 optimal weight: 30.0000 chunk 147 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 144 GLN ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.075181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.046698 restraints weight = 316780.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.048212 restraints weight = 209530.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.047575 restraints weight = 137968.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.046836 restraints weight = 113348.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.046617 restraints weight = 104440.275| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15617 Z= 0.145 Angle : 0.570 5.801 21159 Z= 0.310 Chirality : 0.039 0.144 2373 Planarity : 0.005 0.057 2644 Dihedral : 5.678 77.991 1982 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.19), residues: 1793 helix: 0.35 (0.15), residues: 1116 sheet: -2.70 (0.57), residues: 71 loop : -2.43 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG E 91 TYR 0.026 0.001 TYR E 206 PHE 0.025 0.001 PHE A 255 TRP 0.014 0.001 TRP A 378 HIS 0.010 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00294 (15616) covalent geometry : angle 0.57029 (21159) hydrogen bonds : bond 0.04319 ( 863) hydrogen bonds : angle 4.91703 ( 2523) Misc. bond : bond 0.01647 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 306 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 359 HIS cc_start: -0.0190 (t-90) cc_final: -0.2081 (t70) REVERT: D 29 LEU cc_start: 0.9560 (tt) cc_final: 0.9325 (tt) REVERT: D 33 ASN cc_start: 0.9745 (t0) cc_final: 0.9451 (p0) REVERT: B 76 GLU cc_start: 0.9348 (pt0) cc_final: 0.9115 (pt0) REVERT: B 201 MET cc_start: 0.9181 (tpp) cc_final: 0.8825 (tpp) REVERT: B 319 MET cc_start: 0.9414 (mtm) cc_final: 0.9042 (mtp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.3222 time to fit residues: 53.1397 Evaluate side-chains 98 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 5 optimal weight: 0.1980 chunk 22 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 30 optimal weight: 40.0000 chunk 33 optimal weight: 40.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.074833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.047145 restraints weight = 305796.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.044657 restraints weight = 226490.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.045124 restraints weight = 155024.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.045286 restraints weight = 120123.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.045286 restraints weight = 109898.671| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15617 Z= 0.169 Angle : 0.564 5.878 21159 Z= 0.309 Chirality : 0.038 0.160 2373 Planarity : 0.005 0.057 2644 Dihedral : 5.522 78.163 1982 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.20), residues: 1793 helix: 0.54 (0.15), residues: 1115 sheet: -2.74 (0.57), residues: 73 loop : -2.35 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG E 91 TYR 0.017 0.001 TYR E 206 PHE 0.022 0.001 PHE A 255 TRP 0.014 0.001 TRP A 378 HIS 0.008 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00330 (15616) covalent geometry : angle 0.56423 (21159) hydrogen bonds : bond 0.04172 ( 863) hydrogen bonds : angle 4.88520 ( 2523) Misc. bond : bond 0.01639 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 306 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 359 HIS cc_start: -0.0142 (t-90) cc_final: -0.2272 (t70) REVERT: B 76 GLU cc_start: 0.9380 (pt0) cc_final: 0.9180 (pt0) REVERT: B 201 MET cc_start: 0.9147 (tpp) cc_final: 0.8817 (tpp) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.3011 time to fit residues: 48.7374 Evaluate side-chains 92 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 76 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 154 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 20 optimal weight: 40.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 116 ASN ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 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 = 0.3839 r_free = 0.3839 target = 0.076170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.047163 restraints weight = 308158.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.045514 restraints weight = 196765.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.045796 restraints weight = 143058.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.046304 restraints weight = 123568.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.046662 restraints weight = 111252.698| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15617 Z= 0.125 Angle : 0.530 5.745 21159 Z= 0.286 Chirality : 0.038 0.141 2373 Planarity : 0.004 0.054 2644 Dihedral : 5.368 77.540 1982 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.20), residues: 1793 helix: 0.78 (0.15), residues: 1124 sheet: -2.64 (0.57), residues: 73 loop : -2.27 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.000 ARG E 91 TYR 0.013 0.001 TYR B 447 PHE 0.022 0.001 PHE A 255 TRP 0.013 0.001 TRP A 378 HIS 0.008 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00256 (15616) covalent geometry : angle 0.53035 (21159) hydrogen bonds : bond 0.03958 ( 863) hydrogen bonds : angle 4.66304 ( 2523) Misc. bond : bond 0.01651 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 306 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 359 HIS cc_start: -0.0082 (t-90) cc_final: -0.2320 (t70) REVERT: B 201 MET cc_start: 0.9145 (tpp) cc_final: 0.8821 (tpp) REVERT: B 319 MET cc_start: 0.9398 (mtm) cc_final: 0.8991 (mtp) REVERT: B 443 GLU cc_start: 0.9612 (mt-10) cc_final: 0.9391 (mt-10) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.3095 time to fit residues: 52.2178 Evaluate side-chains 100 residues out of total 1732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 8.9990 chunk 32 optimal weight: 30.0000 chunk 62 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 chunk 142 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 30.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 HIS ** A 307 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 = 0.3804 r_free = 0.3804 target = 0.073449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.044457 restraints weight = 306616.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.044903 restraints weight = 204370.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.045613 restraints weight = 154569.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.044870 restraints weight = 131972.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.044536 restraints weight = 112486.999| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15617 Z= 0.221 Angle : 0.595 6.000 21159 Z= 0.329 Chirality : 0.038 0.156 2373 Planarity : 0.005 0.058 2644 Dihedral : 5.424 78.209 1982 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.20), residues: 1793 helix: 0.57 (0.15), residues: 1118 sheet: -2.59 (0.58), residues: 71 loop : -2.32 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG E 91 TYR 0.015 0.002 TYR B 447 PHE 0.019 0.002 PHE B 324 TRP 0.016 0.002 TRP A 378 HIS 0.010 0.002 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00425 (15616) covalent geometry : angle 0.59490 (21159) hydrogen bonds : bond 0.04199 ( 863) hydrogen bonds : angle 4.89541 ( 2523) Misc. bond : bond 0.01637 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5955.38 seconds wall clock time: 102 minutes 6.57 seconds (6126.57 seconds total)