Starting phenix.real_space_refine on Sat Jun 14 05:18:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bx2_44991/06_2025/9bx2_44991_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bx2_44991/06_2025/9bx2_44991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bx2_44991/06_2025/9bx2_44991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bx2_44991/06_2025/9bx2_44991.map" model { file = "/net/cci-nas-00/data/ceres_data/9bx2_44991/06_2025/9bx2_44991_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bx2_44991/06_2025/9bx2_44991_neut.cif" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 12 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10190 2.51 5 N 2598 2.21 5 O 3066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15954 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 9.11, per 1000 atoms: 0.57 Number of scatterers: 15954 At special positions: 0 Unit cell: (95.046, 140.014, 132.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 12 15.00 Mg 2 11.99 O 3066 8.00 N 2598 7.00 C 10190 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.39 Conformation dependent library (CDL) restraints added in 1.9 seconds 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3688 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 10 sheets defined 64.3% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 27 through 41 removed outlier: 3.554A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.075A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 4.057A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.706A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.873A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.793A pdb=" N GLN A 242 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.639A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 318 through 329 removed outlier: 6.056A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.521A pdb=" N PHE A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 589 removed outlier: 4.273A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 677 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 27 through 41 removed outlier: 3.548A pdb=" N GLU B 31 " --> pdb=" O ASP B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.949A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.960A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.721A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 222 through 237 removed outlier: 3.779A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.573A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 318 through 329 removed outlier: 5.841A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 367 removed outlier: 4.174A pdb=" N VAL B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 424 through 443 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 474 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.565A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 589 removed outlier: 4.402A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 677 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.514A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.889A pdb=" N GLY A 462 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASN A 410 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLY A 464 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 3.736A pdb=" N CYS A 409 " --> pdb=" O CYS A 170 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N CYS A 170 " --> pdb=" O CYS A 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA5, first strand: chain 'A' and resid 655 through 658 Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 removed outlier: 5.890A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 removed outlier: 6.456A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AA9, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB1, first strand: chain 'B' and resid 655 through 659 898 hydrogen bonds defined for protein. 2616 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: 5.33 Time building geometry restraints manager: 4.96 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: 4844 1.33 - 1.46: 2960 1.46 - 1.58: 8319 1.58 - 1.70: 19 1.70 - 1.82: 156 Bond restraints: 16298 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.600 -0.060 1.25e-02 6.40e+03 2.30e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.038 1.20e-02 6.94e+03 1.01e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.032 1.08e-02 8.57e+03 8.87e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.569 -0.031 1.17e-02 7.31e+03 7.21e+00 bond pdb=" CA ILE C 35 " pdb=" CB ILE C 35 " ideal model delta sigma weight residual 1.537 1.569 -0.032 1.21e-02 6.83e+03 6.98e+00 ... (remaining 16293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 21505 2.10 - 4.19: 462 4.19 - 6.29: 34 6.29 - 8.38: 1 8.38 - 10.48: 2 Bond angle restraints: 22004 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.63 -6.09 1.36e+00 5.41e-01 2.00e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.12 -4.41 1.15e+00 7.56e-01 1.47e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.82 -4.32 1.23e+00 6.61e-01 1.23e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.73 -4.02 1.15e+00 7.56e-01 1.22e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.53 3.66 1.06e+00 8.90e-01 1.19e+01 ... (remaining 21999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.31: 9429 34.31 - 68.63: 329 68.63 - 102.94: 48 102.94 - 137.26: 0 137.26 - 171.57: 2 Dihedral angle restraints: 9808 sinusoidal: 4062 harmonic: 5746 Sorted by residual: dihedral pdb=" C2 TTP A 801 " pdb=" C1' TTP A 801 " pdb=" N1 TTP A 801 " pdb=" O4' TTP A 801 " ideal model delta sinusoidal sigma weight residual 301.68 130.11 171.57 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual 301.68 135.73 165.96 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C VAL C 125 " pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual -122.00 -134.38 12.38 0 2.50e+00 1.60e-01 2.45e+01 ... (remaining 9805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2130 0.094 - 0.187: 178 0.187 - 0.281: 33 0.281 - 0.374: 5 0.374 - 0.468: 2 Chirality restraints: 2348 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.47e+00 chirality pdb=" CA TYR C 169 " pdb=" N TYR C 169 " pdb=" C TYR C 169 " pdb=" CB TYR C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.66e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 2345 not shown) Planarity restraints: 2812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 6 " 0.036 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO B 7 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 7 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 7 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO D 75 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " 0.017 2.00e-02 2.50e+03 1.10e-02 2.11e+00 pdb=" CG PHE D 92 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " 0.009 2.00e-02 2.50e+03 ... (remaining 2809 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 132 2.51 - 3.11: 11872 3.11 - 3.70: 26434 3.70 - 4.30: 41217 4.30 - 4.90: 64993 Nonbonded interactions: 144648 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" O1B TTP A 801 " pdb="MG MG A 802 " model vdw 1.919 2.170 nonbonded pdb=" O2A TTP B 801 " pdb="MG MG B 802 " model vdw 1.929 2.170 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 ... (remaining 144643 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' } ncs_group { reference = chain 'C' selection = chain 'D' } 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=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 37.280 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.834 16299 Z= 0.724 Angle : 0.708 10.480 22004 Z= 0.453 Chirality : 0.059 0.468 2348 Planarity : 0.003 0.055 2812 Dihedral : 17.174 171.569 6120 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.40 % Allowed : 14.06 % Favored : 84.54 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.18), residues: 1928 helix: 1.05 (0.15), residues: 1133 sheet: 0.46 (0.39), residues: 146 loop : 0.45 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 PHE 0.021 0.002 PHE C 227 TYR 0.020 0.002 TYR D 179 ARG 0.004 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.16169 ( 896) hydrogen bonds : angle 6.35147 ( 2616) covalent geometry : bond 0.00542 (16298) covalent geometry : angle 0.70754 (22004) Misc. bond : bond 0.83443 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 886 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.7919 (m-80) cc_final: 0.7667 (m-80) REVERT: A 101 TYR cc_start: 0.8052 (m-80) cc_final: 0.7848 (m-80) REVERT: A 147 GLN cc_start: 0.8560 (mt0) cc_final: 0.7467 (mt0) REVERT: A 152 SER cc_start: 0.8560 (p) cc_final: 0.8217 (p) REVERT: A 179 LEU cc_start: 0.9405 (tp) cc_final: 0.9186 (tp) REVERT: A 181 ASP cc_start: 0.8156 (m-30) cc_final: 0.7920 (m-30) REVERT: A 188 ILE cc_start: 0.9049 (mt) cc_final: 0.8827 (mt) REVERT: A 232 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.7977 (m-40) REVERT: A 246 SER cc_start: 0.8278 (m) cc_final: 0.8039 (p) REVERT: A 406 ASP cc_start: 0.7400 (m-30) cc_final: 0.7188 (m-30) REVERT: A 411 LEU cc_start: 0.8475 (mt) cc_final: 0.8057 (mp) REVERT: A 442 THR cc_start: 0.8764 (p) cc_final: 0.8349 (m) REVERT: A 583 SER cc_start: 0.8154 (m) cc_final: 0.7917 (t) REVERT: B 104 TYR cc_start: 0.7704 (m-80) cc_final: 0.7393 (m-80) REVERT: B 116 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7418 (mt-10) REVERT: B 172 LEU cc_start: 0.9029 (mp) cc_final: 0.8485 (mp) REVERT: B 181 ASP cc_start: 0.8383 (m-30) cc_final: 0.7911 (m-30) REVERT: B 227 MET cc_start: 0.7932 (mtp) cc_final: 0.7485 (mtp) REVERT: B 267 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7820 (pt) REVERT: B 276 LYS cc_start: 0.8460 (ptpp) cc_final: 0.8225 (mtmm) REVERT: B 280 ILE cc_start: 0.9081 (pt) cc_final: 0.8853 (pt) REVERT: B 294 GLU cc_start: 0.6773 (mt-10) cc_final: 0.4936 (mt-10) REVERT: B 358 ILE cc_start: 0.9388 (mm) cc_final: 0.9181 (mm) REVERT: B 375 LYS cc_start: 0.9185 (mptp) cc_final: 0.8943 (mmtp) REVERT: B 396 ASP cc_start: 0.7618 (m-30) cc_final: 0.7392 (m-30) REVERT: B 550 MET cc_start: 0.8110 (ttm) cc_final: 0.7657 (mtp) REVERT: B 583 SER cc_start: 0.8125 (m) cc_final: 0.7789 (t) REVERT: B 597 ILE cc_start: 0.9145 (pt) cc_final: 0.8930 (pt) REVERT: B 637 VAL cc_start: 0.9061 (t) cc_final: 0.8855 (t) REVERT: C 26 VAL cc_start: 0.7638 (m) cc_final: 0.7109 (m) REVERT: C 106 SER cc_start: 0.7849 (m) cc_final: 0.7076 (t) REVERT: C 153 LEU cc_start: 0.6349 (tp) cc_final: 0.5524 (tp) REVERT: C 178 PHE cc_start: 0.4601 (m-80) cc_final: 0.4198 (m-10) REVERT: C 229 ILE cc_start: 0.3543 (mt) cc_final: 0.3341 (mt) REVERT: C 316 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7761 (mtmm) REVERT: D 55 TYR cc_start: 0.5619 (t80) cc_final: 0.5412 (t80) REVERT: D 96 MET cc_start: 0.5853 (mmm) cc_final: 0.5391 (mmm) REVERT: D 178 PHE cc_start: 0.6543 (m-80) cc_final: 0.5498 (m-10) REVERT: D 256 VAL cc_start: 0.6468 (t) cc_final: 0.6192 (p) outliers start: 24 outliers final: 4 residues processed: 894 average time/residue: 0.2876 time to fit residues: 371.1358 Evaluate side-chains 564 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 557 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 316 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.9990 chunk 145 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 14 ASN A 49 HIS ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN B 14 ASN B 312 GLN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN C 25 ASN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN C 283 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.135513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.091988 restraints weight = 31787.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.095088 restraints weight = 15019.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.097339 restraints weight = 9216.119| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16299 Z= 0.222 Angle : 0.709 23.642 22004 Z= 0.369 Chirality : 0.045 0.172 2348 Planarity : 0.004 0.054 2812 Dihedral : 9.109 160.571 2232 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.91 % Allowed : 17.74 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.19), residues: 1928 helix: 1.45 (0.15), residues: 1133 sheet: 0.52 (0.40), residues: 128 loop : 0.69 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 124 HIS 0.006 0.001 HIS A 255 PHE 0.028 0.002 PHE D 259 TYR 0.028 0.002 TYR D 262 ARG 0.007 0.001 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.04849 ( 896) hydrogen bonds : angle 5.19447 ( 2616) covalent geometry : bond 0.00499 (16298) covalent geometry : angle 0.70943 (22004) Misc. bond : bond 0.00065 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 578 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8667 (mp0) cc_final: 0.8298 (mp0) REVERT: A 143 LEU cc_start: 0.9400 (tp) cc_final: 0.9142 (tp) REVERT: A 147 GLN cc_start: 0.9443 (mt0) cc_final: 0.9224 (mt0) REVERT: A 157 LEU cc_start: 0.9156 (tt) cc_final: 0.8693 (tp) REVERT: A 174 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7831 (mm-30) REVERT: A 181 ASP cc_start: 0.8758 (m-30) cc_final: 0.8528 (m-30) REVERT: A 214 LYS cc_start: 0.8558 (mmtm) cc_final: 0.8263 (mmtm) REVERT: A 232 ASN cc_start: 0.9130 (OUTLIER) cc_final: 0.8477 (m110) REVERT: A 246 SER cc_start: 0.7639 (m) cc_final: 0.7336 (p) REVERT: A 256 ARG cc_start: 0.8865 (tpt90) cc_final: 0.8616 (tpt90) REVERT: A 348 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8531 (tmm) REVERT: A 393 SER cc_start: 0.8750 (m) cc_final: 0.8475 (p) REVERT: A 509 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8423 (tm-30) REVERT: A 583 SER cc_start: 0.8771 (m) cc_final: 0.8309 (t) REVERT: A 598 MET cc_start: 0.8109 (mtp) cc_final: 0.6903 (mtp) REVERT: A 599 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8210 (pt0) REVERT: A 640 MET cc_start: 0.8953 (tpp) cc_final: 0.8613 (tpp) REVERT: A 686 ARG cc_start: 0.7710 (mtp180) cc_final: 0.7473 (mtp85) REVERT: B 54 LYS cc_start: 0.9507 (tttp) cc_final: 0.9285 (tptt) REVERT: B 64 TYR cc_start: 0.8660 (m-10) cc_final: 0.8434 (m-10) REVERT: B 102 ASN cc_start: 0.9305 (m-40) cc_final: 0.8835 (m110) REVERT: B 109 ASN cc_start: 0.9372 (OUTLIER) cc_final: 0.9069 (m110) REVERT: B 172 LEU cc_start: 0.8904 (mp) cc_final: 0.8685 (mp) REVERT: B 184 ARG cc_start: 0.9100 (tpp-160) cc_final: 0.8835 (tpp80) REVERT: B 317 MET cc_start: 0.8585 (mtm) cc_final: 0.8260 (mtt) REVERT: B 318 ASP cc_start: 0.8506 (t0) cc_final: 0.8274 (p0) REVERT: B 334 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8951 (ptpt) REVERT: B 349 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9082 (mp) REVERT: B 350 ARG cc_start: 0.8842 (mtp-110) cc_final: 0.8611 (mtp-110) REVERT: B 466 MET cc_start: 0.8875 (ptt) cc_final: 0.8386 (ptp) REVERT: B 515 ASP cc_start: 0.9111 (m-30) cc_final: 0.8881 (m-30) REVERT: B 550 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7780 (mtp) REVERT: B 583 SER cc_start: 0.8910 (m) cc_final: 0.8658 (t) REVERT: B 588 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8622 (tp40) REVERT: B 599 GLU cc_start: 0.8732 (pt0) cc_final: 0.8517 (pm20) REVERT: B 602 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8273 (tt0) REVERT: B 604 ARG cc_start: 0.9075 (mmm160) cc_final: 0.8747 (mmm160) REVERT: C 20 MET cc_start: 0.9316 (mpp) cc_final: 0.9096 (tmm) REVERT: C 26 VAL cc_start: 0.9446 (m) cc_final: 0.9069 (m) REVERT: C 29 PHE cc_start: 0.6973 (p90) cc_final: 0.6694 (p90) REVERT: C 30 TRP cc_start: 0.7290 (p-90) cc_final: 0.7088 (p-90) REVERT: C 89 VAL cc_start: 0.8248 (t) cc_final: 0.7766 (t) REVERT: C 92 PHE cc_start: 0.9105 (t80) cc_final: 0.8790 (t80) REVERT: C 93 MET cc_start: 0.8431 (mtt) cc_final: 0.8152 (mtt) REVERT: C 96 MET cc_start: 0.8082 (mmm) cc_final: 0.7626 (mmm) REVERT: C 118 ILE cc_start: 0.8530 (mt) cc_final: 0.7923 (pt) REVERT: C 124 TRP cc_start: 0.7681 (t60) cc_final: 0.7147 (t60) REVERT: C 162 TYR cc_start: 0.8765 (m-10) cc_final: 0.8220 (m-10) REVERT: C 185 MET cc_start: 0.2883 (mtm) cc_final: 0.2636 (pmm) REVERT: C 212 ILE cc_start: 0.7277 (mm) cc_final: 0.6787 (mm) REVERT: C 229 ILE cc_start: 0.5433 (mt) cc_final: 0.5122 (mt) REVERT: C 239 GLU cc_start: 0.8718 (tp30) cc_final: 0.8351 (tp30) REVERT: C 243 THR cc_start: 0.7500 (p) cc_final: 0.6810 (t) REVERT: C 273 PHE cc_start: 0.4930 (OUTLIER) cc_final: 0.3930 (m-80) REVERT: C 285 ILE cc_start: 0.6910 (tp) cc_final: 0.6155 (tp) REVERT: D 20 MET cc_start: 0.9343 (mmm) cc_final: 0.8882 (ptm) REVERT: D 21 PHE cc_start: 0.8275 (m-80) cc_final: 0.7948 (m-10) REVERT: D 25 ASN cc_start: 0.9514 (m-40) cc_final: 0.9246 (m-40) REVERT: D 56 MET cc_start: 0.8490 (ptt) cc_final: 0.8203 (mmp) REVERT: D 71 ASN cc_start: 0.8929 (m110) cc_final: 0.8715 (p0) REVERT: D 76 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8202 (mt) REVERT: D 96 MET cc_start: 0.7475 (mmm) cc_final: 0.7151 (mmm) REVERT: D 162 TYR cc_start: 0.9079 (m-10) cc_final: 0.8798 (m-80) REVERT: D 178 PHE cc_start: 0.8773 (m-80) cc_final: 0.7964 (m-10) REVERT: D 320 PHE cc_start: 0.8610 (m-80) cc_final: 0.8249 (m-80) outliers start: 67 outliers final: 34 residues processed: 617 average time/residue: 0.2834 time to fit residues: 257.7476 Evaluate side-chains 559 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 515 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 273 PHE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 250 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 191 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 175 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN B 645 GLN C 84 HIS C 127 GLN C 216 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN D 71 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.128698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.086693 restraints weight = 32261.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.089793 restraints weight = 15361.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.091803 restraints weight = 9170.130| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16299 Z= 0.259 Angle : 0.691 15.023 22004 Z= 0.357 Chirality : 0.045 0.170 2348 Planarity : 0.004 0.050 2812 Dihedral : 8.992 147.193 2226 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.61 % Allowed : 19.54 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.18), residues: 1928 helix: 1.30 (0.15), residues: 1130 sheet: 0.06 (0.41), residues: 134 loop : 0.68 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP D 30 HIS 0.005 0.001 HIS D 201 PHE 0.030 0.002 PHE C 122 TYR 0.036 0.002 TYR D 142 ARG 0.007 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04465 ( 896) hydrogen bonds : angle 5.13807 ( 2616) covalent geometry : bond 0.00577 (16298) covalent geometry : angle 0.69087 (22004) Misc. bond : bond 0.00077 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 544 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8643 (mp0) cc_final: 0.8423 (mp0) REVERT: A 143 LEU cc_start: 0.9408 (tp) cc_final: 0.9145 (tp) REVERT: A 147 GLN cc_start: 0.9345 (mt0) cc_final: 0.9091 (mt0) REVERT: A 157 LEU cc_start: 0.9264 (tt) cc_final: 0.9059 (tp) REVERT: A 161 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7620 (mtm-85) REVERT: A 164 ARG cc_start: 0.8267 (ptt90) cc_final: 0.8026 (ptt90) REVERT: A 174 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7835 (mm-30) REVERT: A 181 ASP cc_start: 0.8795 (m-30) cc_final: 0.8557 (m-30) REVERT: A 214 LYS cc_start: 0.8544 (mmtm) cc_final: 0.8286 (mmtm) REVERT: A 232 ASN cc_start: 0.9162 (OUTLIER) cc_final: 0.8470 (m110) REVERT: A 334 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8514 (ptpt) REVERT: A 348 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8567 (tmm) REVERT: A 383 SER cc_start: 0.8984 (m) cc_final: 0.8628 (t) REVERT: A 393 SER cc_start: 0.8858 (m) cc_final: 0.8571 (p) REVERT: A 415 ASN cc_start: 0.9136 (t0) cc_final: 0.8912 (t0) REVERT: A 509 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8422 (tm-30) REVERT: A 512 GLU cc_start: 0.8887 (pm20) cc_final: 0.8681 (pm20) REVERT: A 588 GLN cc_start: 0.9270 (mm-40) cc_final: 0.8982 (tp40) REVERT: A 598 MET cc_start: 0.8191 (mtp) cc_final: 0.6843 (mtp) REVERT: A 599 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8189 (pt0) REVERT: A 686 ARG cc_start: 0.7820 (mtp180) cc_final: 0.7608 (mtp85) REVERT: B 102 ASN cc_start: 0.9300 (m-40) cc_final: 0.8875 (m110) REVERT: B 104 TYR cc_start: 0.9006 (m-80) cc_final: 0.8591 (m-80) REVERT: B 109 ASN cc_start: 0.9423 (OUTLIER) cc_final: 0.8965 (m-40) REVERT: B 121 ARG cc_start: 0.9428 (OUTLIER) cc_final: 0.9211 (tpt170) REVERT: B 172 LEU cc_start: 0.8994 (mp) cc_final: 0.8439 (mp) REVERT: B 184 ARG cc_start: 0.9136 (tpp-160) cc_final: 0.8892 (tpp80) REVERT: B 235 ARG cc_start: 0.8836 (ttp-110) cc_final: 0.8052 (ttm110) REVERT: B 238 ASP cc_start: 0.8002 (t0) cc_final: 0.7183 (t0) REVERT: B 274 ARG cc_start: 0.6731 (ttp-110) cc_final: 0.6058 (ttp-110) REVERT: B 322 MET cc_start: 0.9100 (mmm) cc_final: 0.8886 (mmm) REVERT: B 334 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8753 (ptpt) REVERT: B 381 LEU cc_start: 0.9386 (tt) cc_final: 0.9113 (tp) REVERT: B 415 ASN cc_start: 0.9166 (t0) cc_final: 0.8859 (t0) REVERT: B 466 MET cc_start: 0.9109 (ptt) cc_final: 0.8815 (ptp) REVERT: B 515 ASP cc_start: 0.9133 (m-30) cc_final: 0.8870 (m-30) REVERT: B 550 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8020 (mtp) REVERT: B 570 MET cc_start: 0.8508 (mtp) cc_final: 0.8275 (mtp) REVERT: B 578 ILE cc_start: 0.9152 (mt) cc_final: 0.8900 (mt) REVERT: B 588 GLN cc_start: 0.8973 (mm-40) cc_final: 0.8558 (mm-40) REVERT: B 599 GLU cc_start: 0.8750 (pt0) cc_final: 0.8063 (pt0) REVERT: B 610 LYS cc_start: 0.8390 (mmmt) cc_final: 0.8014 (mmmt) REVERT: B 612 TYR cc_start: 0.8858 (m-80) cc_final: 0.8618 (m-80) REVERT: B 686 ARG cc_start: 0.7999 (mmt180) cc_final: 0.7673 (mpt180) REVERT: C 89 VAL cc_start: 0.8236 (t) cc_final: 0.7666 (t) REVERT: C 92 PHE cc_start: 0.9168 (t80) cc_final: 0.8696 (t80) REVERT: C 93 MET cc_start: 0.8580 (mtt) cc_final: 0.7949 (mtt) REVERT: C 95 MET cc_start: 0.8727 (tmm) cc_final: 0.8099 (tmm) REVERT: C 96 MET cc_start: 0.8196 (mmm) cc_final: 0.7453 (mmm) REVERT: C 109 PHE cc_start: 0.8414 (m-10) cc_final: 0.8156 (m-80) REVERT: C 124 TRP cc_start: 0.7873 (t60) cc_final: 0.7161 (t60) REVERT: C 129 LYS cc_start: 0.9409 (mmmt) cc_final: 0.8930 (mmmt) REVERT: C 162 TYR cc_start: 0.8840 (m-10) cc_final: 0.8316 (m-80) REVERT: C 185 MET cc_start: 0.2877 (mtm) cc_final: 0.1618 (pmm) REVERT: C 229 ILE cc_start: 0.5439 (mt) cc_final: 0.5237 (mm) REVERT: D 21 PHE cc_start: 0.8462 (m-80) cc_final: 0.8231 (m-10) REVERT: D 25 ASN cc_start: 0.9594 (m-40) cc_final: 0.9316 (m-40) REVERT: D 56 MET cc_start: 0.8605 (ptt) cc_final: 0.8343 (mmp) REVERT: D 71 ASN cc_start: 0.8919 (m-40) cc_final: 0.8453 (p0) REVERT: D 96 MET cc_start: 0.7396 (mmm) cc_final: 0.7156 (mmm) REVERT: D 110 MET cc_start: 0.8805 (ppp) cc_final: 0.8594 (ppp) REVERT: D 178 PHE cc_start: 0.8530 (m-10) cc_final: 0.8297 (m-10) REVERT: D 259 PHE cc_start: 0.8079 (t80) cc_final: 0.7873 (t80) REVERT: D 261 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6756 (ptm-80) outliers start: 79 outliers final: 49 residues processed: 584 average time/residue: 0.2857 time to fit residues: 244.4504 Evaluate side-chains 568 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 509 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 261 ARG Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 153 optimal weight: 20.0000 chunk 136 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN C 127 GLN C 238 ASN C 283 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.133256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.091395 restraints weight = 32379.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.094733 restraints weight = 15082.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.096785 restraints weight = 8960.292| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16299 Z= 0.137 Angle : 0.636 15.273 22004 Z= 0.325 Chirality : 0.043 0.181 2348 Planarity : 0.003 0.049 2812 Dihedral : 8.464 138.664 2220 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.21 % Allowed : 21.00 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.19), residues: 1928 helix: 1.33 (0.15), residues: 1125 sheet: 0.50 (0.45), residues: 112 loop : 0.36 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 30 HIS 0.009 0.001 HIS D 80 PHE 0.050 0.002 PHE C 122 TYR 0.038 0.002 TYR D 142 ARG 0.005 0.001 ARG D 261 Details of bonding type rmsd hydrogen bonds : bond 0.04118 ( 896) hydrogen bonds : angle 4.99592 ( 2616) covalent geometry : bond 0.00303 (16298) covalent geometry : angle 0.63607 (22004) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 560 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.9132 (m-80) cc_final: 0.8919 (m-80) REVERT: A 115 LEU cc_start: 0.8953 (mp) cc_final: 0.8441 (mp) REVERT: A 119 GLU cc_start: 0.8582 (mp0) cc_final: 0.8233 (mp0) REVERT: A 164 ARG cc_start: 0.8194 (ptt90) cc_final: 0.7619 (ptt90) REVERT: A 174 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7817 (mm-30) REVERT: A 214 LYS cc_start: 0.8457 (mmtm) cc_final: 0.8137 (mmtm) REVERT: A 232 ASN cc_start: 0.9068 (m110) cc_final: 0.8618 (m110) REVERT: A 256 ARG cc_start: 0.8923 (tpt90) cc_final: 0.8350 (tpt90) REVERT: A 334 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8261 (ptpt) REVERT: A 348 MET cc_start: 0.8853 (ttp) cc_final: 0.8549 (tmm) REVERT: A 362 ASP cc_start: 0.8441 (m-30) cc_final: 0.7815 (m-30) REVERT: A 383 SER cc_start: 0.8863 (m) cc_final: 0.8575 (t) REVERT: A 393 SER cc_start: 0.8873 (m) cc_final: 0.8236 (p) REVERT: A 415 ASN cc_start: 0.9109 (t0) cc_final: 0.8866 (t0) REVERT: A 435 SER cc_start: 0.9560 (OUTLIER) cc_final: 0.9257 (t) REVERT: A 598 MET cc_start: 0.8157 (mtp) cc_final: 0.6879 (mtp) REVERT: A 599 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8120 (mt-10) REVERT: A 602 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7342 (tp30) REVERT: A 604 ARG cc_start: 0.8519 (mtp85) cc_final: 0.7979 (mmp80) REVERT: A 612 TYR cc_start: 0.8914 (m-80) cc_final: 0.8675 (m-80) REVERT: B 52 LYS cc_start: 0.9232 (tppt) cc_final: 0.8781 (tppt) REVERT: B 56 ASP cc_start: 0.9066 (m-30) cc_final: 0.8797 (m-30) REVERT: B 102 ASN cc_start: 0.9296 (m-40) cc_final: 0.8873 (m110) REVERT: B 121 ARG cc_start: 0.9352 (OUTLIER) cc_final: 0.9119 (tpt170) REVERT: B 172 LEU cc_start: 0.8955 (mp) cc_final: 0.8700 (mp) REVERT: B 184 ARG cc_start: 0.9151 (tpp-160) cc_final: 0.8814 (tpp80) REVERT: B 235 ARG cc_start: 0.8895 (ttp-110) cc_final: 0.8612 (ttp-110) REVERT: B 238 ASP cc_start: 0.7887 (t0) cc_final: 0.7165 (t70) REVERT: B 415 ASN cc_start: 0.9191 (t0) cc_final: 0.8914 (t0) REVERT: B 466 MET cc_start: 0.8896 (ptt) cc_final: 0.8488 (ptp) REVERT: B 474 GLN cc_start: 0.8684 (mt0) cc_final: 0.8385 (mt0) REVERT: B 515 ASP cc_start: 0.9111 (m-30) cc_final: 0.8835 (m-30) REVERT: B 550 MET cc_start: 0.8278 (ttm) cc_final: 0.8001 (mtp) REVERT: B 578 ILE cc_start: 0.9109 (mt) cc_final: 0.8873 (mt) REVERT: B 588 GLN cc_start: 0.8889 (mm-40) cc_final: 0.7975 (mm-40) REVERT: B 599 GLU cc_start: 0.8399 (pt0) cc_final: 0.7905 (pm20) REVERT: B 615 MET cc_start: 0.9220 (mmp) cc_final: 0.8934 (mmp) REVERT: B 639 ASP cc_start: 0.8508 (m-30) cc_final: 0.8096 (m-30) REVERT: C 29 PHE cc_start: 0.6804 (p90) cc_final: 0.6593 (p90) REVERT: C 89 VAL cc_start: 0.8222 (t) cc_final: 0.7591 (t) REVERT: C 92 PHE cc_start: 0.9276 (t80) cc_final: 0.8815 (t80) REVERT: C 93 MET cc_start: 0.8691 (mtt) cc_final: 0.8341 (mtt) REVERT: C 95 MET cc_start: 0.8716 (tmm) cc_final: 0.8011 (tmm) REVERT: C 96 MET cc_start: 0.8261 (mmm) cc_final: 0.7302 (mmm) REVERT: C 109 PHE cc_start: 0.8469 (m-10) cc_final: 0.8102 (m-80) REVERT: C 124 TRP cc_start: 0.8046 (t60) cc_final: 0.7238 (t60) REVERT: C 129 LYS cc_start: 0.9449 (mmmt) cc_final: 0.9226 (mmmt) REVERT: C 162 TYR cc_start: 0.8766 (m-10) cc_final: 0.8114 (m-10) REVERT: C 185 MET cc_start: 0.3257 (mtm) cc_final: 0.2196 (pmm) REVERT: C 197 ASP cc_start: 0.8670 (t70) cc_final: 0.8203 (t70) REVERT: C 239 GLU cc_start: 0.9122 (tp30) cc_final: 0.8855 (tp30) REVERT: C 268 LEU cc_start: 0.8460 (tp) cc_final: 0.8210 (tp) REVERT: C 269 MET cc_start: 0.9174 (tmm) cc_final: 0.8653 (mmt) REVERT: C 270 ASN cc_start: 0.9149 (m-40) cc_final: 0.8825 (m-40) REVERT: D 20 MET cc_start: 0.9295 (mmm) cc_final: 0.8857 (ptm) REVERT: D 21 PHE cc_start: 0.8499 (m-80) cc_final: 0.8287 (m-10) REVERT: D 25 ASN cc_start: 0.9549 (m-40) cc_final: 0.9286 (m-40) REVERT: D 46 TYR cc_start: 0.8556 (m-80) cc_final: 0.8187 (m-10) REVERT: D 53 ASP cc_start: 0.8245 (m-30) cc_final: 0.7987 (m-30) REVERT: D 71 ASN cc_start: 0.8830 (m-40) cc_final: 0.8433 (p0) REVERT: D 79 GLU cc_start: 0.8463 (tm-30) cc_final: 0.7069 (mm-30) REVERT: D 109 PHE cc_start: 0.8241 (m-80) cc_final: 0.7880 (m-80) REVERT: D 178 PHE cc_start: 0.8719 (m-10) cc_final: 0.8248 (m-10) REVERT: D 213 TYR cc_start: 0.6610 (t80) cc_final: 0.6357 (t80) REVERT: D 214 ASN cc_start: 0.8239 (m-40) cc_final: 0.7853 (m110) REVERT: D 224 LEU cc_start: 0.8213 (mt) cc_final: 0.8003 (mt) REVERT: D 227 PHE cc_start: 0.7968 (m-10) cc_final: 0.7764 (m-80) REVERT: D 261 ARG cc_start: 0.7129 (ttm-80) cc_final: 0.6769 (ptm160) outliers start: 55 outliers final: 32 residues processed: 587 average time/residue: 0.2762 time to fit residues: 240.1627 Evaluate side-chains 548 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 511 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 109 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 188 optimal weight: 20.0000 chunk 102 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 143 optimal weight: 20.0000 chunk 45 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN C 249 GLN ** D 23 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 = 0.3603 r_free = 0.3603 target = 0.129616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.087749 restraints weight = 33180.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.090869 restraints weight = 15291.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.092947 restraints weight = 9174.342| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16299 Z= 0.238 Angle : 0.666 14.305 22004 Z= 0.344 Chirality : 0.044 0.173 2348 Planarity : 0.004 0.046 2812 Dihedral : 8.583 143.911 2217 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.26 % Allowed : 21.06 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.19), residues: 1928 helix: 1.27 (0.15), residues: 1137 sheet: -0.34 (0.40), residues: 142 loop : 0.46 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP C 30 HIS 0.005 0.001 HIS A 255 PHE 0.026 0.002 PHE D 172 TYR 0.041 0.002 TYR A 571 ARG 0.007 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 896) hydrogen bonds : angle 5.07935 ( 2616) covalent geometry : bond 0.00527 (16298) covalent geometry : angle 0.66646 (22004) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 525 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8632 (mp0) cc_final: 0.8394 (mp0) REVERT: A 161 ARG cc_start: 0.8436 (mmm-85) cc_final: 0.8004 (mtm-85) REVERT: A 164 ARG cc_start: 0.8352 (ptt90) cc_final: 0.7365 (ptt90) REVERT: A 174 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7858 (mm-30) REVERT: A 181 ASP cc_start: 0.8815 (m-30) cc_final: 0.8536 (m-30) REVERT: A 191 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8142 (mm-40) REVERT: A 214 LYS cc_start: 0.8496 (mmtm) cc_final: 0.8194 (mmtm) REVERT: A 286 ASP cc_start: 0.7966 (m-30) cc_final: 0.7745 (m-30) REVERT: A 334 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.8393 (ptpt) REVERT: A 335 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8174 (mt-10) REVERT: A 348 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8582 (tmm) REVERT: A 362 ASP cc_start: 0.8441 (m-30) cc_final: 0.7837 (m-30) REVERT: A 393 SER cc_start: 0.8861 (m) cc_final: 0.8346 (p) REVERT: A 415 ASN cc_start: 0.9005 (t0) cc_final: 0.8728 (t0) REVERT: A 599 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.7998 (pt0) REVERT: A 602 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7140 (tp30) REVERT: A 604 ARG cc_start: 0.8602 (mtp85) cc_final: 0.7974 (mmp80) REVERT: A 612 TYR cc_start: 0.9065 (m-80) cc_final: 0.8813 (m-80) REVERT: B 78 LYS cc_start: 0.9193 (pttp) cc_final: 0.8785 (pttm) REVERT: B 102 ASN cc_start: 0.9276 (m-40) cc_final: 0.8850 (m110) REVERT: B 104 TYR cc_start: 0.9020 (m-80) cc_final: 0.8704 (m-80) REVERT: B 172 LEU cc_start: 0.9008 (mp) cc_final: 0.8761 (mp) REVERT: B 179 LEU cc_start: 0.9549 (tp) cc_final: 0.9075 (tt) REVERT: B 181 ASP cc_start: 0.8703 (m-30) cc_final: 0.8319 (m-30) REVERT: B 184 ARG cc_start: 0.9140 (tpp-160) cc_final: 0.8863 (tpp80) REVERT: B 238 ASP cc_start: 0.8061 (t0) cc_final: 0.7164 (t0) REVERT: B 274 ARG cc_start: 0.6756 (ttp-110) cc_final: 0.6077 (ttp-110) REVERT: B 322 MET cc_start: 0.9134 (mmm) cc_final: 0.8893 (mmm) REVERT: B 466 MET cc_start: 0.9067 (ptt) cc_final: 0.8723 (ptp) REVERT: B 515 ASP cc_start: 0.9163 (m-30) cc_final: 0.8886 (m-30) REVERT: B 550 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7963 (mtp) REVERT: B 570 MET cc_start: 0.8491 (mtp) cc_final: 0.8155 (mtp) REVERT: B 588 GLN cc_start: 0.8986 (mm-40) cc_final: 0.7936 (mm-40) REVERT: B 599 GLU cc_start: 0.8423 (pt0) cc_final: 0.7935 (pm20) REVERT: B 604 ARG cc_start: 0.8949 (mmm160) cc_final: 0.8608 (mmm160) REVERT: B 610 LYS cc_start: 0.8500 (mmmt) cc_final: 0.8241 (mmmt) REVERT: B 639 ASP cc_start: 0.8503 (m-30) cc_final: 0.8088 (m-30) REVERT: B 686 ARG cc_start: 0.7951 (mmt180) cc_final: 0.7610 (mpt180) REVERT: C 17 PHE cc_start: 0.7865 (p90) cc_final: 0.7597 (p90) REVERT: C 43 THR cc_start: 0.0156 (OUTLIER) cc_final: -0.0129 (p) REVERT: C 89 VAL cc_start: 0.8354 (t) cc_final: 0.7820 (t) REVERT: C 92 PHE cc_start: 0.9326 (t80) cc_final: 0.8844 (t80) REVERT: C 93 MET cc_start: 0.8874 (mtt) cc_final: 0.8497 (mtt) REVERT: C 95 MET cc_start: 0.8810 (tmm) cc_final: 0.8029 (tmm) REVERT: C 96 MET cc_start: 0.8319 (mmm) cc_final: 0.7621 (mmm) REVERT: C 162 TYR cc_start: 0.8793 (m-10) cc_final: 0.8205 (m-10) REVERT: C 185 MET cc_start: 0.3703 (mtm) cc_final: 0.2704 (pmm) REVERT: C 239 GLU cc_start: 0.9144 (tp30) cc_final: 0.8878 (tp30) REVERT: D 20 MET cc_start: 0.9337 (mmm) cc_final: 0.8871 (ptm) REVERT: D 21 PHE cc_start: 0.8538 (m-80) cc_final: 0.8328 (m-10) REVERT: D 25 ASN cc_start: 0.9563 (m-40) cc_final: 0.9318 (m-40) REVERT: D 46 TYR cc_start: 0.8630 (m-80) cc_final: 0.8034 (m-10) REVERT: D 56 MET cc_start: 0.9263 (mmp) cc_final: 0.8627 (ptp) REVERT: D 79 GLU cc_start: 0.8513 (tm-30) cc_final: 0.6960 (mm-30) REVERT: D 109 PHE cc_start: 0.8274 (m-80) cc_final: 0.8064 (m-80) REVERT: D 110 MET cc_start: 0.8676 (ppp) cc_final: 0.8463 (ppp) REVERT: D 224 LEU cc_start: 0.8196 (mt) cc_final: 0.7782 (mt) REVERT: D 227 PHE cc_start: 0.8169 (m-10) cc_final: 0.7841 (m-80) REVERT: D 261 ARG cc_start: 0.7207 (ttm-80) cc_final: 0.6842 (ttt-90) outliers start: 73 outliers final: 49 residues processed: 557 average time/residue: 0.2796 time to fit residues: 230.1657 Evaluate side-chains 528 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 473 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 143 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 182 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 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 = 0.3625 r_free = 0.3625 target = 0.132140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.091152 restraints weight = 32761.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.094399 restraints weight = 14966.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.096458 restraints weight = 8813.830| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16299 Z= 0.228 Angle : 0.688 18.879 22004 Z= 0.350 Chirality : 0.044 0.289 2348 Planarity : 0.004 0.048 2812 Dihedral : 8.566 143.996 2217 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.14 % Allowed : 21.70 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.19), residues: 1928 helix: 1.18 (0.15), residues: 1138 sheet: -0.40 (0.41), residues: 142 loop : 0.43 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP C 30 HIS 0.005 0.001 HIS A 255 PHE 0.035 0.002 PHE D 168 TYR 0.038 0.002 TYR D 142 ARG 0.007 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 896) hydrogen bonds : angle 5.12937 ( 2616) covalent geometry : bond 0.00509 (16298) covalent geometry : angle 0.68750 (22004) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 497 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8377 (mt0) REVERT: A 117 ARG cc_start: 0.8620 (mmm160) cc_final: 0.8244 (mmm160) REVERT: A 119 GLU cc_start: 0.8625 (mp0) cc_final: 0.8423 (mp0) REVERT: A 161 ARG cc_start: 0.8398 (mmm-85) cc_final: 0.7922 (mtm-85) REVERT: A 174 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7935 (mm-30) REVERT: A 181 ASP cc_start: 0.8762 (m-30) cc_final: 0.8518 (m-30) REVERT: A 214 LYS cc_start: 0.8466 (mmtm) cc_final: 0.8183 (mmtm) REVERT: A 238 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.7134 (m-30) REVERT: A 286 ASP cc_start: 0.7979 (m-30) cc_final: 0.7696 (m-30) REVERT: A 334 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.8438 (ptpt) REVERT: A 335 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8096 (mt-10) REVERT: A 348 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8688 (tmm) REVERT: A 362 ASP cc_start: 0.8422 (m-30) cc_final: 0.7705 (m-30) REVERT: A 393 SER cc_start: 0.8764 (m) cc_final: 0.8332 (p) REVERT: A 415 ASN cc_start: 0.8956 (t0) cc_final: 0.8724 (t0) REVERT: A 446 ARG cc_start: 0.7742 (mmp80) cc_final: 0.7138 (mmp80) REVERT: A 599 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8002 (pt0) REVERT: A 602 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7421 (tp30) REVERT: A 604 ARG cc_start: 0.8596 (mtp85) cc_final: 0.8319 (mmp80) REVERT: B 78 LYS cc_start: 0.9200 (pttp) cc_final: 0.8795 (pttm) REVERT: B 102 ASN cc_start: 0.9271 (m-40) cc_final: 0.8854 (m110) REVERT: B 104 TYR cc_start: 0.9021 (m-80) cc_final: 0.8680 (m-80) REVERT: B 109 ASN cc_start: 0.9416 (OUTLIER) cc_final: 0.9171 (m110) REVERT: B 172 LEU cc_start: 0.9017 (mp) cc_final: 0.8442 (mp) REVERT: B 181 ASP cc_start: 0.8739 (m-30) cc_final: 0.8356 (m-30) REVERT: B 184 ARG cc_start: 0.9166 (tpp-160) cc_final: 0.8862 (tpp80) REVERT: B 235 ARG cc_start: 0.8870 (ttp-110) cc_final: 0.8072 (ttm110) REVERT: B 238 ASP cc_start: 0.7958 (t0) cc_final: 0.7064 (t0) REVERT: B 322 MET cc_start: 0.9132 (mmm) cc_final: 0.8878 (mmm) REVERT: B 466 MET cc_start: 0.9012 (ptt) cc_final: 0.8683 (ptp) REVERT: B 515 ASP cc_start: 0.9121 (m-30) cc_final: 0.8837 (m-30) REVERT: B 570 MET cc_start: 0.8387 (mtp) cc_final: 0.8061 (mtp) REVERT: B 586 TYR cc_start: 0.9178 (m-80) cc_final: 0.8570 (m-80) REVERT: B 588 GLN cc_start: 0.8936 (mm-40) cc_final: 0.7923 (mm-40) REVERT: B 599 GLU cc_start: 0.8425 (pt0) cc_final: 0.7137 (pm20) REVERT: B 602 GLU cc_start: 0.8192 (tp30) cc_final: 0.7813 (tp30) REVERT: B 610 LYS cc_start: 0.8552 (mmmt) cc_final: 0.8260 (mmmt) REVERT: B 615 MET cc_start: 0.9194 (mmp) cc_final: 0.8838 (mmp) REVERT: B 639 ASP cc_start: 0.8491 (m-30) cc_final: 0.8081 (m-30) REVERT: C 17 PHE cc_start: 0.8109 (p90) cc_final: 0.7883 (p90) REVERT: C 89 VAL cc_start: 0.8466 (t) cc_final: 0.7931 (t) REVERT: C 93 MET cc_start: 0.8958 (mtt) cc_final: 0.8579 (mtt) REVERT: C 158 VAL cc_start: 0.9578 (t) cc_final: 0.9004 (m) REVERT: C 162 TYR cc_start: 0.8686 (m-10) cc_final: 0.8235 (m-10) REVERT: C 239 GLU cc_start: 0.9187 (tp30) cc_final: 0.8938 (tp30) REVERT: D 20 MET cc_start: 0.9308 (mmm) cc_final: 0.8924 (ptm) REVERT: D 21 PHE cc_start: 0.8644 (m-80) cc_final: 0.8396 (m-10) REVERT: D 25 ASN cc_start: 0.9582 (m-40) cc_final: 0.9280 (m-40) REVERT: D 46 TYR cc_start: 0.8716 (m-80) cc_final: 0.8154 (m-10) REVERT: D 51 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8310 (mm-30) REVERT: D 56 MET cc_start: 0.9247 (mmp) cc_final: 0.8640 (ptp) REVERT: D 79 GLU cc_start: 0.8598 (tm-30) cc_final: 0.7000 (mm-30) REVERT: D 109 PHE cc_start: 0.8413 (m-80) cc_final: 0.8201 (m-80) REVERT: D 110 MET cc_start: 0.8564 (ppp) cc_final: 0.8324 (ppp) REVERT: D 134 LYS cc_start: 0.7766 (pttt) cc_final: 0.6653 (pttp) REVERT: D 174 TYR cc_start: 0.8736 (t80) cc_final: 0.8323 (t80) REVERT: D 224 LEU cc_start: 0.8116 (mt) cc_final: 0.7787 (mt) REVERT: D 227 PHE cc_start: 0.8145 (m-10) cc_final: 0.7863 (m-80) REVERT: D 261 ARG cc_start: 0.7170 (ttm-80) cc_final: 0.6891 (ptm-80) outliers start: 71 outliers final: 51 residues processed: 528 average time/residue: 0.2908 time to fit residues: 230.2732 Evaluate side-chains 529 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 471 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 276 TYR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 196 ARG Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 250 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 7 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 84 optimal weight: 0.0980 chunk 185 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 HIS D 23 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.133104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.092879 restraints weight = 32732.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.096022 restraints weight = 14969.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.098052 restraints weight = 8922.611| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.5860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16299 Z= 0.133 Angle : 0.670 19.074 22004 Z= 0.336 Chirality : 0.044 0.362 2348 Planarity : 0.004 0.055 2812 Dihedral : 8.292 138.034 2217 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.92 % Allowed : 24.04 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.19), residues: 1928 helix: 1.13 (0.15), residues: 1146 sheet: 0.10 (0.43), residues: 126 loop : 0.36 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 30 HIS 0.005 0.001 HIS C 201 PHE 0.059 0.002 PHE C 109 TYR 0.042 0.002 TYR D 142 ARG 0.007 0.001 ARG B 274 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 896) hydrogen bonds : angle 5.02478 ( 2616) covalent geometry : bond 0.00297 (16298) covalent geometry : angle 0.66956 (22004) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 530 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8466 (mt0) REVERT: A 65 GLU cc_start: 0.8561 (mm-30) cc_final: 0.7648 (mp0) REVERT: A 95 MET cc_start: 0.9045 (tpp) cc_final: 0.8839 (tpp) REVERT: A 115 LEU cc_start: 0.8983 (mp) cc_final: 0.8398 (mt) REVERT: A 119 GLU cc_start: 0.8561 (mp0) cc_final: 0.8265 (mp0) REVERT: A 164 ARG cc_start: 0.8255 (ptt90) cc_final: 0.7983 (ptt90) REVERT: A 174 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7941 (mm-30) REVERT: A 181 ASP cc_start: 0.8709 (m-30) cc_final: 0.8471 (m-30) REVERT: A 214 LYS cc_start: 0.8346 (mmtm) cc_final: 0.7983 (mmtm) REVERT: A 256 ARG cc_start: 0.8923 (tpt90) cc_final: 0.8287 (tpt90) REVERT: A 286 ASP cc_start: 0.7897 (m-30) cc_final: 0.7658 (m-30) REVERT: A 334 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.8364 (ptpt) REVERT: A 348 MET cc_start: 0.8883 (ttp) cc_final: 0.8641 (tmm) REVERT: A 350 ARG cc_start: 0.8705 (mtp85) cc_final: 0.8082 (mtp85) REVERT: A 362 ASP cc_start: 0.8485 (m-30) cc_final: 0.7753 (m-30) REVERT: A 393 SER cc_start: 0.8784 (m) cc_final: 0.8469 (p) REVERT: A 483 GLU cc_start: 0.8909 (mp0) cc_final: 0.8523 (pm20) REVERT: A 509 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8362 (tm-30) REVERT: A 598 MET cc_start: 0.8011 (mtp) cc_final: 0.7107 (mtp) REVERT: A 599 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.7963 (pt0) REVERT: A 602 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7267 (tp30) REVERT: A 604 ARG cc_start: 0.8549 (mtp85) cc_final: 0.8279 (mmp80) REVERT: A 612 TYR cc_start: 0.8925 (m-80) cc_final: 0.8541 (m-80) REVERT: A 627 LYS cc_start: 0.8851 (tttt) cc_final: 0.8640 (tttt) REVERT: A 686 ARG cc_start: 0.7548 (mtp85) cc_final: 0.7280 (mtp-110) REVERT: B 78 LYS cc_start: 0.9198 (pttp) cc_final: 0.8807 (pttm) REVERT: B 102 ASN cc_start: 0.9253 (m-40) cc_final: 0.8900 (m110) REVERT: B 104 TYR cc_start: 0.8949 (m-80) cc_final: 0.8630 (m-80) REVERT: B 172 LEU cc_start: 0.8893 (mp) cc_final: 0.8614 (mp) REVERT: B 181 ASP cc_start: 0.8617 (m-30) cc_final: 0.8147 (m-30) REVERT: B 184 ARG cc_start: 0.9135 (tpp-160) cc_final: 0.8727 (tpp80) REVERT: B 238 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7096 (t70) REVERT: B 250 TYR cc_start: 0.9221 (m-80) cc_final: 0.8917 (m-80) REVERT: B 274 ARG cc_start: 0.6605 (ttp-110) cc_final: 0.5918 (ttp-110) REVERT: B 466 MET cc_start: 0.8873 (ptt) cc_final: 0.8544 (ptp) REVERT: B 515 ASP cc_start: 0.9096 (m-30) cc_final: 0.8798 (m-30) REVERT: B 570 MET cc_start: 0.8488 (mtp) cc_final: 0.8239 (mtp) REVERT: B 586 TYR cc_start: 0.9110 (m-80) cc_final: 0.8668 (m-80) REVERT: B 588 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8029 (mm-40) REVERT: B 599 GLU cc_start: 0.8382 (pt0) cc_final: 0.7855 (pm20) REVERT: B 604 ARG cc_start: 0.8807 (mmm160) cc_final: 0.8489 (mmm160) REVERT: B 610 LYS cc_start: 0.8548 (mmmt) cc_final: 0.8215 (mmmt) REVERT: B 639 ASP cc_start: 0.8571 (m-30) cc_final: 0.8107 (m-30) REVERT: C 43 THR cc_start: -0.0009 (OUTLIER) cc_final: -0.0840 (p) REVERT: C 89 VAL cc_start: 0.8485 (t) cc_final: 0.8010 (t) REVERT: C 93 MET cc_start: 0.8920 (mtt) cc_final: 0.8683 (mtt) REVERT: C 158 VAL cc_start: 0.9622 (t) cc_final: 0.8971 (m) REVERT: C 162 TYR cc_start: 0.8669 (m-10) cc_final: 0.8220 (m-10) REVERT: C 226 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8673 (pp20) REVERT: C 239 GLU cc_start: 0.9215 (tp30) cc_final: 0.8953 (tp30) REVERT: D 20 MET cc_start: 0.9327 (mmm) cc_final: 0.8952 (ptm) REVERT: D 25 ASN cc_start: 0.9556 (m-40) cc_final: 0.9297 (m-40) REVERT: D 46 TYR cc_start: 0.8682 (m-80) cc_final: 0.8050 (m-10) REVERT: D 51 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8337 (mm-30) REVERT: D 56 MET cc_start: 0.9247 (mmp) cc_final: 0.8638 (ptp) REVERT: D 79 GLU cc_start: 0.8419 (tm-30) cc_final: 0.7022 (mm-30) REVERT: D 110 MET cc_start: 0.8533 (ppp) cc_final: 0.8206 (ppp) REVERT: D 134 LYS cc_start: 0.7800 (pttt) cc_final: 0.6789 (pttp) REVERT: D 174 TYR cc_start: 0.8765 (t80) cc_final: 0.8445 (t80) REVERT: D 224 LEU cc_start: 0.8169 (mt) cc_final: 0.7933 (mt) REVERT: D 227 PHE cc_start: 0.8211 (m-10) cc_final: 0.7931 (m-80) REVERT: D 239 GLU cc_start: 0.6202 (OUTLIER) cc_final: 0.5990 (pp20) REVERT: D 261 ARG cc_start: 0.7228 (ttm-80) cc_final: 0.7025 (ptm-80) outliers start: 50 outliers final: 33 residues processed: 554 average time/residue: 0.2760 time to fit residues: 226.5394 Evaluate side-chains 530 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 490 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 196 ARG Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 250 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 146 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 646 GLN ** D 28 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 = 0.3637 r_free = 0.3637 target = 0.132084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.091782 restraints weight = 32491.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.094941 restraints weight = 15049.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.097019 restraints weight = 8869.997| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.5998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16299 Z= 0.152 Angle : 0.695 18.044 22004 Z= 0.350 Chirality : 0.045 0.321 2348 Planarity : 0.004 0.054 2812 Dihedral : 8.266 138.807 2216 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.80 % Allowed : 25.03 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.19), residues: 1928 helix: 1.11 (0.15), residues: 1144 sheet: 0.11 (0.43), residues: 126 loop : 0.29 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 30 HIS 0.005 0.001 HIS C 201 PHE 0.052 0.002 PHE C 109 TYR 0.040 0.002 TYR D 142 ARG 0.007 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 896) hydrogen bonds : angle 5.08768 ( 2616) covalent geometry : bond 0.00344 (16298) covalent geometry : angle 0.69537 (22004) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 504 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8413 (mt0) REVERT: A 65 GLU cc_start: 0.8662 (mm-30) cc_final: 0.7788 (mp0) REVERT: A 115 LEU cc_start: 0.9052 (mp) cc_final: 0.8485 (mt) REVERT: A 119 GLU cc_start: 0.8582 (mp0) cc_final: 0.8292 (mp0) REVERT: A 174 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7892 (mm-30) REVERT: A 181 ASP cc_start: 0.8688 (m-30) cc_final: 0.8451 (m-30) REVERT: A 191 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7978 (mm-40) REVERT: A 214 LYS cc_start: 0.8382 (mmtm) cc_final: 0.8072 (mmtm) REVERT: A 334 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8331 (ptpt) REVERT: A 348 MET cc_start: 0.8906 (ttp) cc_final: 0.8681 (tmm) REVERT: A 350 ARG cc_start: 0.8777 (mtp85) cc_final: 0.8101 (mtp85) REVERT: A 362 ASP cc_start: 0.8475 (m-30) cc_final: 0.7588 (m-30) REVERT: A 483 GLU cc_start: 0.8947 (mp0) cc_final: 0.8499 (pm20) REVERT: A 509 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8359 (tm-30) REVERT: A 599 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8016 (pt0) REVERT: A 602 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7201 (tp30) REVERT: A 604 ARG cc_start: 0.8585 (mtp85) cc_final: 0.8293 (mmp80) REVERT: A 612 TYR cc_start: 0.8940 (m-80) cc_final: 0.8446 (m-80) REVERT: A 686 ARG cc_start: 0.7574 (mtp85) cc_final: 0.7362 (mtp85) REVERT: B 78 LYS cc_start: 0.9189 (pttp) cc_final: 0.8822 (pttm) REVERT: B 102 ASN cc_start: 0.9198 (m-40) cc_final: 0.8858 (m110) REVERT: B 172 LEU cc_start: 0.8927 (mp) cc_final: 0.8689 (mp) REVERT: B 181 ASP cc_start: 0.8580 (m-30) cc_final: 0.8138 (m-30) REVERT: B 184 ARG cc_start: 0.9089 (tpp-160) cc_final: 0.8879 (tpp80) REVERT: B 238 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7100 (t70) REVERT: B 250 TYR cc_start: 0.9229 (m-80) cc_final: 0.8936 (m-80) REVERT: B 274 ARG cc_start: 0.6921 (ttp-110) cc_final: 0.5866 (ttp-110) REVERT: B 312 GLN cc_start: 0.8591 (mt0) cc_final: 0.8229 (pt0) REVERT: B 466 MET cc_start: 0.8766 (ptt) cc_final: 0.8488 (ptt) REVERT: B 515 ASP cc_start: 0.9099 (m-30) cc_final: 0.8787 (m-30) REVERT: B 570 MET cc_start: 0.8523 (mtp) cc_final: 0.8251 (mtp) REVERT: B 586 TYR cc_start: 0.9097 (m-80) cc_final: 0.8753 (m-80) REVERT: B 588 GLN cc_start: 0.8949 (mm-40) cc_final: 0.8141 (mm-40) REVERT: B 599 GLU cc_start: 0.8428 (pt0) cc_final: 0.7867 (pm20) REVERT: B 604 ARG cc_start: 0.8825 (mmm160) cc_final: 0.8542 (mmm160) REVERT: B 610 LYS cc_start: 0.8534 (mmmt) cc_final: 0.8235 (mmmt) REVERT: B 639 ASP cc_start: 0.8555 (m-30) cc_final: 0.8100 (m-30) REVERT: B 684 TYR cc_start: 0.7609 (OUTLIER) cc_final: 0.7361 (m-10) REVERT: B 686 ARG cc_start: 0.7877 (mmt180) cc_final: 0.7656 (mpt90) REVERT: C 17 PHE cc_start: 0.7506 (p90) cc_final: 0.7282 (p90) REVERT: C 20 MET cc_start: 0.9234 (tmm) cc_final: 0.8827 (tmm) REVERT: C 56 MET cc_start: 0.2377 (ptt) cc_final: 0.2118 (ptt) REVERT: C 89 VAL cc_start: 0.8656 (t) cc_final: 0.8159 (t) REVERT: C 124 TRP cc_start: 0.8187 (t60) cc_final: 0.7745 (t60) REVERT: C 158 VAL cc_start: 0.9623 (t) cc_final: 0.8967 (m) REVERT: C 162 TYR cc_start: 0.8654 (m-10) cc_final: 0.8198 (m-10) REVERT: C 226 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8630 (pp20) REVERT: C 239 GLU cc_start: 0.9165 (tp30) cc_final: 0.8928 (tp30) REVERT: D 20 MET cc_start: 0.9295 (mmm) cc_final: 0.8990 (ptm) REVERT: D 25 ASN cc_start: 0.9583 (m-40) cc_final: 0.9338 (m-40) REVERT: D 46 TYR cc_start: 0.8696 (m-80) cc_final: 0.8039 (m-10) REVERT: D 51 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8400 (mm-30) REVERT: D 56 MET cc_start: 0.9320 (mmp) cc_final: 0.8597 (ptp) REVERT: D 79 GLU cc_start: 0.8440 (tm-30) cc_final: 0.7014 (mm-30) REVERT: D 109 PHE cc_start: 0.8203 (m-80) cc_final: 0.7880 (m-80) REVERT: D 110 MET cc_start: 0.8459 (ppp) cc_final: 0.8181 (ppp) REVERT: D 134 LYS cc_start: 0.7803 (pttt) cc_final: 0.6817 (pttp) REVERT: D 157 MET cc_start: 0.6625 (ppp) cc_final: 0.6248 (ppp) REVERT: D 174 TYR cc_start: 0.8845 (t80) cc_final: 0.8497 (t80) REVERT: D 224 LEU cc_start: 0.8141 (mt) cc_final: 0.7914 (mt) REVERT: D 227 PHE cc_start: 0.8257 (m-10) cc_final: 0.7953 (m-80) outliers start: 48 outliers final: 39 residues processed: 528 average time/residue: 0.2701 time to fit residues: 210.9521 Evaluate side-chains 542 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 497 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 276 TYR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 196 ARG Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 250 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 140 optimal weight: 20.0000 chunk 110 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 1 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 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 = 0.3630 r_free = 0.3630 target = 0.133205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.092503 restraints weight = 32895.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.095672 restraints weight = 15289.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.097701 restraints weight = 9084.011| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.6142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 16299 Z= 0.189 Angle : 0.726 20.224 22004 Z= 0.367 Chirality : 0.046 0.400 2348 Planarity : 0.004 0.052 2812 Dihedral : 8.339 141.224 2216 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.03 % Allowed : 25.32 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.19), residues: 1928 helix: 1.06 (0.15), residues: 1144 sheet: -0.01 (0.44), residues: 128 loop : 0.26 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 30 HIS 0.005 0.001 HIS C 201 PHE 0.049 0.002 PHE C 109 TYR 0.041 0.002 TYR D 142 ARG 0.007 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03929 ( 896) hydrogen bonds : angle 5.15259 ( 2616) covalent geometry : bond 0.00433 (16298) covalent geometry : angle 0.72555 (22004) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 485 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8439 (mt0) REVERT: A 119 GLU cc_start: 0.8596 (mp0) cc_final: 0.8275 (mp0) REVERT: A 139 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8182 (mm-30) REVERT: A 161 ARG cc_start: 0.8217 (mmm-85) cc_final: 0.7830 (mtm-85) REVERT: A 181 ASP cc_start: 0.8672 (m-30) cc_final: 0.8432 (m-30) REVERT: A 214 LYS cc_start: 0.8384 (mmtm) cc_final: 0.8051 (mmtm) REVERT: A 317 MET cc_start: 0.8218 (mtt) cc_final: 0.7970 (mtt) REVERT: A 334 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8320 (ptpt) REVERT: A 350 ARG cc_start: 0.8800 (mtp85) cc_final: 0.8090 (mtp85) REVERT: A 393 SER cc_start: 0.8481 (p) cc_final: 0.7338 (t) REVERT: A 453 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.8959 (ttt-90) REVERT: A 483 GLU cc_start: 0.8965 (mp0) cc_final: 0.8520 (pm20) REVERT: A 509 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8359 (tm-30) REVERT: A 599 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.7967 (pt0) REVERT: A 602 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7269 (tp30) REVERT: A 604 ARG cc_start: 0.8611 (mtp85) cc_final: 0.8340 (mmp80) REVERT: A 612 TYR cc_start: 0.8946 (m-80) cc_final: 0.8453 (m-80) REVERT: B 102 ASN cc_start: 0.9187 (m-40) cc_final: 0.8855 (m110) REVERT: B 181 ASP cc_start: 0.8641 (m-30) cc_final: 0.8282 (m-30) REVERT: B 184 ARG cc_start: 0.9128 (tpp-160) cc_final: 0.8911 (tpp80) REVERT: B 202 ASN cc_start: 0.9163 (t0) cc_final: 0.8931 (t0) REVERT: B 238 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7125 (t70) REVERT: B 274 ARG cc_start: 0.6433 (ttp-110) cc_final: 0.5800 (ttp-110) REVERT: B 276 LYS cc_start: 0.8842 (mmmt) cc_final: 0.8455 (mmmt) REVERT: B 312 GLN cc_start: 0.8612 (mt0) cc_final: 0.8306 (pt0) REVERT: B 466 MET cc_start: 0.8832 (ptt) cc_final: 0.8550 (ptt) REVERT: B 515 ASP cc_start: 0.9129 (m-30) cc_final: 0.8801 (m-30) REVERT: B 570 MET cc_start: 0.8493 (mtp) cc_final: 0.8220 (mtp) REVERT: B 586 TYR cc_start: 0.9077 (m-80) cc_final: 0.8810 (m-80) REVERT: B 588 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8145 (mm-40) REVERT: B 599 GLU cc_start: 0.8463 (pt0) cc_final: 0.7958 (pm20) REVERT: B 639 ASP cc_start: 0.8551 (m-30) cc_final: 0.8107 (m-30) REVERT: B 684 TYR cc_start: 0.7585 (OUTLIER) cc_final: 0.7332 (m-10) REVERT: C 20 MET cc_start: 0.9239 (tmm) cc_final: 0.8812 (tmm) REVERT: C 56 MET cc_start: 0.2256 (ptt) cc_final: 0.2018 (ptt) REVERT: C 124 TRP cc_start: 0.8165 (t60) cc_final: 0.7733 (t60) REVERT: C 145 ILE cc_start: 0.8577 (mm) cc_final: 0.7921 (tp) REVERT: C 158 VAL cc_start: 0.9629 (t) cc_final: 0.8991 (m) REVERT: C 162 TYR cc_start: 0.8698 (m-10) cc_final: 0.8281 (m-10) REVERT: C 226 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8613 (pp20) REVERT: C 239 GLU cc_start: 0.9234 (tp30) cc_final: 0.9015 (tp30) REVERT: C 269 MET cc_start: 0.9031 (tmm) cc_final: 0.8600 (mpp) REVERT: C 287 LEU cc_start: 0.4889 (OUTLIER) cc_final: 0.4676 (mt) REVERT: D 21 PHE cc_start: 0.8606 (m-80) cc_final: 0.8357 (m-80) REVERT: D 25 ASN cc_start: 0.9588 (m-40) cc_final: 0.9338 (m-40) REVERT: D 46 TYR cc_start: 0.8696 (m-80) cc_final: 0.8058 (m-10) REVERT: D 51 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8401 (mm-30) REVERT: D 56 MET cc_start: 0.9305 (mmp) cc_final: 0.8634 (ptp) REVERT: D 79 GLU cc_start: 0.8410 (tm-30) cc_final: 0.6998 (mm-30) REVERT: D 109 PHE cc_start: 0.8370 (m-80) cc_final: 0.7954 (m-80) REVERT: D 134 LYS cc_start: 0.7845 (pttt) cc_final: 0.6927 (pttp) REVERT: D 174 TYR cc_start: 0.8872 (t80) cc_final: 0.8519 (t80) REVERT: D 227 PHE cc_start: 0.8370 (m-10) cc_final: 0.8083 (m-80) outliers start: 52 outliers final: 37 residues processed: 511 average time/residue: 0.2836 time to fit residues: 214.2274 Evaluate side-chains 521 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 476 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 276 TYR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 196 ARG Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 250 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 180 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 190 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 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 = 0.3610 r_free = 0.3610 target = 0.131723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.091245 restraints weight = 33274.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.094336 restraints weight = 15416.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.096382 restraints weight = 9151.450| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.6228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 16299 Z= 0.222 Angle : 0.757 19.727 22004 Z= 0.385 Chirality : 0.048 0.388 2348 Planarity : 0.004 0.050 2812 Dihedral : 8.503 142.903 2216 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.51 % Allowed : 26.20 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.19), residues: 1928 helix: 0.98 (0.15), residues: 1154 sheet: -0.60 (0.41), residues: 148 loop : 0.21 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP C 30 HIS 0.005 0.001 HIS C 201 PHE 0.047 0.002 PHE C 109 TYR 0.039 0.002 TYR D 142 ARG 0.008 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 896) hydrogen bonds : angle 5.24716 ( 2616) covalent geometry : bond 0.00503 (16298) covalent geometry : angle 0.75742 (22004) Misc. bond : bond 0.00003 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 485 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.9418 (tp) cc_final: 0.9138 (tp) REVERT: A 117 ARG cc_start: 0.8524 (mmm160) cc_final: 0.8222 (mmm160) REVERT: A 119 GLU cc_start: 0.8586 (mp0) cc_final: 0.8294 (mp0) REVERT: A 139 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8194 (mm-30) REVERT: A 161 ARG cc_start: 0.8290 (mmm-85) cc_final: 0.7643 (mtm-85) REVERT: A 174 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7972 (mm-30) REVERT: A 181 ASP cc_start: 0.8693 (m-30) cc_final: 0.8412 (m-30) REVERT: A 214 LYS cc_start: 0.8441 (mmtm) cc_final: 0.8143 (mmtm) REVERT: A 317 MET cc_start: 0.8285 (mtt) cc_final: 0.8049 (mtt) REVERT: A 334 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.8338 (ptpt) REVERT: A 350 ARG cc_start: 0.8797 (mtp85) cc_final: 0.8051 (mtp85) REVERT: A 446 ARG cc_start: 0.7699 (mmp80) cc_final: 0.7095 (mmp-170) REVERT: A 453 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8974 (ttt-90) REVERT: A 483 GLU cc_start: 0.8947 (mp0) cc_final: 0.8483 (pm20) REVERT: A 509 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8393 (tm-30) REVERT: A 598 MET cc_start: 0.8126 (mtp) cc_final: 0.7333 (mtp) REVERT: A 604 ARG cc_start: 0.8603 (mtp85) cc_final: 0.8328 (mmp80) REVERT: A 686 ARG cc_start: 0.7637 (mtp85) cc_final: 0.7175 (mtp-110) REVERT: B 102 ASN cc_start: 0.9221 (m-40) cc_final: 0.8898 (m110) REVERT: B 104 TYR cc_start: 0.9181 (m-80) cc_final: 0.8781 (m-80) REVERT: B 181 ASP cc_start: 0.8651 (m-30) cc_final: 0.8336 (m-30) REVERT: B 202 ASN cc_start: 0.9161 (t0) cc_final: 0.8954 (t0) REVERT: B 238 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7126 (t70) REVERT: B 274 ARG cc_start: 0.6493 (ttp-110) cc_final: 0.5564 (ttp-110) REVERT: B 312 GLN cc_start: 0.8657 (mt0) cc_final: 0.8302 (pt0) REVERT: B 362 ASP cc_start: 0.8270 (m-30) cc_final: 0.8018 (m-30) REVERT: B 515 ASP cc_start: 0.9156 (m-30) cc_final: 0.8807 (m-30) REVERT: B 570 MET cc_start: 0.8367 (mtp) cc_final: 0.8066 (mtp) REVERT: B 586 TYR cc_start: 0.9104 (m-80) cc_final: 0.8830 (m-80) REVERT: B 588 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8118 (mm-40) REVERT: B 602 GLU cc_start: 0.8296 (tp30) cc_final: 0.7600 (tp30) REVERT: B 604 ARG cc_start: 0.8658 (mmm160) cc_final: 0.8291 (mmm160) REVERT: B 639 ASP cc_start: 0.8490 (m-30) cc_final: 0.8035 (m-30) REVERT: B 684 TYR cc_start: 0.7601 (OUTLIER) cc_final: 0.7263 (m-10) REVERT: C 17 PHE cc_start: 0.7624 (p90) cc_final: 0.7034 (p90) REVERT: C 20 MET cc_start: 0.9210 (tmm) cc_final: 0.8869 (tmm) REVERT: C 124 TRP cc_start: 0.8176 (t60) cc_final: 0.7715 (t60) REVERT: C 145 ILE cc_start: 0.8648 (mm) cc_final: 0.8126 (tp) REVERT: C 158 VAL cc_start: 0.9618 (t) cc_final: 0.9001 (m) REVERT: C 162 TYR cc_start: 0.8713 (m-10) cc_final: 0.8298 (m-10) REVERT: C 226 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8573 (pp20) REVERT: C 239 GLU cc_start: 0.9192 (tp30) cc_final: 0.8981 (tp30) REVERT: C 243 THR cc_start: 0.7339 (t) cc_final: 0.6493 (t) REVERT: C 269 MET cc_start: 0.8988 (tmm) cc_final: 0.8560 (mpp) REVERT: C 287 LEU cc_start: 0.4915 (OUTLIER) cc_final: 0.4694 (mt) REVERT: D 20 MET cc_start: 0.9404 (mmm) cc_final: 0.9181 (ptm) REVERT: D 25 ASN cc_start: 0.9588 (m-40) cc_final: 0.9310 (m-40) REVERT: D 51 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8546 (mm-30) REVERT: D 76 ILE cc_start: 0.7813 (mt) cc_final: 0.7517 (mt) REVERT: D 109 PHE cc_start: 0.8440 (m-80) cc_final: 0.8106 (m-80) REVERT: D 134 LYS cc_start: 0.7883 (pttt) cc_final: 0.6997 (pttp) REVERT: D 174 TYR cc_start: 0.8926 (t80) cc_final: 0.8561 (t80) REVERT: D 185 MET cc_start: 0.6553 (ptm) cc_final: 0.6178 (ptm) REVERT: D 227 PHE cc_start: 0.8403 (m-10) cc_final: 0.8106 (m-80) outliers start: 43 outliers final: 34 residues processed: 509 average time/residue: 0.2804 time to fit residues: 211.0971 Evaluate side-chains 510 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 471 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 276 TYR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 196 ARG Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 239 GLU Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 250 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 186 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 140 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.134700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.094734 restraints weight = 33101.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.097977 restraints weight = 15124.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.100091 restraints weight = 8839.451| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.6426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16299 Z= 0.149 Angle : 0.740 19.226 22004 Z= 0.372 Chirality : 0.046 0.373 2348 Planarity : 0.004 0.048 2812 Dihedral : 8.246 138.141 2216 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.10 % Allowed : 27.01 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.19), residues: 1928 helix: 0.97 (0.15), residues: 1155 sheet: -0.08 (0.44), residues: 128 loop : 0.06 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 30 HIS 0.005 0.001 HIS A 255 PHE 0.045 0.002 PHE C 109 TYR 0.045 0.002 TYR C 55 ARG 0.013 0.001 ARG B 274 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 896) hydrogen bonds : angle 5.18132 ( 2616) covalent geometry : bond 0.00342 (16298) covalent geometry : angle 0.73971 (22004) Misc. bond : bond 0.00009 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6498.75 seconds wall clock time: 113 minutes 17.89 seconds (6797.89 seconds total)