Starting phenix.real_space_refine on Wed Sep 17 13:16:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fuw_50780/09_2025/9fuw_50780.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fuw_50780/09_2025/9fuw_50780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fuw_50780/09_2025/9fuw_50780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fuw_50780/09_2025/9fuw_50780.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fuw_50780/09_2025/9fuw_50780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fuw_50780/09_2025/9fuw_50780.map" } resolution = 3.8 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5590 2.51 5 N 1536 2.21 5 O 1642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8822 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4411 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 13, 'TRANS': 555} Chain: "A" Number of atoms: 4411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4411 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 13, 'TRANS': 555} Time building chain proxies: 2.37, per 1000 atoms: 0.27 Number of scatterers: 8822 At special positions: 0 Unit cell: (121.04, 111.52, 140.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1642 8.00 N 1536 7.00 C 5590 6.00 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: 0.93 Conformation dependent library (CDL) restraints added in 352.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 5 sheets defined 68.4% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'B' and resid 16 through 21 removed outlier: 3.879A pdb=" N ILE B 20 " --> pdb=" O LEU B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 55 removed outlier: 4.534A pdb=" N ASP B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 61 through 107 Proline residue: B 68 - end of helix removed outlier: 3.593A pdb=" N VAL B 92 " --> pdb=" O CYS B 88 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR B 99 " --> pdb=" O LYS B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 119 removed outlier: 3.670A pdb=" N PHE B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 164 removed outlier: 3.503A pdb=" N ASP B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER B 132 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 212 Proline residue: B 176 - end of helix removed outlier: 4.095A pdb=" N THR B 199 " --> pdb=" O ASN B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 221 Processing helix chain 'B' and resid 222 through 250 Processing helix chain 'B' and resid 251 through 272 Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.757A pdb=" N ILE B 284 " --> pdb=" O THR B 280 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 310 through 323 Processing helix chain 'B' and resid 381 through 391 removed outlier: 3.586A pdb=" N ALA B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER B 387 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 Processing helix chain 'B' and resid 432 through 438 Processing helix chain 'B' and resid 446 through 457 Processing helix chain 'B' and resid 459 through 464 Processing helix chain 'B' and resid 468 through 472 removed outlier: 3.664A pdb=" N ASP B 471 " --> pdb=" O ASN B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 498 Processing helix chain 'B' and resid 515 through 528 Processing helix chain 'B' and resid 538 through 545 Processing helix chain 'B' and resid 561 through 568 Processing helix chain 'B' and resid 571 through 580 Processing helix chain 'A' and resid 16 through 21 removed outlier: 3.902A pdb=" N ILE A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 54 removed outlier: 3.674A pdb=" N LEU A 36 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 45 " --> pdb=" O ASP A 41 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 65 through 107 removed outlier: 3.837A pdb=" N LEU A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 72 " --> pdb=" O PRO A 68 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 92 " --> pdb=" O CYS A 88 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR A 99 " --> pdb=" O LYS A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 117 removed outlier: 3.995A pdb=" N PHE A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 146 removed outlier: 4.478A pdb=" N LEU A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER A 126 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 163 removed outlier: 3.815A pdb=" N ILE A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ILE A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 213 removed outlier: 3.640A pdb=" N LEU A 174 " --> pdb=" O ILE A 170 " (cutoff:3.500A) Proline residue: A 176 - end of helix removed outlier: 3.770A pdb=" N ASN A 198 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR A 199 " --> pdb=" O ASN A 195 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET A 200 " --> pdb=" O MET A 196 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 221 Processing helix chain 'A' and resid 222 through 250 Processing helix chain 'A' and resid 250 through 272 removed outlier: 3.670A pdb=" N ILE A 254 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 302 removed outlier: 3.901A pdb=" N THR A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N MET A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Proline residue: A 297 - end of helix Processing helix chain 'A' and resid 303 through 323 removed outlier: 3.616A pdb=" N GLN A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.938A pdb=" N ILE A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 Processing helix chain 'A' and resid 432 through 438 Processing helix chain 'A' and resid 446 through 457 Processing helix chain 'A' and resid 459 through 465 Processing helix chain 'A' and resid 468 through 472 removed outlier: 3.760A pdb=" N ASP A 471 " --> pdb=" O ASN A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 498 Processing helix chain 'A' and resid 515 through 529 removed outlier: 4.445A pdb=" N ASN A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 544 removed outlier: 3.592A pdb=" N ILE A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 568 removed outlier: 3.663A pdb=" N HIS A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 579 Processing sheet with id=AA1, first strand: chain 'B' and resid 401 through 402 Processing sheet with id=AA2, first strand: chain 'B' and resid 419 through 422 removed outlier: 6.977A pdb=" N ALA B 420 " --> pdb=" O ILE B 503 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 548 through 551 removed outlier: 6.602A pdb=" N ILE B 548 " --> pdb=" O ARG B 559 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ARG B 559 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL B 550 " --> pdb=" O VAL B 557 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 342 through 345 removed outlier: 4.063A pdb=" N ARG A 345 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLU A 399 " --> pdb=" O ARG A 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 419 through 422 removed outlier: 6.143A pdb=" N LEU A 502 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ILE A 535 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU A 504 " --> pdb=" O ILE A 535 " (cutoff:3.500A) 544 hydrogen bonds defined for protein. 1614 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.56 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2110 1.33 - 1.45: 1695 1.45 - 1.58: 5040 1.58 - 1.70: 1 1.70 - 1.82: 104 Bond restraints: 8950 Sorted by residual: bond pdb=" N ILE B 20 " pdb=" CA ILE B 20 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.19e-02 7.06e+03 9.27e+00 bond pdb=" N ARG A 14 " pdb=" CA ARG A 14 " ideal model delta sigma weight residual 1.458 1.498 -0.041 1.35e-02 5.49e+03 9.07e+00 bond pdb=" N THR B 283 " pdb=" CA THR B 283 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.21e-02 6.83e+03 8.21e+00 bond pdb=" N ALA B 21 " pdb=" CA ALA B 21 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.04e-02 9.25e+03 7.98e+00 bond pdb=" N GLN A 309 " pdb=" CA GLN A 309 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.23e-02 6.61e+03 7.24e+00 ... (remaining 8945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 11727 1.89 - 3.78: 308 3.78 - 5.67: 46 5.67 - 7.55: 8 7.55 - 9.44: 3 Bond angle restraints: 12092 Sorted by residual: angle pdb=" N PHE A 308 " pdb=" CA PHE A 308 " pdb=" C PHE A 308 " ideal model delta sigma weight residual 111.28 102.00 9.28 1.09e+00 8.42e-01 7.25e+01 angle pdb=" N ARG A 310 " pdb=" CA ARG A 310 " pdb=" C ARG A 310 " ideal model delta sigma weight residual 111.07 104.00 7.07 1.07e+00 8.73e-01 4.37e+01 angle pdb=" CA PHE A 13 " pdb=" C PHE A 13 " pdb=" O PHE A 13 " ideal model delta sigma weight residual 120.82 114.46 6.36 1.05e+00 9.07e-01 3.67e+01 angle pdb=" N PHE A 13 " pdb=" CA PHE A 13 " pdb=" C PHE A 13 " ideal model delta sigma weight residual 111.07 117.25 -6.18 1.07e+00 8.73e-01 3.33e+01 angle pdb=" N ALA A 314 " pdb=" CA ALA A 314 " pdb=" C ALA A 314 " ideal model delta sigma weight residual 111.28 105.30 5.98 1.09e+00 8.42e-01 3.01e+01 ... (remaining 12087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4673 17.90 - 35.81: 586 35.81 - 53.71: 160 53.71 - 71.62: 24 71.62 - 89.52: 11 Dihedral angle restraints: 5454 sinusoidal: 2164 harmonic: 3290 Sorted by residual: dihedral pdb=" CA ARG B 14 " pdb=" C ARG B 14 " pdb=" N ARG B 15 " pdb=" CA ARG B 15 " ideal model delta harmonic sigma weight residual 180.00 151.29 28.71 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" C PHE A 308 " pdb=" N PHE A 308 " pdb=" CA PHE A 308 " pdb=" CB PHE A 308 " ideal model delta harmonic sigma weight residual -122.60 -108.85 -13.75 0 2.50e+00 1.60e-01 3.02e+01 dihedral pdb=" C THR A 12 " pdb=" N THR A 12 " pdb=" CA THR A 12 " pdb=" CB THR A 12 " ideal model delta harmonic sigma weight residual -122.00 -133.88 11.88 0 2.50e+00 1.60e-01 2.26e+01 ... (remaining 5451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1339 0.079 - 0.159: 93 0.159 - 0.238: 3 0.238 - 0.318: 0 0.318 - 0.397: 5 Chirality restraints: 1440 Sorted by residual: chirality pdb=" CA ARG A 14 " pdb=" N ARG A 14 " pdb=" C ARG A 14 " pdb=" CB ARG A 14 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA LEU A 16 " pdb=" N LEU A 16 " pdb=" C LEU A 16 " pdb=" CB LEU A 16 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CA PHE A 308 " pdb=" N PHE A 308 " pdb=" C PHE A 308 " pdb=" CB PHE A 308 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.14e+00 ... (remaining 1437 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 351 " -0.039 5.00e-02 4.00e+02 5.83e-02 5.45e+00 pdb=" N PRO A 352 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 352 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 352 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 13 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.37e+00 pdb=" C PHE A 13 " -0.040 2.00e-02 2.50e+03 pdb=" O PHE A 13 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG A 14 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 307 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C GLN A 307 " -0.036 2.00e-02 2.50e+03 pdb=" O GLN A 307 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE A 308 " 0.012 2.00e-02 2.50e+03 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1593 2.76 - 3.29: 9860 3.29 - 3.83: 15065 3.83 - 4.36: 16926 4.36 - 4.90: 28110 Nonbonded interactions: 71554 Sorted by model distance: nonbonded pdb=" O THR A 123 " pdb=" OG SER A 126 " model vdw 2.221 3.040 nonbonded pdb=" NH1 ARG B 61 " pdb=" O SER A 271 " model vdw 2.241 3.120 nonbonded pdb=" O ILE B 128 " pdb=" OG SER B 132 " model vdw 2.249 3.040 nonbonded pdb=" O GLN B 202 " pdb=" OG1 THR B 205 " model vdw 2.252 3.040 nonbonded pdb=" OD1 ASN B 198 " pdb=" N THR B 199 " model vdw 2.254 3.120 ... (remaining 71549 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 5.610 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.190 Find NCS groups from input model: 0.130 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: 17.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 : 0.004 0.045 8950 Z= 0.232 Angle : 0.730 9.442 12092 Z= 0.454 Chirality : 0.045 0.397 1440 Planarity : 0.004 0.058 1532 Dihedral : 17.186 89.522 3326 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.73 % Favored : 94.18 % Rotamer: Outliers : 0.31 % Allowed : 30.99 % Favored : 68.70 % Cbeta Deviations : 0.19 % 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 aren not related in a simple way. whole: -0.15 (0.25), residues: 1134 helix: 0.66 (0.19), residues: 752 sheet: -3.38 (0.96), residues: 24 loop : -1.37 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 310 TYR 0.011 0.001 TYR A 410 PHE 0.023 0.002 PHE A 308 TRP 0.010 0.001 TRP A 66 HIS 0.005 0.001 HIS A 562 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 8950) covalent geometry : angle 0.73035 (12092) hydrogen bonds : bond 0.13865 ( 544) hydrogen bonds : angle 6.29488 ( 1614) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 129 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: B 458 TYR cc_start: 0.8501 (m-80) cc_final: 0.8278 (m-10) outliers start: 3 outliers final: 1 residues processed: 131 average time/residue: 0.0924 time to fit residues: 17.4132 Evaluate side-chains 118 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN A 417 ASN ** A 436 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 = 0.3836 r_free = 0.3836 target = 0.107981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.080913 restraints weight = 25729.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.083451 restraints weight = 13363.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.085096 restraints weight = 8781.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.086143 restraints weight = 6706.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.086805 restraints weight = 5649.937| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 8950 Z= 0.201 Angle : 0.680 8.342 12092 Z= 0.354 Chirality : 0.043 0.168 1440 Planarity : 0.004 0.039 1532 Dihedral : 5.132 44.476 1241 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.24 % Allowed : 27.58 % Favored : 68.18 % 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 aren not related in a simple way. whole: 0.23 (0.25), residues: 1134 helix: 0.90 (0.19), residues: 778 sheet: -3.25 (0.97), residues: 24 loop : -1.26 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 517 TYR 0.018 0.002 TYR A 439 PHE 0.017 0.002 PHE A 56 TRP 0.015 0.001 TRP A 66 HIS 0.007 0.001 HIS A 562 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 8950) covalent geometry : angle 0.67965 (12092) hydrogen bonds : bond 0.04476 ( 544) hydrogen bonds : angle 4.87749 ( 1614) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 ARG cc_start: 0.7568 (mtt180) cc_final: 0.7336 (mtt180) REVERT: B 284 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.8998 (tp) REVERT: B 458 TYR cc_start: 0.8465 (m-80) cc_final: 0.8223 (m-10) REVERT: A 170 ILE cc_start: 0.9225 (tp) cc_final: 0.8892 (tp) REVERT: A 324 SER cc_start: 0.8251 (OUTLIER) cc_final: 0.7942 (t) REVERT: A 402 MET cc_start: 0.7762 (tpt) cc_final: 0.7449 (tpt) REVERT: A 456 MET cc_start: 0.8577 (mmm) cc_final: 0.8346 (mmm) outliers start: 41 outliers final: 25 residues processed: 161 average time/residue: 0.0797 time to fit residues: 19.1098 Evaluate side-chains 149 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 576 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 51 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN A 427 HIS A 436 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.111008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.084699 restraints weight = 25585.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.087376 restraints weight = 12707.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.089151 restraints weight = 8123.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.090204 restraints weight = 6102.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.090928 restraints weight = 5116.722| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 8950 Z= 0.149 Angle : 0.617 11.584 12092 Z= 0.317 Chirality : 0.041 0.171 1440 Planarity : 0.004 0.031 1532 Dihedral : 4.864 40.331 1241 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.29 % Favored : 94.62 % Rotamer: Outliers : 3.10 % Allowed : 29.96 % Favored : 66.94 % 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 aren not related in a simple way. whole: 0.40 (0.26), residues: 1134 helix: 1.03 (0.19), residues: 782 sheet: -3.24 (0.96), residues: 24 loop : -1.25 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 517 TYR 0.029 0.002 TYR A 439 PHE 0.014 0.002 PHE A 462 TRP 0.013 0.001 TRP A 66 HIS 0.005 0.001 HIS A 562 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 8950) covalent geometry : angle 0.61664 (12092) hydrogen bonds : bond 0.04067 ( 544) hydrogen bonds : angle 4.60870 ( 1614) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 458 TYR cc_start: 0.8294 (m-80) cc_final: 0.8080 (m-10) REVERT: A 170 ILE cc_start: 0.9289 (tp) cc_final: 0.8907 (tp) REVERT: A 456 MET cc_start: 0.8508 (mmm) cc_final: 0.8122 (ttt) outliers start: 30 outliers final: 18 residues processed: 153 average time/residue: 0.0789 time to fit residues: 18.1679 Evaluate side-chains 136 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 576 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 13 optimal weight: 0.5980 chunk 89 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 66 optimal weight: 0.0980 chunk 36 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 85 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 417 ASN ** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.112355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.086045 restraints weight = 25815.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.088772 restraints weight = 12773.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.090542 restraints weight = 8103.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.091661 restraints weight = 6070.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.092291 restraints weight = 5057.276| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 8950 Z= 0.128 Angle : 0.603 9.778 12092 Z= 0.308 Chirality : 0.040 0.178 1440 Planarity : 0.003 0.030 1532 Dihedral : 4.664 33.968 1241 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.85 % Favored : 95.06 % Rotamer: Outliers : 3.41 % Allowed : 30.58 % Favored : 66.01 % 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 aren not related in a simple way. whole: 0.51 (0.26), residues: 1134 helix: 1.15 (0.19), residues: 772 sheet: -3.21 (0.95), residues: 24 loop : -1.23 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 517 TYR 0.024 0.001 TYR A 439 PHE 0.032 0.001 PHE A 349 TRP 0.012 0.001 TRP A 66 HIS 0.004 0.001 HIS A 562 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8950) covalent geometry : angle 0.60324 (12092) hydrogen bonds : bond 0.03741 ( 544) hydrogen bonds : angle 4.41541 ( 1614) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7904 (tmm) cc_final: 0.6991 (tmm) REVERT: A 170 ILE cc_start: 0.9314 (tp) cc_final: 0.8931 (tp) REVERT: A 349 PHE cc_start: 0.7575 (t80) cc_final: 0.6765 (t80) REVERT: A 456 MET cc_start: 0.8499 (mmm) cc_final: 0.8230 (mmm) REVERT: A 466 MET cc_start: 0.8361 (mmm) cc_final: 0.8024 (mmt) REVERT: A 480 LEU cc_start: 0.9017 (tp) cc_final: 0.8737 (tt) outliers start: 33 outliers final: 18 residues processed: 164 average time/residue: 0.0794 time to fit residues: 19.4739 Evaluate side-chains 142 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 541 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 83 optimal weight: 0.3980 chunk 16 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.112944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.086674 restraints weight = 26078.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.089414 restraints weight = 13091.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.091077 restraints weight = 8381.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.092265 restraints weight = 6353.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.093038 restraints weight = 5287.155| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 8950 Z= 0.133 Angle : 0.614 9.694 12092 Z= 0.311 Chirality : 0.041 0.144 1440 Planarity : 0.003 0.029 1532 Dihedral : 4.507 20.065 1238 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.94 % Favored : 94.97 % Rotamer: Outliers : 3.62 % Allowed : 30.89 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.26), residues: 1134 helix: 1.18 (0.19), residues: 760 sheet: -3.26 (0.93), residues: 24 loop : -1.28 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 517 TYR 0.020 0.001 TYR B 439 PHE 0.022 0.002 PHE B 116 TRP 0.013 0.001 TRP A 66 HIS 0.004 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8950) covalent geometry : angle 0.61379 (12092) hydrogen bonds : bond 0.03642 ( 544) hydrogen bonds : angle 4.36660 ( 1614) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 ARG cc_start: 0.7451 (mtt180) cc_final: 0.7246 (mtt180) REVERT: B 312 MET cc_start: 0.3836 (tpt) cc_final: 0.3556 (tpt) REVERT: A 170 ILE cc_start: 0.9315 (tp) cc_final: 0.8935 (tp) REVERT: A 324 SER cc_start: 0.8035 (OUTLIER) cc_final: 0.7720 (t) REVERT: A 349 PHE cc_start: 0.7462 (t80) cc_final: 0.6702 (t80) REVERT: A 480 LEU cc_start: 0.9048 (tp) cc_final: 0.8765 (tt) REVERT: A 481 LEU cc_start: 0.8832 (mt) cc_final: 0.8604 (mt) outliers start: 35 outliers final: 26 residues processed: 161 average time/residue: 0.0828 time to fit residues: 19.5954 Evaluate side-chains 149 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 541 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 109 optimal weight: 10.0000 chunk 95 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 53 optimal weight: 0.0070 chunk 14 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.113972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.087698 restraints weight = 26705.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.090562 restraints weight = 13194.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.092406 restraints weight = 8370.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.093585 restraints weight = 6262.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.094219 restraints weight = 5214.775| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 8950 Z= 0.123 Angle : 0.615 8.722 12092 Z= 0.311 Chirality : 0.041 0.182 1440 Planarity : 0.003 0.028 1532 Dihedral : 4.410 18.902 1238 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.76 % Favored : 95.15 % Rotamer: Outliers : 2.89 % Allowed : 31.51 % Favored : 65.60 % 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 aren not related in a simple way. whole: 0.50 (0.26), residues: 1134 helix: 1.16 (0.19), residues: 772 sheet: -3.26 (0.94), residues: 24 loop : -1.26 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 517 TYR 0.014 0.001 TYR B 410 PHE 0.032 0.001 PHE B 116 TRP 0.012 0.001 TRP A 66 HIS 0.006 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8950) covalent geometry : angle 0.61457 (12092) hydrogen bonds : bond 0.03575 ( 544) hydrogen bonds : angle 4.28895 ( 1614) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8156 (pt) REVERT: B 61 ARG cc_start: 0.7596 (mtt180) cc_final: 0.7353 (mtt180) REVERT: A 98 MET cc_start: 0.7720 (tmm) cc_final: 0.7101 (tmm) REVERT: A 170 ILE cc_start: 0.9279 (tp) cc_final: 0.8897 (tp) REVERT: A 349 PHE cc_start: 0.7519 (t80) cc_final: 0.6845 (t80) REVERT: A 456 MET cc_start: 0.8600 (mmm) cc_final: 0.7958 (tpt) REVERT: A 480 LEU cc_start: 0.9054 (tp) cc_final: 0.8736 (tt) REVERT: A 481 LEU cc_start: 0.8801 (mt) cc_final: 0.8537 (mt) outliers start: 28 outliers final: 21 residues processed: 152 average time/residue: 0.0866 time to fit residues: 19.0758 Evaluate side-chains 140 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 576 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 88 optimal weight: 20.0000 chunk 65 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 427 HIS ** A 485 GLN ** 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 = 0.3931 r_free = 0.3931 target = 0.113172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.087260 restraints weight = 26115.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.090030 restraints weight = 12906.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.091851 restraints weight = 8178.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.092903 restraints weight = 6102.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.093672 restraints weight = 5106.056| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 8950 Z= 0.139 Angle : 0.637 9.787 12092 Z= 0.319 Chirality : 0.041 0.163 1440 Planarity : 0.003 0.029 1532 Dihedral : 4.395 18.645 1238 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.67 % Favored : 95.24 % Rotamer: Outliers : 3.93 % Allowed : 31.10 % Favored : 64.98 % 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 aren not related in a simple way. whole: 0.47 (0.26), residues: 1134 helix: 1.17 (0.19), residues: 784 sheet: -3.33 (0.93), residues: 24 loop : -1.46 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 517 TYR 0.018 0.001 TYR B 130 PHE 0.018 0.001 PHE B 116 TRP 0.014 0.001 TRP A 66 HIS 0.004 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8950) covalent geometry : angle 0.63668 (12092) hydrogen bonds : bond 0.03581 ( 544) hydrogen bonds : angle 4.28297 ( 1614) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 410 TYR cc_start: 0.7795 (OUTLIER) cc_final: 0.7399 (m-80) REVERT: A 98 MET cc_start: 0.7755 (tmm) cc_final: 0.7297 (tmm) REVERT: A 170 ILE cc_start: 0.9296 (tp) cc_final: 0.8922 (tp) REVERT: A 312 MET cc_start: 0.7014 (mmm) cc_final: 0.6401 (ttt) REVERT: A 324 SER cc_start: 0.8037 (OUTLIER) cc_final: 0.7724 (t) REVERT: A 349 PHE cc_start: 0.7516 (t80) cc_final: 0.7011 (t80) REVERT: A 456 MET cc_start: 0.8459 (mmm) cc_final: 0.8133 (tpt) REVERT: A 480 LEU cc_start: 0.9040 (tp) cc_final: 0.8709 (tt) REVERT: A 481 LEU cc_start: 0.8781 (mt) cc_final: 0.8514 (mt) outliers start: 38 outliers final: 31 residues processed: 154 average time/residue: 0.0781 time to fit residues: 17.8188 Evaluate side-chains 152 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 410 TYR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 458 TYR Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 576 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 88 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.114354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.088752 restraints weight = 26211.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.091582 restraints weight = 12866.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.093423 restraints weight = 8138.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.094607 restraints weight = 6048.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.095259 restraints weight = 5013.677| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 8950 Z= 0.141 Angle : 0.656 10.280 12092 Z= 0.324 Chirality : 0.041 0.147 1440 Planarity : 0.003 0.029 1532 Dihedral : 4.384 18.443 1238 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.76 % Favored : 95.15 % Rotamer: Outliers : 3.82 % Allowed : 32.13 % Favored : 64.05 % 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 aren not related in a simple way. whole: 0.45 (0.26), residues: 1134 helix: 1.15 (0.19), residues: 784 sheet: -3.11 (0.96), residues: 24 loop : -1.49 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 517 TYR 0.016 0.001 TYR B 572 PHE 0.020 0.001 PHE B 116 TRP 0.013 0.001 TRP A 66 HIS 0.004 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8950) covalent geometry : angle 0.65594 (12092) hydrogen bonds : bond 0.03656 ( 544) hydrogen bonds : angle 4.27425 ( 1614) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 410 TYR cc_start: 0.7766 (OUTLIER) cc_final: 0.7297 (m-80) REVERT: B 460 MET cc_start: 0.8371 (ptp) cc_final: 0.8088 (pmm) REVERT: A 170 ILE cc_start: 0.9312 (tp) cc_final: 0.8935 (tp) REVERT: A 312 MET cc_start: 0.6929 (mmm) cc_final: 0.6484 (ttt) REVERT: A 349 PHE cc_start: 0.7508 (t80) cc_final: 0.7011 (t80) REVERT: A 456 MET cc_start: 0.8418 (mmm) cc_final: 0.8180 (ttt) REVERT: A 480 LEU cc_start: 0.9049 (tp) cc_final: 0.8697 (tt) REVERT: A 481 LEU cc_start: 0.8750 (mt) cc_final: 0.8539 (mt) outliers start: 37 outliers final: 31 residues processed: 156 average time/residue: 0.0785 time to fit residues: 18.0155 Evaluate side-chains 155 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 410 TYR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 458 TYR Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 576 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 109 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.114232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.088268 restraints weight = 26819.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.091131 restraints weight = 13397.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.092919 restraints weight = 8566.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.094127 restraints weight = 6455.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.094786 restraints weight = 5394.985| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 8950 Z= 0.148 Angle : 0.681 10.355 12092 Z= 0.331 Chirality : 0.042 0.224 1440 Planarity : 0.003 0.029 1532 Dihedral : 4.387 18.373 1238 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.85 % Favored : 95.06 % Rotamer: Outliers : 3.82 % Allowed : 32.44 % Favored : 63.74 % 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 aren not related in a simple way. whole: 0.43 (0.26), residues: 1134 helix: 1.15 (0.19), residues: 782 sheet: -3.11 (0.96), residues: 24 loop : -1.50 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 517 TYR 0.021 0.001 TYR B 130 PHE 0.014 0.001 PHE A 429 TRP 0.014 0.001 TRP A 66 HIS 0.015 0.002 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8950) covalent geometry : angle 0.68088 (12092) hydrogen bonds : bond 0.03714 ( 544) hydrogen bonds : angle 4.30083 ( 1614) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 410 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.7378 (m-80) REVERT: B 460 MET cc_start: 0.8392 (ptp) cc_final: 0.8099 (pmm) REVERT: A 98 MET cc_start: 0.7880 (tmm) cc_final: 0.7401 (tmm) REVERT: A 170 ILE cc_start: 0.9312 (tp) cc_final: 0.8937 (tp) REVERT: A 312 MET cc_start: 0.6973 (mmm) cc_final: 0.6456 (ttt) REVERT: A 339 THR cc_start: 0.8417 (m) cc_final: 0.8053 (p) REVERT: A 349 PHE cc_start: 0.7530 (t80) cc_final: 0.6991 (t80) REVERT: A 456 MET cc_start: 0.8419 (mmm) cc_final: 0.8211 (ttt) REVERT: A 480 LEU cc_start: 0.9092 (tp) cc_final: 0.8767 (tt) REVERT: A 481 LEU cc_start: 0.8802 (mt) cc_final: 0.8571 (mt) outliers start: 37 outliers final: 32 residues processed: 148 average time/residue: 0.0897 time to fit residues: 19.5243 Evaluate side-chains 153 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 410 TYR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 458 TYR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 576 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 47 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 82 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 108 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 ASN A 427 HIS ** A 485 GLN ** 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 = 0.3965 r_free = 0.3965 target = 0.114907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.089370 restraints weight = 26253.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.092242 restraints weight = 12784.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.094102 restraints weight = 8026.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.095274 restraints weight = 5962.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.095974 restraints weight = 4944.755| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 8950 Z= 0.132 Angle : 0.680 10.887 12092 Z= 0.329 Chirality : 0.041 0.159 1440 Planarity : 0.003 0.028 1532 Dihedral : 4.352 18.173 1238 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.85 % Favored : 95.06 % Rotamer: Outliers : 3.41 % Allowed : 32.85 % Favored : 63.74 % 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 aren not related in a simple way. whole: 0.45 (0.26), residues: 1134 helix: 1.15 (0.19), residues: 782 sheet: -3.03 (0.97), residues: 24 loop : -1.46 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 517 TYR 0.016 0.001 TYR B 572 PHE 0.023 0.001 PHE A 429 TRP 0.019 0.001 TRP A 66 HIS 0.013 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8950) covalent geometry : angle 0.67968 (12092) hydrogen bonds : bond 0.03651 ( 544) hydrogen bonds : angle 4.25273 ( 1614) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 410 TYR cc_start: 0.7786 (OUTLIER) cc_final: 0.7319 (m-80) REVERT: B 460 MET cc_start: 0.8315 (ptp) cc_final: 0.8069 (pmm) REVERT: A 170 ILE cc_start: 0.9300 (tp) cc_final: 0.8929 (tp) REVERT: A 312 MET cc_start: 0.7128 (mmm) cc_final: 0.6906 (mmm) REVERT: A 324 SER cc_start: 0.7959 (OUTLIER) cc_final: 0.7637 (t) REVERT: A 339 THR cc_start: 0.8374 (m) cc_final: 0.8017 (p) REVERT: A 349 PHE cc_start: 0.7367 (t80) cc_final: 0.6850 (t80) REVERT: A 456 MET cc_start: 0.8346 (mmm) cc_final: 0.8074 (ttt) REVERT: A 480 LEU cc_start: 0.9098 (tp) cc_final: 0.8768 (tt) REVERT: A 481 LEU cc_start: 0.8818 (mt) cc_final: 0.8580 (mt) outliers start: 33 outliers final: 29 residues processed: 147 average time/residue: 0.0776 time to fit residues: 17.1825 Evaluate side-chains 150 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 410 TYR Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 458 TYR Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 576 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 80 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 49 optimal weight: 0.0470 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 94 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.115320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.089863 restraints weight = 25908.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.092714 restraints weight = 12704.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.094553 restraints weight = 8004.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.095719 restraints weight = 5957.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.096380 restraints weight = 4948.910| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 8950 Z= 0.126 Angle : 0.672 10.878 12092 Z= 0.327 Chirality : 0.041 0.158 1440 Planarity : 0.003 0.028 1532 Dihedral : 4.293 17.720 1238 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.94 % Favored : 94.97 % Rotamer: Outliers : 3.41 % Allowed : 33.06 % Favored : 63.53 % 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 aren not related in a simple way. whole: 0.45 (0.26), residues: 1134 helix: 1.17 (0.19), residues: 778 sheet: -3.00 (0.97), residues: 24 loop : -1.49 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 517 TYR 0.024 0.001 TYR B 130 PHE 0.017 0.001 PHE A 429 TRP 0.021 0.001 TRP A 66 HIS 0.011 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8950) covalent geometry : angle 0.67237 (12092) hydrogen bonds : bond 0.03565 ( 544) hydrogen bonds : angle 4.19585 ( 1614) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1938.12 seconds wall clock time: 34 minutes 5.73 seconds (2045.73 seconds total)