Starting phenix.real_space_refine on Thu Mar 5 14:57:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6p7v_20270/03_2026/6p7v_20270.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p7v_20270/03_2026/6p7v_20270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6p7v_20270/03_2026/6p7v_20270.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p7v_20270/03_2026/6p7v_20270.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6p7v_20270/03_2026/6p7v_20270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p7v_20270/03_2026/6p7v_20270.map" } resolution = 4.0 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 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 56 5.16 5 C 7501 2.51 5 N 1906 2.21 5 O 2069 1.98 5 H 11620 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.01s 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: 23152 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 5437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 5437 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain breaks: 1 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: 7679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 7679 Classifications: {'peptide': 457} Link IDs: {'PTRANS': 14, 'TRANS': 442} Chain breaks: 6 Time building chain proxies: 3.85, per 1000 atoms: 0.17 Number of scatterers: 23152 At special positions: 0 Unit cell: (96.5055, 112.413, 127.26, 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 56 16.00 O 2069 8.00 N 1906 7.00 C 7501 6.00 H 11620 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=0, symmetry=0 Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 666.5 milliseconds 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2696 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 5 sheets defined 69.5% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 11 through 22 removed outlier: 3.897A pdb=" N ARG C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 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 201 removed outlier: 4.446A pdb=" N GLU C 199 " --> pdb=" O PRO C 196 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER C 200 " --> pdb=" O CYS C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 219 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 372 removed outlier: 3.655A pdb=" N GLU C 372 " --> pdb=" O ARG C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 27 Processing helix chain 'D' and resid 29 through 36 removed outlier: 3.553A pdb=" N GLN D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 131 through 148 removed outlier: 3.718A pdb=" N LEU D 135 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 156 removed outlier: 3.869A 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 removed outlier: 3.512A pdb=" N GLU B 103 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 133 removed outlier: 3.574A pdb=" N ILE B 122 " --> pdb=" O SER B 118 " (cutoff:3.500A) 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: 3.675A pdb=" N ILE B 206 " --> pdb=" O PRO B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 218 removed outlier: 3.917A 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 271 removed outlier: 3.564A pdb=" N GLN B 265 " --> pdb=" O VAL B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'B' and resid 279 through 298 removed outlier: 3.541A 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 342 through 346 removed outlier: 3.540A pdb=" N ASN B 346 " --> pdb=" O HIS B 343 " (cutoff:3.500A) 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: 3.711A pdb=" N THR B 479 " --> pdb=" O TYR B 475 " (cutoff:3.500A) removed outlier: 3.855A 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: 3.738A pdb=" N VAL B 485 " --> pdb=" O HIS B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 522 removed outlier: 3.524A pdb=" N LEU B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 548 Processing helix chain 'B' and resid 560 through 578 removed outlier: 4.301A 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 removed outlier: 3.623A pdb=" N ILE A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) 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: 3.767A pdb=" N ILE A 206 " --> pdb=" O PRO A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 232 through 256 removed outlier: 3.683A pdb=" N ARG A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 272 removed outlier: 4.122A 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 298 removed outlier: 3.516A pdb=" N GLY A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 333 Processing helix chain 'A' and resid 373 through 390 removed outlier: 3.677A pdb=" N SER A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) 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: 3.584A pdb=" N THR A 479 " --> pdb=" O TYR A 475 " (cutoff:3.500A) removed outlier: 3.653A 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: 3.722A pdb=" N VAL A 485 " --> pdb=" O HIS A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 522 Processing helix chain 'A' and resid 525 through 548 removed outlier: 3.538A pdb=" N ILE A 529 " --> pdb=" O LEU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 578 removed outlier: 3.821A 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 'C' and resid 105 through 111 removed outlier: 3.748A pdb=" N VAL C 129 " --> pdb=" O ILE C 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 178 through 179 removed outlier: 7.091A pdb=" N ILE C 178 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU C 207 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 276 through 277 removed outlier: 6.837A pdb=" N ILE C 276 " --> pdb=" O ILE C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 365 through 366 removed outlier: 6.661A pdb=" N LEU C 365 " --> pdb=" O ILE C 389 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 16 through 21 695 hydrogen bonds defined for protein. 2052 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: 4.69 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 11591 1.02 - 1.22: 33 1.22 - 1.42: 4993 1.42 - 1.62: 6709 1.62 - 1.82: 83 Bond restraints: 23409 Sorted by residual: bond pdb=" CA ASN B 106 " pdb=" CB ASN B 106 " ideal model delta sigma weight residual 1.526 1.471 0.055 1.76e-02 3.23e+03 9.93e+00 bond pdb=" CG1 ILE A 254 " pdb=" CD1 ILE A 254 " ideal model delta sigma weight residual 1.513 1.405 0.108 3.90e-02 6.57e+02 7.67e+00 bond pdb=" CB VAL B 329 " pdb=" CG1 VAL B 329 " ideal model delta sigma weight residual 1.521 1.447 0.074 3.30e-02 9.18e+02 5.05e+00 bond pdb=" CG LEU A 282 " pdb=" CD1 LEU A 282 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.86e+00 bond pdb=" CA ILE B 254 " pdb=" C ILE B 254 " ideal model delta sigma weight residual 1.524 1.499 0.025 1.18e-02 7.18e+03 4.61e+00 ... (remaining 23404 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 41322 2.96 - 5.92: 926 5.92 - 8.88: 83 8.88 - 11.84: 2 11.84 - 14.80: 2 Bond angle restraints: 42335 Sorted by residual: angle pdb=" C GLY A 134 " pdb=" N TRP A 135 " pdb=" CA TRP A 135 " ideal model delta sigma weight residual 121.19 129.89 -8.70 1.59e+00 3.96e-01 2.99e+01 angle pdb=" N LEU B 257 " pdb=" CA LEU B 257 " pdb=" C LEU B 257 " ideal model delta sigma weight residual 108.22 112.98 -4.76 9.00e-01 1.23e+00 2.80e+01 angle pdb=" C PHE B 522 " pdb=" N ASP B 523 " pdb=" CA ASP B 523 " ideal model delta sigma weight residual 119.78 126.22 -6.44 1.24e+00 6.50e-01 2.70e+01 angle pdb=" C PHE A 117 " pdb=" CA PHE A 117 " pdb=" HA PHE A 117 " ideal model delta sigma weight residual 109.00 94.20 14.80 3.00e+00 1.11e-01 2.43e+01 angle pdb=" CA ARG A 575 " pdb=" CB ARG A 575 " pdb=" CG ARG A 575 " ideal model delta sigma weight residual 114.10 123.67 -9.57 2.00e+00 2.50e-01 2.29e+01 ... (remaining 42330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 9299 17.66 - 35.32: 1279 35.32 - 52.97: 249 52.97 - 70.63: 73 70.63 - 88.29: 17 Dihedral angle restraints: 10917 sinusoidal: 5877 harmonic: 5040 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 180.00 140.21 39.79 0 5.00e+00 4.00e-02 6.33e+01 dihedral pdb=" CA PHE C 201 " pdb=" C PHE C 201 " pdb=" N ASN C 202 " pdb=" CA ASN C 202 " ideal model delta harmonic sigma weight residual 180.00 -149.83 -30.17 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA PHE B 117 " pdb=" C PHE B 117 " pdb=" N SER B 118 " pdb=" CA SER B 118 " ideal model delta harmonic sigma weight residual 180.00 150.64 29.36 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 10914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1307 0.060 - 0.121: 388 0.121 - 0.181: 88 0.181 - 0.242: 13 0.242 - 0.302: 3 Chirality restraints: 1799 Sorted by residual: chirality pdb=" CG LEU A 185 " pdb=" CB LEU A 185 " pdb=" CD1 LEU A 185 " pdb=" CD2 LEU A 185 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CG LEU A 268 " pdb=" CB LEU A 268 " pdb=" CD1 LEU A 268 " pdb=" CD2 LEU A 268 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA LEU A 268 " pdb=" N LEU A 268 " pdb=" C LEU A 268 " pdb=" CB LEU A 268 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 1796 not shown) Planarity restraints: 3304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 211 " 0.028 2.00e-02 2.50e+03 5.69e-02 3.24e+01 pdb=" C ASP A 211 " -0.098 2.00e-02 2.50e+03 pdb=" O ASP A 211 " 0.037 2.00e-02 2.50e+03 pdb=" N ILE A 212 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 110 " -0.021 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" C PHE A 110 " 0.073 2.00e-02 2.50e+03 pdb=" O PHE A 110 " -0.027 2.00e-02 2.50e+03 pdb=" N TYR A 111 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 532 " -0.020 2.00e-02 2.50e+03 4.09e-02 1.67e+01 pdb=" C PHE A 532 " 0.071 2.00e-02 2.50e+03 pdb=" O PHE A 532 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE A 533 " -0.024 2.00e-02 2.50e+03 ... (remaining 3301 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 4643 2.29 - 2.87: 54009 2.87 - 3.44: 60588 3.44 - 4.02: 77798 4.02 - 4.60: 121085 Nonbonded interactions: 318123 Sorted by model distance: nonbonded pdb=" O LEU A 270 " pdb=" HG1 THR A 273 " model vdw 1.712 2.450 nonbonded pdb=" O VAL C 341 " pdb=" HG1 THR C 344 " model vdw 1.716 2.450 nonbonded pdb=" O SER D 12 " pdb=" H GLY D 15 " model vdw 1.738 2.450 nonbonded pdb=" OE1 GLU A 477 " pdb=" H GLU A 477 " model vdw 1.740 2.450 nonbonded pdb=" OD2 ASP B 330 " pdb=" H LEU B 342 " model vdw 1.743 2.450 ... (remaining 318118 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' 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.160 Extract box with map and model: 0.350 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 19.670 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 : 0.011 0.108 11789 Z= 0.479 Angle : 1.207 12.578 15945 Z= 0.683 Chirality : 0.060 0.302 1799 Planarity : 0.008 0.075 1981 Dihedral : 15.861 85.657 4372 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.79 % Favored : 89.99 % Rotamer: Outliers : 0.08 % Allowed : 4.59 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.19 (0.19), residues: 1348 helix: -1.27 (0.14), residues: 874 sheet: -2.61 (0.88), residues: 36 loop : -3.71 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 615 TYR 0.054 0.004 TYR A 111 PHE 0.039 0.004 PHE A 444 TRP 0.044 0.004 TRP A 378 HIS 0.019 0.004 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.01083 (11789) covalent geometry : angle 1.20677 (15945) hydrogen bonds : bond 0.12112 ( 695) hydrogen bonds : angle 6.16399 ( 2052) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.724 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: C 91 ASP cc_start: 0.9264 (t0) cc_final: 0.8893 (p0) REVERT: C 116 GLU cc_start: 0.6877 (tt0) cc_final: 0.6319 (mp0) REVERT: C 244 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7606 (mt-10) REVERT: D 76 GLN cc_start: 0.9395 (tt0) cc_final: 0.8997 (tp-100) REVERT: D 132 LYS cc_start: 0.9495 (mmtt) cc_final: 0.9227 (mmmt) REVERT: B 277 GLN cc_start: 0.9312 (mp10) cc_final: 0.9091 (mp10) REVERT: B 330 ASP cc_start: 0.8087 (t0) cc_final: 0.7824 (t70) REVERT: A 76 GLU cc_start: 0.8957 (pt0) cc_final: 0.8691 (pt0) REVERT: A 295 LYS cc_start: 0.9452 (mttt) cc_final: 0.9174 (mttp) REVERT: A 330 ASP cc_start: 0.8841 (t70) cc_final: 0.8460 (t70) REVERT: A 436 MET cc_start: 0.9074 (mmm) cc_final: 0.8655 (mtm) outliers start: 1 outliers final: 1 residues processed: 182 average time/residue: 0.2608 time to fit residues: 66.3519 Evaluate side-chains 114 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 175 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 160 ASN ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 ASN B 307 ASN B 346 ASN B 431 GLN ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN ** A 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.074860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.058625 restraints weight = 162717.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.061425 restraints weight = 73072.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.063212 restraints weight = 42910.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.064218 restraints weight = 30139.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.065032 restraints weight = 24289.611| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11789 Z= 0.139 Angle : 0.667 6.708 15945 Z= 0.356 Chirality : 0.040 0.160 1799 Planarity : 0.005 0.053 1981 Dihedral : 6.719 31.786 1500 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.49 % Favored : 92.43 % Rotamer: Outliers : 0.69 % Allowed : 9.25 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.50 (0.22), residues: 1348 helix: 0.17 (0.16), residues: 867 sheet: -2.66 (0.71), residues: 51 loop : -3.21 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 252 TYR 0.023 0.002 TYR C 177 PHE 0.015 0.002 PHE A 110 TRP 0.018 0.002 TRP B 79 HIS 0.007 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00288 (11789) covalent geometry : angle 0.66654 (15945) hydrogen bonds : bond 0.05064 ( 695) hydrogen bonds : angle 4.99619 ( 2052) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.710 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: C 91 ASP cc_start: 0.9261 (t0) cc_final: 0.8841 (p0) REVERT: C 116 GLU cc_start: 0.6563 (tt0) cc_final: 0.6321 (mp0) REVERT: C 206 MET cc_start: 0.7773 (mtt) cc_final: 0.7502 (mtt) REVERT: C 244 GLU cc_start: 0.8596 (mt-10) cc_final: 0.7949 (mt-10) REVERT: C 352 GLU cc_start: 0.7892 (tt0) cc_final: 0.7298 (tm-30) REVERT: C 376 LYS cc_start: 0.8661 (tttt) cc_final: 0.8445 (mttt) REVERT: D 76 GLN cc_start: 0.9392 (tt0) cc_final: 0.9032 (tp-100) REVERT: B 76 GLU cc_start: 0.9108 (pt0) cc_final: 0.8771 (pt0) REVERT: B 277 GLN cc_start: 0.9321 (mp10) cc_final: 0.9107 (mp10) REVERT: B 400 MET cc_start: 0.9333 (mtm) cc_final: 0.8882 (mtp) REVERT: A 76 GLU cc_start: 0.8895 (pt0) cc_final: 0.8595 (pt0) REVERT: A 330 ASP cc_start: 0.8833 (t70) cc_final: 0.8576 (t70) REVERT: A 436 MET cc_start: 0.8897 (mmm) cc_final: 0.8517 (mtm) outliers start: 9 outliers final: 4 residues processed: 156 average time/residue: 0.2237 time to fit residues: 51.0476 Evaluate side-chains 120 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 126 PHE Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 308 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 13 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 111 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 125 optimal weight: 0.0870 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.073220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.056881 restraints weight = 165355.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.059624 restraints weight = 74302.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.061368 restraints weight = 43849.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.062441 restraints weight = 31075.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.063082 restraints weight = 24936.467| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11789 Z= 0.165 Angle : 0.604 6.487 15945 Z= 0.329 Chirality : 0.038 0.141 1799 Planarity : 0.004 0.046 1981 Dihedral : 5.982 28.241 1499 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.12 % Favored : 90.80 % Rotamer: Outliers : 1.07 % Allowed : 11.70 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.75 (0.23), residues: 1348 helix: 0.81 (0.17), residues: 874 sheet: -2.57 (0.62), residues: 65 loop : -3.08 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 99 TYR 0.018 0.001 TYR C 177 PHE 0.013 0.001 PHE A 110 TRP 0.017 0.002 TRP B 79 HIS 0.009 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00333 (11789) covalent geometry : angle 0.60429 (15945) hydrogen bonds : bond 0.04689 ( 695) hydrogen bonds : angle 4.74888 ( 2052) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.641 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: C 91 ASP cc_start: 0.9330 (t0) cc_final: 0.8884 (p0) REVERT: C 206 MET cc_start: 0.7750 (mtt) cc_final: 0.7526 (mtt) REVERT: C 352 GLU cc_start: 0.7923 (tt0) cc_final: 0.7459 (tm-30) REVERT: D 33 ASN cc_start: 0.8932 (t0) cc_final: 0.8705 (t0) REVERT: D 76 GLN cc_start: 0.9517 (tt0) cc_final: 0.9050 (tp-100) REVERT: B 76 GLU cc_start: 0.9202 (pt0) cc_final: 0.8695 (pt0) REVERT: B 277 GLN cc_start: 0.9387 (mp10) cc_final: 0.9149 (mp10) REVERT: B 330 ASP cc_start: 0.8789 (t0) cc_final: 0.8575 (t70) REVERT: B 400 MET cc_start: 0.9375 (mtm) cc_final: 0.8760 (mtp) REVERT: A 76 GLU cc_start: 0.8904 (pt0) cc_final: 0.8615 (pt0) REVERT: A 330 ASP cc_start: 0.9001 (t70) cc_final: 0.8669 (t70) REVERT: A 436 MET cc_start: 0.8913 (mmm) cc_final: 0.8538 (mtm) outliers start: 14 outliers final: 11 residues processed: 136 average time/residue: 0.2010 time to fit residues: 41.7612 Evaluate side-chains 119 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 126 PHE Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 536 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 134 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 98 optimal weight: 0.0040 chunk 121 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.073618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.057409 restraints weight = 164880.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.060157 restraints weight = 73442.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.061945 restraints weight = 43374.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.063038 restraints weight = 30527.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.063424 restraints weight = 24395.861| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11789 Z= 0.123 Angle : 0.559 5.868 15945 Z= 0.301 Chirality : 0.037 0.139 1799 Planarity : 0.004 0.047 1981 Dihedral : 5.594 28.688 1499 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.49 % Favored : 92.43 % Rotamer: Outliers : 1.07 % Allowed : 13.30 % Favored : 85.63 % 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: -0.28 (0.23), residues: 1348 helix: 1.20 (0.17), residues: 883 sheet: -2.46 (0.63), residues: 65 loop : -3.05 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 92 TYR 0.014 0.001 TYR A 331 PHE 0.010 0.001 PHE A 324 TRP 0.018 0.001 TRP B 79 HIS 0.007 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00255 (11789) covalent geometry : angle 0.55898 (15945) hydrogen bonds : bond 0.04296 ( 695) hydrogen bonds : angle 4.48244 ( 2052) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.672 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: C 91 ASP cc_start: 0.9359 (t0) cc_final: 0.8682 (t70) REVERT: C 206 MET cc_start: 0.7653 (mtt) cc_final: 0.7432 (mtt) REVERT: C 352 GLU cc_start: 0.7888 (tt0) cc_final: 0.7489 (tm-30) REVERT: D 33 ASN cc_start: 0.8942 (t0) cc_final: 0.8698 (t0) REVERT: D 76 GLN cc_start: 0.9384 (tt0) cc_final: 0.9055 (tp-100) REVERT: B 76 GLU cc_start: 0.9229 (pt0) cc_final: 0.8687 (pt0) REVERT: B 135 TRP cc_start: 0.7356 (t60) cc_final: 0.6750 (t60) REVERT: B 277 GLN cc_start: 0.9386 (mp10) cc_final: 0.9136 (mp10) REVERT: B 400 MET cc_start: 0.9400 (mtm) cc_final: 0.8744 (mtp) REVERT: A 76 GLU cc_start: 0.8885 (pt0) cc_final: 0.8601 (pt0) REVERT: A 111 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.7780 (m-80) REVERT: A 330 ASP cc_start: 0.9018 (t70) cc_final: 0.8689 (t70) REVERT: A 436 MET cc_start: 0.8889 (mmm) cc_final: 0.8498 (mtm) REVERT: A 458 CYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8618 (m) outliers start: 14 outliers final: 10 residues processed: 134 average time/residue: 0.2122 time to fit residues: 43.0002 Evaluate side-chains 127 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 536 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 70 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.073609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.057290 restraints weight = 165032.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.060074 restraints weight = 73252.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.061843 restraints weight = 43038.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.062940 restraints weight = 30364.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.063546 restraints weight = 24322.637| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11789 Z= 0.118 Angle : 0.536 5.467 15945 Z= 0.288 Chirality : 0.037 0.137 1799 Planarity : 0.004 0.046 1981 Dihedral : 5.285 28.399 1499 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 1.07 % Allowed : 13.84 % Favored : 85.09 % 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: 0.08 (0.24), residues: 1348 helix: 1.49 (0.17), residues: 884 sheet: -2.44 (0.63), residues: 66 loop : -2.92 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 92 TYR 0.014 0.001 TYR A 331 PHE 0.009 0.001 PHE A 324 TRP 0.018 0.001 TRP B 79 HIS 0.007 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00243 (11789) covalent geometry : angle 0.53604 (15945) hydrogen bonds : bond 0.04123 ( 695) hydrogen bonds : angle 4.32651 ( 2052) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.662 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: C 343 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8946 (mm-40) REVERT: C 352 GLU cc_start: 0.8029 (tt0) cc_final: 0.7671 (tm-30) REVERT: D 33 ASN cc_start: 0.8974 (t0) cc_final: 0.8743 (t0) REVERT: D 76 GLN cc_start: 0.9403 (tt0) cc_final: 0.9064 (tp-100) REVERT: B 76 GLU cc_start: 0.9268 (pt0) cc_final: 0.8722 (pt0) REVERT: B 277 GLN cc_start: 0.9428 (mp10) cc_final: 0.9147 (mp10) REVERT: B 400 MET cc_start: 0.9421 (mtm) cc_final: 0.8716 (mtp) REVERT: A 76 GLU cc_start: 0.8889 (pt0) cc_final: 0.8609 (pt0) REVERT: A 111 TYR cc_start: 0.8195 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: A 276 LEU cc_start: 0.8809 (mt) cc_final: 0.8482 (tp) REVERT: A 330 ASP cc_start: 0.8961 (t70) cc_final: 0.8662 (t70) REVERT: A 436 MET cc_start: 0.8882 (mmm) cc_final: 0.8444 (mtm) REVERT: A 458 CYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8574 (m) outliers start: 14 outliers final: 8 residues processed: 132 average time/residue: 0.2103 time to fit residues: 41.7358 Evaluate side-chains 127 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 536 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 50 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 GLN ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN C 260 GLN B 272 ASN ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN A 346 ASN A 431 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.071168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.054845 restraints weight = 170004.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.057465 restraints weight = 75922.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.059163 restraints weight = 45290.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.060221 restraints weight = 32288.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.060754 restraints weight = 26098.679| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11789 Z= 0.219 Angle : 0.605 6.080 15945 Z= 0.331 Chirality : 0.038 0.148 1799 Planarity : 0.004 0.046 1981 Dihedral : 5.315 27.510 1499 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.27 % Favored : 90.65 % Rotamer: Outliers : 1.68 % Allowed : 13.76 % Favored : 84.56 % 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: 0.05 (0.24), residues: 1348 helix: 1.48 (0.17), residues: 885 sheet: -2.70 (0.64), residues: 62 loop : -2.94 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 99 TYR 0.021 0.002 TYR B 137 PHE 0.012 0.002 PHE B 267 TRP 0.019 0.002 TRP B 79 HIS 0.010 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00450 (11789) covalent geometry : angle 0.60471 (15945) hydrogen bonds : bond 0.04528 ( 695) hydrogen bonds : angle 4.62065 ( 2052) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.649 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: C 91 ASP cc_start: 0.9415 (t0) cc_final: 0.8980 (p0) REVERT: C 198 MET cc_start: 0.9201 (tmm) cc_final: 0.8980 (tmm) REVERT: C 352 GLU cc_start: 0.8338 (tt0) cc_final: 0.7749 (tm-30) REVERT: D 33 ASN cc_start: 0.8976 (t0) cc_final: 0.8774 (t0) REVERT: D 76 GLN cc_start: 0.9454 (tt0) cc_final: 0.9117 (tp-100) REVERT: B 76 GLU cc_start: 0.9286 (pt0) cc_final: 0.8736 (pt0) REVERT: B 111 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.6881 (t80) REVERT: B 254 ILE cc_start: 0.8311 (mt) cc_final: 0.8109 (mt) REVERT: B 277 GLN cc_start: 0.9460 (mp10) cc_final: 0.9156 (mp10) REVERT: B 390 SER cc_start: 0.8262 (m) cc_final: 0.7931 (p) REVERT: A 76 GLU cc_start: 0.8879 (pt0) cc_final: 0.8617 (pt0) REVERT: A 330 ASP cc_start: 0.9057 (t70) cc_final: 0.8778 (t70) REVERT: A 436 MET cc_start: 0.8918 (mmm) cc_final: 0.8546 (mtm) REVERT: A 458 CYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8633 (m) outliers start: 22 outliers final: 13 residues processed: 132 average time/residue: 0.2046 time to fit residues: 41.3913 Evaluate side-chains 123 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 536 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 94 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 118 optimal weight: 0.5980 chunk 123 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 134 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN A 156 ASN ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.072130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.055774 restraints weight = 167377.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.058453 restraints weight = 74548.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.060154 restraints weight = 44339.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.061244 restraints weight = 31599.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.061832 restraints weight = 25464.723| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11789 Z= 0.136 Angle : 0.550 5.535 15945 Z= 0.296 Chirality : 0.037 0.137 1799 Planarity : 0.004 0.046 1981 Dihedral : 5.162 27.872 1499 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.94 % Favored : 91.99 % Rotamer: Outliers : 1.15 % Allowed : 14.45 % Favored : 84.40 % 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: 0.33 (0.24), residues: 1348 helix: 1.67 (0.17), residues: 885 sheet: -2.42 (0.70), residues: 56 loop : -2.81 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 99 TYR 0.016 0.001 TYR B 137 PHE 0.010 0.001 PHE A 324 TRP 0.019 0.001 TRP B 79 HIS 0.011 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00283 (11789) covalent geometry : angle 0.54966 (15945) hydrogen bonds : bond 0.04209 ( 695) hydrogen bonds : angle 4.36517 ( 2052) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.544 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: C 198 MET cc_start: 0.9160 (tmm) cc_final: 0.8933 (tmm) REVERT: C 352 GLU cc_start: 0.8350 (tt0) cc_final: 0.7759 (tm-30) REVERT: D 76 GLN cc_start: 0.9426 (tt0) cc_final: 0.9077 (tp-100) REVERT: B 76 GLU cc_start: 0.9273 (pt0) cc_final: 0.8720 (pt0) REVERT: B 277 GLN cc_start: 0.9438 (mp10) cc_final: 0.9144 (mp10) REVERT: B 390 SER cc_start: 0.8130 (m) cc_final: 0.7757 (p) REVERT: B 400 MET cc_start: 0.9382 (mtm) cc_final: 0.8887 (mtp) REVERT: A 76 GLU cc_start: 0.8858 (pt0) cc_final: 0.8600 (pt0) REVERT: A 201 MET cc_start: 0.8528 (tpp) cc_final: 0.8093 (tpp) REVERT: A 276 LEU cc_start: 0.8853 (mt) cc_final: 0.8559 (tp) REVERT: A 330 ASP cc_start: 0.9011 (t70) cc_final: 0.8736 (t70) REVERT: A 436 MET cc_start: 0.8905 (mmm) cc_final: 0.8511 (mtm) REVERT: A 458 CYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8622 (m) outliers start: 15 outliers final: 12 residues processed: 130 average time/residue: 0.1907 time to fit residues: 38.2084 Evaluate side-chains 130 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain B residue 610 PHE Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 536 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 76 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 119 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 107 GLN ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.072452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.056045 restraints weight = 165762.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.058756 restraints weight = 73746.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.060479 restraints weight = 43534.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.061581 restraints weight = 30982.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.062173 restraints weight = 24922.539| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11789 Z= 0.125 Angle : 0.549 5.894 15945 Z= 0.292 Chirality : 0.037 0.136 1799 Planarity : 0.004 0.046 1981 Dihedral : 5.022 27.642 1499 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.79 % Favored : 92.14 % Rotamer: Outliers : 1.38 % Allowed : 14.37 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.51 (0.24), residues: 1348 helix: 1.78 (0.18), residues: 886 sheet: -2.04 (0.69), residues: 60 loop : -2.73 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 99 TYR 0.016 0.001 TYR B 137 PHE 0.022 0.001 PHE C 120 TRP 0.018 0.001 TRP B 79 HIS 0.011 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00263 (11789) covalent geometry : angle 0.54861 (15945) hydrogen bonds : bond 0.04064 ( 695) hydrogen bonds : angle 4.24771 ( 2052) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.665 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: C 198 MET cc_start: 0.9178 (tmm) cc_final: 0.8927 (tmm) REVERT: C 352 GLU cc_start: 0.8325 (tt0) cc_final: 0.7785 (tm-30) REVERT: D 76 GLN cc_start: 0.9431 (tt0) cc_final: 0.9088 (tp-100) REVERT: B 76 GLU cc_start: 0.9239 (pt0) cc_final: 0.8692 (pt0) REVERT: B 277 GLN cc_start: 0.9437 (mp10) cc_final: 0.9131 (mp10) REVERT: B 390 SER cc_start: 0.8094 (m) cc_final: 0.7733 (p) REVERT: B 400 MET cc_start: 0.9431 (mtm) cc_final: 0.8898 (mtp) REVERT: A 76 GLU cc_start: 0.8855 (pt0) cc_final: 0.8603 (pt0) REVERT: A 111 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.7601 (m-10) REVERT: A 201 MET cc_start: 0.8535 (tpp) cc_final: 0.8051 (tpp) REVERT: A 276 LEU cc_start: 0.8852 (mt) cc_final: 0.8578 (tp) REVERT: A 330 ASP cc_start: 0.9012 (t70) cc_final: 0.8751 (t70) REVERT: A 436 MET cc_start: 0.8911 (mmm) cc_final: 0.8518 (mtm) REVERT: A 458 CYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8606 (m) outliers start: 18 outliers final: 14 residues processed: 132 average time/residue: 0.2002 time to fit residues: 39.8976 Evaluate side-chains 131 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain B residue 610 PHE Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 536 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 85 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.070588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.054363 restraints weight = 167403.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.056956 restraints weight = 75089.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.058604 restraints weight = 44536.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.059668 restraints weight = 31787.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.060344 restraints weight = 25644.637| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11789 Z= 0.190 Angle : 0.580 6.076 15945 Z= 0.315 Chirality : 0.038 0.137 1799 Planarity : 0.004 0.044 1981 Dihedral : 5.056 27.016 1499 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.23 % Favored : 91.69 % Rotamer: Outliers : 1.30 % Allowed : 14.53 % Favored : 84.17 % 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: 0.40 (0.24), residues: 1348 helix: 1.71 (0.17), residues: 886 sheet: -2.41 (0.70), residues: 56 loop : -2.76 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 99 TYR 0.017 0.001 TYR B 137 PHE 0.011 0.001 PHE A 494 TRP 0.019 0.002 TRP B 79 HIS 0.010 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00394 (11789) covalent geometry : angle 0.58007 (15945) hydrogen bonds : bond 0.04291 ( 695) hydrogen bonds : angle 4.43176 ( 2052) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.678 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: C 198 MET cc_start: 0.9189 (tmm) cc_final: 0.8890 (tmm) REVERT: C 352 GLU cc_start: 0.8510 (tt0) cc_final: 0.7904 (tm-30) REVERT: C 372 GLU cc_start: 0.8336 (mp0) cc_final: 0.8132 (mp0) REVERT: D 76 GLN cc_start: 0.9461 (tt0) cc_final: 0.9130 (tp-100) REVERT: B 76 GLU cc_start: 0.9250 (pt0) cc_final: 0.8712 (pt0) REVERT: B 277 GLN cc_start: 0.9461 (mp10) cc_final: 0.9111 (mp10) REVERT: B 390 SER cc_start: 0.8186 (m) cc_final: 0.7777 (p) REVERT: A 76 GLU cc_start: 0.8818 (pt0) cc_final: 0.8563 (pt0) REVERT: A 111 TYR cc_start: 0.8094 (OUTLIER) cc_final: 0.7566 (m-10) REVERT: A 201 MET cc_start: 0.8490 (tpp) cc_final: 0.8063 (tpp) REVERT: A 330 ASP cc_start: 0.9055 (t70) cc_final: 0.8805 (t70) REVERT: A 436 MET cc_start: 0.8944 (mmm) cc_final: 0.8558 (mtm) outliers start: 17 outliers final: 16 residues processed: 127 average time/residue: 0.1997 time to fit residues: 38.3215 Evaluate side-chains 134 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 104 PHE Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain B residue 610 PHE Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 536 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 51 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 118 optimal weight: 0.0870 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 106 optimal weight: 0.3980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** 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 = 0.3669 r_free = 0.3669 target = 0.072254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.055959 restraints weight = 165653.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.058658 restraints weight = 72962.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.060347 restraints weight = 43165.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.061446 restraints weight = 30696.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.062042 restraints weight = 24765.394| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11789 Z= 0.109 Angle : 0.539 6.624 15945 Z= 0.286 Chirality : 0.037 0.139 1799 Planarity : 0.004 0.046 1981 Dihedral : 4.892 27.324 1499 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.64 % Favored : 92.28 % Rotamer: Outliers : 1.22 % Allowed : 14.83 % Favored : 83.94 % 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: 0.65 (0.24), residues: 1348 helix: 1.89 (0.17), residues: 888 sheet: -2.10 (0.64), residues: 69 loop : -2.67 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 99 TYR 0.015 0.001 TYR B 236 PHE 0.013 0.001 PHE C 120 TRP 0.019 0.001 TRP B 79 HIS 0.008 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00230 (11789) covalent geometry : angle 0.53910 (15945) hydrogen bonds : bond 0.03965 ( 695) hydrogen bonds : angle 4.12953 ( 2052) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.616 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: C 198 MET cc_start: 0.9158 (tmm) cc_final: 0.8855 (tmm) REVERT: C 352 GLU cc_start: 0.8398 (tt0) cc_final: 0.7855 (tm-30) REVERT: D 76 GLN cc_start: 0.9441 (tt0) cc_final: 0.9077 (tp-100) REVERT: B 76 GLU cc_start: 0.9219 (pt0) cc_final: 0.8682 (pt0) REVERT: B 277 GLN cc_start: 0.9437 (mp10) cc_final: 0.9139 (mp10) REVERT: B 390 SER cc_start: 0.8008 (m) cc_final: 0.7554 (p) REVERT: A 76 GLU cc_start: 0.8828 (pt0) cc_final: 0.8591 (pt0) REVERT: A 111 TYR cc_start: 0.7911 (OUTLIER) cc_final: 0.7385 (m-10) REVERT: A 201 MET cc_start: 0.8532 (tpp) cc_final: 0.8079 (tpp) REVERT: A 276 LEU cc_start: 0.8843 (mt) cc_final: 0.8573 (tp) REVERT: A 330 ASP cc_start: 0.9006 (t70) cc_final: 0.8763 (t70) REVERT: A 436 MET cc_start: 0.8900 (mmm) cc_final: 0.8502 (mtm) REVERT: A 458 CYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8581 (m) outliers start: 16 outliers final: 14 residues processed: 136 average time/residue: 0.2135 time to fit residues: 43.5398 Evaluate side-chains 135 residues out of total 1308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 104 PHE Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 137 TYR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain A residue 111 TYR Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 458 CYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 536 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 115 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN A 156 ASN ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.070916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.054711 restraints weight = 167214.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.057300 restraints weight = 74151.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.058969 restraints weight = 44117.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.060042 restraints weight = 31398.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.060581 restraints weight = 25317.838| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11789 Z= 0.169 Angle : 0.568 8.648 15945 Z= 0.305 Chirality : 0.037 0.136 1799 Planarity : 0.004 0.045 1981 Dihedral : 4.902 26.730 1499 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.38 % Favored : 91.54 % Rotamer: Outliers : 1.45 % Allowed : 14.91 % Favored : 83.64 % 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: 0.58 (0.24), residues: 1348 helix: 1.84 (0.17), residues: 888 sheet: -2.34 (0.71), residues: 56 loop : -2.67 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 99 TYR 0.016 0.001 TYR B 137 PHE 0.010 0.001 PHE A 494 TRP 0.018 0.001 TRP B 79 HIS 0.008 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00353 (11789) covalent geometry : angle 0.56847 (15945) hydrogen bonds : bond 0.04133 ( 695) hydrogen bonds : angle 4.28372 ( 2052) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3263.90 seconds wall clock time: 56 minutes 27.92 seconds (3387.92 seconds total)