Starting phenix.real_space_refine on Thu Sep 18 09:41:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bx2_44991/09_2025/9bx2_44991_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bx2_44991/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9bx2_44991/09_2025/9bx2_44991_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bx2_44991/09_2025/9bx2_44991_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bx2_44991/09_2025/9bx2_44991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bx2_44991/09_2025/9bx2_44991.map" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.62, per 1000 atoms: 0.23 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: 1.55 Conformation dependent library (CDL) restraints added in 527.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.47 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: 3.34 Time building geometry restraints manager: 1.95 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: 0.03 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.590 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.300 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.004 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.009 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00542 (16298) covalent geometry : angle 0.70754 (22004) hydrogen bonds : bond 0.16169 ( 896) hydrogen bonds : angle 6.35147 ( 2616) 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 : 0.579 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: A 37 PHE cc_start: 0.7919 (m-80) cc_final: 0.7670 (m-80) REVERT: A 101 TYR cc_start: 0.8052 (m-80) cc_final: 0.7846 (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: 0.8218 (p) REVERT: A 179 LEU cc_start: 0.9405 (tp) cc_final: 0.9188 (tp) REVERT: A 181 ASP cc_start: 0.8156 (m-30) cc_final: 0.7915 (m-30) REVERT: A 188 ILE cc_start: 0.9049 (mt) cc_final: 0.8829 (mt) REVERT: A 232 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.7971 (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: 0.7190 (m-30) REVERT: A 411 LEU cc_start: 0.8475 (mt) cc_final: 0.8056 (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: 0.7926 (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: 0.7417 (mt-10) REVERT: B 172 LEU cc_start: 0.9029 (mp) cc_final: 0.8479 (mp) REVERT: B 181 ASP cc_start: 0.8383 (m-30) cc_final: 0.7907 (m-30) REVERT: B 227 MET cc_start: 0.7932 (mtp) cc_final: 0.7487 (mtp) REVERT: B 267 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7823 (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: 0.8833 (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: 0.9164 (mm) REVERT: B 375 LYS cc_start: 0.9185 (mptp) cc_final: 0.8940 (mmtp) REVERT: B 396 ASP cc_start: 0.7618 (m-30) cc_final: 0.7396 (m-30) REVERT: B 550 MET cc_start: 0.8110 (ttm) cc_final: 0.7664 (mtp) REVERT: B 583 SER cc_start: 0.8125 (m) cc_final: 0.7778 (t) REVERT: B 597 ILE cc_start: 0.9145 (pt) cc_final: 0.8926 (pt) REVERT: B 637 VAL cc_start: 0.9061 (t) cc_final: 0.8850 (t) REVERT: C 26 VAL cc_start: 0.7638 (m) cc_final: 0.7122 (m) REVERT: C 106 SER cc_start: 0.7849 (m) cc_final: 0.7089 (t) REVERT: C 153 LEU cc_start: 0.6349 (tp) cc_final: 0.5530 (tp) REVERT: C 229 ILE cc_start: 0.3543 (mt) cc_final: 0.3299 (mt) REVERT: C 316 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7776 (mtmm) REVERT: D 55 TYR cc_start: 0.5619 (t80) cc_final: 0.5408 (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: 0.5485 (m-10) REVERT: D 256 VAL cc_start: 0.6468 (t) cc_final: 0.6261 (p) outliers start: 24 outliers final: 4 residues processed: 894 average time/residue: 0.1324 time to fit residues: 172.7002 Evaluate side-chains 547 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 540 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 474 GLN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN C 25 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS 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 28 GLN D 71 ASN D 80 HIS ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.133829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.090344 restraints weight = 32070.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.093460 restraints weight = 15076.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.095628 restraints weight = 9230.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.097023 restraints weight = 6381.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.097903 restraints weight = 5028.376| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 16299 Z= 0.252 Angle : 0.703 10.135 22004 Z= 0.372 Chirality : 0.045 0.173 2348 Planarity : 0.004 0.053 2812 Dihedral : 9.154 161.966 2232 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.08 % Allowed : 17.97 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.19), residues: 1928 helix: 1.48 (0.15), residues: 1133 sheet: 0.38 (0.40), residues: 134 loop : 0.75 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 331 TYR 0.035 0.002 TYR D 262 PHE 0.022 0.002 PHE D 259 TRP 0.028 0.003 TRP C 124 HIS 0.006 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00569 (16298) covalent geometry : angle 0.70281 (22004) hydrogen bonds : bond 0.05115 ( 896) hydrogen bonds : angle 5.25304 ( 2616) Misc. bond : bond 0.00031 ( 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 642 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 572 time to evaluate : 0.541 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: A 143 LEU cc_start: 0.9403 (tp) cc_final: 0.9144 (tp) REVERT: A 147 GLN cc_start: 0.9446 (mt0) cc_final: 0.9212 (mt0) REVERT: A 157 LEU cc_start: 0.9148 (tt) cc_final: 0.8728 (tp) REVERT: A 174 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7718 (mm-30) REVERT: A 181 ASP cc_start: 0.8745 (m-30) cc_final: 0.8497 (m-30) REVERT: A 214 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8243 (mmtm) REVERT: A 232 ASN cc_start: 0.9115 (OUTLIER) cc_final: 0.8481 (m110) REVERT: A 246 SER cc_start: 0.7468 (m) cc_final: 0.7182 (p) REVERT: A 256 ARG cc_start: 0.8911 (tpt90) cc_final: 0.8650 (tpt90) REVERT: A 348 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8514 (tmm) REVERT: A 393 SER cc_start: 0.8768 (m) cc_final: 0.8480 (p) REVERT: A 446 ARG cc_start: 0.7900 (mmm160) cc_final: 0.7525 (mmp-170) REVERT: A 509 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8377 (tm-30) REVERT: A 583 SER cc_start: 0.8787 (m) cc_final: 0.8323 (t) REVERT: A 598 MET cc_start: 0.8067 (mtp) cc_final: 0.7791 (mtp) REVERT: A 599 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8243 (pt0) REVERT: A 658 LEU cc_start: 0.9558 (mp) cc_final: 0.9272 (mt) REVERT: A 686 ARG cc_start: 0.7716 (mtp180) cc_final: 0.7496 (mtp85) REVERT: B 64 TYR cc_start: 0.8645 (m-10) cc_final: 0.8408 (m-10) REVERT: B 102 ASN cc_start: 0.9293 (m-40) cc_final: 0.8829 (m110) REVERT: B 109 ASN cc_start: 0.9334 (OUTLIER) cc_final: 0.9032 (m110) REVERT: B 172 LEU cc_start: 0.8872 (mp) cc_final: 0.8671 (mp) REVERT: B 184 ARG cc_start: 0.9118 (tpp-160) cc_final: 0.8844 (tpp80) REVERT: B 317 MET cc_start: 0.8597 (mtm) cc_final: 0.8304 (mtt) REVERT: B 318 ASP cc_start: 0.8518 (t0) cc_final: 0.8270 (p0) REVERT: B 334 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8937 (ptpt) REVERT: B 349 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9024 (mp) REVERT: B 466 MET cc_start: 0.8958 (ptt) cc_final: 0.8736 (ptp) REVERT: B 515 ASP cc_start: 0.9075 (m-30) cc_final: 0.8861 (m-30) REVERT: B 550 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7744 (mtp) REVERT: B 583 SER cc_start: 0.8935 (m) cc_final: 0.8660 (t) REVERT: B 599 GLU cc_start: 0.8697 (pt0) cc_final: 0.8428 (pt0) REVERT: B 604 ARG cc_start: 0.9048 (mmm160) cc_final: 0.8551 (mmm160) REVERT: B 610 LYS cc_start: 0.8411 (mmmt) cc_final: 0.8113 (mmmm) REVERT: C 20 MET cc_start: 0.9335 (mpp) cc_final: 0.8550 (tmm) REVERT: C 26 VAL cc_start: 0.9462 (m) cc_final: 0.9104 (m) REVERT: C 29 PHE cc_start: 0.6937 (p90) cc_final: 0.6647 (p90) REVERT: C 30 TRP cc_start: 0.7290 (p-90) cc_final: 0.7050 (p-90) REVERT: C 89 VAL cc_start: 0.8274 (t) cc_final: 0.7828 (t) REVERT: C 92 PHE cc_start: 0.9054 (t80) cc_final: 0.8787 (t80) REVERT: C 96 MET cc_start: 0.8146 (mmm) cc_final: 0.7770 (mmm) REVERT: C 118 ILE cc_start: 0.8523 (mt) cc_final: 0.7971 (pt) REVERT: C 124 TRP cc_start: 0.7626 (t60) cc_final: 0.7163 (t60) REVERT: C 162 TYR cc_start: 0.8833 (m-10) cc_final: 0.8356 (m-80) REVERT: C 212 ILE cc_start: 0.7219 (mm) cc_final: 0.6698 (mm) REVERT: C 229 ILE cc_start: 0.5123 (mt) cc_final: 0.4892 (mt) REVERT: D 20 MET cc_start: 0.9371 (mmm) cc_final: 0.8888 (ptm) REVERT: D 21 PHE cc_start: 0.8317 (m-80) cc_final: 0.7990 (m-10) REVERT: D 25 ASN cc_start: 0.9494 (m-40) cc_final: 0.9220 (m-40) REVERT: D 30 TRP cc_start: 0.8014 (p-90) cc_final: 0.7165 (p-90) REVERT: D 76 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8148 (mt) REVERT: D 96 MET cc_start: 0.7554 (mmm) cc_final: 0.7201 (mmm) REVERT: D 162 TYR cc_start: 0.9037 (m-10) cc_final: 0.8770 (m-80) REVERT: D 178 PHE cc_start: 0.8730 (m-10) cc_final: 0.7983 (m-10) REVERT: D 227 PHE cc_start: 0.7853 (m-10) cc_final: 0.7589 (m-80) REVERT: D 259 PHE cc_start: 0.8359 (t80) cc_final: 0.8114 (t80) REVERT: D 265 ASN cc_start: 0.7330 (m110) cc_final: 0.7116 (m110) REVERT: D 273 PHE cc_start: 0.6713 (m-80) cc_final: 0.6213 (t80) REVERT: D 320 PHE cc_start: 0.8667 (m-80) cc_final: 0.8348 (m-80) outliers start: 70 outliers final: 36 residues processed: 611 average time/residue: 0.1207 time to fit residues: 109.7274 Evaluate side-chains 538 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 494 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 687 THR Chi-restraints excluded: chain C residue 18 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 230 ASP Chi-restraints excluded: chain C residue 255 ASP 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 239 GLU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 181 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 156 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 91 ASN C 127 GLN C 216 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN D 23 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.135536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.092158 restraints weight = 32166.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.095464 restraints weight = 14950.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.097604 restraints weight = 8911.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.098949 restraints weight = 6260.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.099782 restraints weight = 4906.260| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 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 = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16299 Z= 0.156 Angle : 0.650 9.689 22004 Z= 0.336 Chirality : 0.043 0.178 2348 Planarity : 0.004 0.051 2812 Dihedral : 8.710 142.031 2222 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.38 % Allowed : 19.43 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.18), residues: 1928 helix: 1.42 (0.15), residues: 1128 sheet: 1.17 (0.46), residues: 102 loop : 0.52 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 261 TYR 0.041 0.002 TYR D 142 PHE 0.028 0.002 PHE C 122 TRP 0.019 0.002 TRP C 44 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00349 (16298) covalent geometry : angle 0.64988 (22004) hydrogen bonds : bond 0.04405 ( 896) hydrogen bonds : angle 5.05237 ( 2616) Misc. bond : bond 0.00140 ( 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: 58 poor density : 565 time to evaluate : 0.651 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 115 LEU cc_start: 0.8906 (mp) cc_final: 0.8512 (mt) REVERT: A 139 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8329 (mm-30) REVERT: A 157 LEU cc_start: 0.9243 (tt) cc_final: 0.8767 (tp) REVERT: A 161 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7707 (mtm-85) REVERT: A 174 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7690 (mm-30) REVERT: A 214 LYS cc_start: 0.8465 (mmtm) cc_final: 0.8165 (mmtm) REVERT: A 232 ASN cc_start: 0.9069 (OUTLIER) cc_final: 0.8476 (m-40) REVERT: A 286 ASP cc_start: 0.8158 (m-30) cc_final: 0.7885 (m-30) REVERT: A 334 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8237 (ptpt) REVERT: A 348 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8546 (tmm) REVERT: A 362 ASP cc_start: 0.8363 (m-30) cc_final: 0.7743 (m-30) REVERT: A 393 SER cc_start: 0.8843 (m) cc_final: 0.8554 (p) REVERT: A 415 ASN cc_start: 0.9075 (t0) cc_final: 0.8848 (t0) REVERT: A 446 ARG cc_start: 0.7959 (mmm160) cc_final: 0.7745 (mmp80) REVERT: A 509 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8360 (tm-30) REVERT: A 598 MET cc_start: 0.8112 (mtp) cc_final: 0.7780 (mtp) REVERT: A 599 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8258 (pt0) REVERT: B 8 LYS cc_start: 0.9164 (tppt) cc_final: 0.8964 (tppt) REVERT: B 102 ASN cc_start: 0.9280 (m-40) cc_final: 0.8855 (m110) REVERT: B 121 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9121 (tpt170) REVERT: B 172 LEU cc_start: 0.8934 (mp) cc_final: 0.8689 (mp) REVERT: B 184 ARG cc_start: 0.9128 (tpp-160) cc_final: 0.8832 (tpp80) REVERT: B 238 ASP cc_start: 0.7855 (t0) cc_final: 0.7208 (t70) REVERT: B 381 LEU cc_start: 0.9375 (tt) cc_final: 0.9137 (tp) REVERT: B 415 ASN cc_start: 0.9117 (t0) cc_final: 0.8769 (t0) REVERT: B 466 MET cc_start: 0.8791 (ptt) cc_final: 0.8304 (ptp) REVERT: B 515 ASP cc_start: 0.9073 (m-30) cc_final: 0.8822 (m-30) REVERT: B 550 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8052 (mtp) REVERT: B 570 MET cc_start: 0.8506 (mtp) cc_final: 0.8295 (mtp) REVERT: B 583 SER cc_start: 0.8902 (m) cc_final: 0.8657 (t) REVERT: B 588 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8432 (mm-40) REVERT: B 599 GLU cc_start: 0.8654 (pt0) cc_final: 0.8042 (pm20) REVERT: B 604 ARG cc_start: 0.9032 (mmm160) cc_final: 0.8570 (mmm160) REVERT: B 612 TYR cc_start: 0.8755 (m-80) cc_final: 0.8549 (m-80) REVERT: C 20 MET cc_start: 0.9537 (mpp) cc_final: 0.9237 (ppp) REVERT: C 26 VAL cc_start: 0.9364 (m) cc_final: 0.9070 (m) REVERT: C 29 PHE cc_start: 0.6990 (p90) cc_final: 0.6755 (p90) REVERT: C 89 VAL cc_start: 0.8299 (t) cc_final: 0.8028 (t) REVERT: C 92 PHE cc_start: 0.9152 (t80) cc_final: 0.8652 (t80) REVERT: C 93 MET cc_start: 0.8651 (mtt) cc_final: 0.8116 (mtt) REVERT: C 95 MET cc_start: 0.8729 (tmm) cc_final: 0.8172 (tmm) REVERT: C 96 MET cc_start: 0.8207 (mmm) cc_final: 0.7502 (mmm) REVERT: C 109 PHE cc_start: 0.8393 (m-10) cc_final: 0.8098 (m-80) REVERT: C 118 ILE cc_start: 0.8320 (mt) cc_final: 0.8118 (pt) REVERT: C 124 TRP cc_start: 0.7879 (t60) cc_final: 0.7200 (t60) REVERT: C 129 LYS cc_start: 0.9430 (mmmt) cc_final: 0.8985 (mmmt) REVERT: C 162 TYR cc_start: 0.8824 (m-10) cc_final: 0.8256 (m-80) REVERT: C 178 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.8061 (m-10) REVERT: D 21 PHE cc_start: 0.8383 (m-80) cc_final: 0.8053 (m-10) REVERT: D 25 ASN cc_start: 0.9634 (m-40) cc_final: 0.9394 (m-40) REVERT: D 79 GLU cc_start: 0.8428 (tm-30) cc_final: 0.6884 (mm-30) REVERT: D 96 MET cc_start: 0.7301 (mmm) cc_final: 0.6986 (mmm) REVERT: D 174 TYR cc_start: 0.8604 (OUTLIER) cc_final: 0.8353 (t80) REVERT: D 195 LEU cc_start: 0.8662 (mm) cc_final: 0.8450 (mm) REVERT: D 213 TYR cc_start: 0.6905 (t80) cc_final: 0.6464 (t80) REVERT: D 214 ASN cc_start: 0.8187 (m-40) cc_final: 0.7781 (m110) REVERT: D 227 PHE cc_start: 0.7869 (m-10) cc_final: 0.7572 (m-10) REVERT: D 259 PHE cc_start: 0.8235 (t80) cc_final: 0.7958 (t80) REVERT: D 273 PHE cc_start: 0.6479 (m-80) cc_final: 0.6208 (t80) REVERT: D 320 PHE cc_start: 0.8638 (m-80) cc_final: 0.8380 (m-80) outliers start: 58 outliers final: 32 residues processed: 593 average time/residue: 0.1248 time to fit residues: 110.0246 Evaluate side-chains 541 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 500 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 460 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 590 SER 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 121 ARG Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 266 LYS 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 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 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 178 PHE 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 139 VAL Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 250 VAL 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: 2.9990 chunk 30 optimal weight: 0.9980 chunk 147 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 89 optimal weight: 0.1980 chunk 54 optimal weight: 5.9990 chunk 145 optimal weight: 20.0000 chunk 172 optimal weight: 9.9990 chunk 134 optimal weight: 0.7980 chunk 171 optimal weight: 6.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 ASN B 418 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.132734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.090747 restraints weight = 32899.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.094018 restraints weight = 15340.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.096050 restraints weight = 9076.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.097311 restraints weight = 6367.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.098241 restraints weight = 5032.577| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16299 Z= 0.184 Angle : 0.645 9.406 22004 Z= 0.333 Chirality : 0.043 0.198 2348 Planarity : 0.004 0.048 2812 Dihedral : 8.504 141.415 2220 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.68 % Allowed : 20.13 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.19), residues: 1928 helix: 1.37 (0.15), residues: 1131 sheet: 0.44 (0.44), residues: 112 loop : 0.45 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 261 TYR 0.039 0.002 TYR D 142 PHE 0.052 0.002 PHE C 122 TRP 0.023 0.003 TRP D 30 HIS 0.010 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00411 (16298) covalent geometry : angle 0.64535 (22004) hydrogen bonds : bond 0.04168 ( 896) hydrogen bonds : angle 4.99229 ( 2616) Misc. bond : bond 0.00044 ( 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 610 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 547 time to evaluate : 0.624 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 115 LEU cc_start: 0.9010 (mp) cc_final: 0.8607 (mp) REVERT: A 135 GLU cc_start: 0.8607 (mp0) cc_final: 0.8380 (mp0) REVERT: A 139 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8388 (mm-30) REVERT: A 157 LEU cc_start: 0.9197 (tt) cc_final: 0.8621 (tp) REVERT: A 174 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7776 (mm-30) REVERT: A 181 ASP cc_start: 0.8812 (m-30) cc_final: 0.8547 (m-30) REVERT: A 191 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8138 (mm-40) REVERT: A 238 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.7295 (m-30) REVERT: A 286 ASP cc_start: 0.8125 (m-30) cc_final: 0.7884 (m-30) REVERT: A 317 MET cc_start: 0.8481 (mtt) cc_final: 0.8191 (mtt) REVERT: A 348 MET cc_start: 0.8813 (ttp) cc_final: 0.8513 (tmm) REVERT: A 362 ASP cc_start: 0.8431 (m-30) cc_final: 0.7637 (m-30) REVERT: A 379 SER cc_start: 0.9107 (t) cc_final: 0.8894 (t) REVERT: A 383 SER cc_start: 0.8845 (m) cc_final: 0.8521 (t) REVERT: A 393 SER cc_start: 0.8879 (m) cc_final: 0.8167 (p) REVERT: A 415 ASN cc_start: 0.9153 (t0) cc_final: 0.8894 (t0) REVERT: A 509 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8386 (tm-30) REVERT: A 598 MET cc_start: 0.8205 (mtp) cc_final: 0.7766 (mtp) REVERT: A 599 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.7970 (pt0) REVERT: A 602 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7109 (tp30) REVERT: A 604 ARG cc_start: 0.8518 (mtp85) cc_final: 0.7953 (mmp80) REVERT: A 640 MET cc_start: 0.8975 (tpp) cc_final: 0.8679 (tpp) REVERT: B 52 LYS cc_start: 0.9220 (tppt) cc_final: 0.8800 (tppt) REVERT: B 56 ASP cc_start: 0.9013 (m-30) cc_final: 0.8755 (m-30) REVERT: B 78 LYS cc_start: 0.9151 (pttm) cc_final: 0.8843 (pttt) REVERT: B 102 ASN cc_start: 0.9290 (m-40) cc_final: 0.8874 (m110) REVERT: B 104 TYR cc_start: 0.8935 (m-80) cc_final: 0.8495 (m-80) REVERT: B 109 ASN cc_start: 0.9404 (OUTLIER) cc_final: 0.9076 (m-40) REVERT: B 121 ARG cc_start: 0.9366 (OUTLIER) cc_final: 0.9145 (tpt170) REVERT: B 172 LEU cc_start: 0.8977 (mp) cc_final: 0.8402 (mp) REVERT: B 179 LEU cc_start: 0.9560 (tp) cc_final: 0.9102 (tt) REVERT: B 184 ARG cc_start: 0.9135 (tpp-160) cc_final: 0.8823 (tpp80) REVERT: B 238 ASP cc_start: 0.7882 (t0) cc_final: 0.7206 (t70) REVERT: B 274 ARG cc_start: 0.6584 (ttp-110) cc_final: 0.6025 (ttp-110) REVERT: B 317 MET cc_start: 0.8414 (mtm) cc_final: 0.8120 (mtt) REVERT: B 334 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8836 (ptpt) REVERT: B 381 LEU cc_start: 0.9363 (tt) cc_final: 0.9095 (tp) REVERT: B 415 ASN cc_start: 0.9217 (t0) cc_final: 0.8882 (t0) REVERT: B 466 MET cc_start: 0.8929 (ptt) cc_final: 0.8186 (ptp) REVERT: B 515 ASP cc_start: 0.9101 (m-30) cc_final: 0.8864 (m-30) REVERT: B 550 MET cc_start: 0.8289 (ttm) cc_final: 0.7948 (mtp) REVERT: B 578 ILE cc_start: 0.9146 (mt) cc_final: 0.8917 (mt) REVERT: B 588 GLN cc_start: 0.8924 (mm-40) cc_final: 0.7977 (mm-40) REVERT: B 599 GLU cc_start: 0.8523 (pt0) cc_final: 0.8046 (pm20) REVERT: B 610 LYS cc_start: 0.8300 (mmmm) cc_final: 0.8023 (mmmt) REVERT: B 639 ASP cc_start: 0.8434 (m-30) cc_final: 0.8058 (m-30) REVERT: C 20 MET cc_start: 0.9575 (mpp) cc_final: 0.9372 (ppp) REVERT: C 26 VAL cc_start: 0.9365 (m) cc_final: 0.9083 (m) REVERT: C 29 PHE cc_start: 0.6833 (p90) cc_final: 0.6628 (p90) REVERT: C 89 VAL cc_start: 0.8337 (t) cc_final: 0.8045 (t) REVERT: C 92 PHE cc_start: 0.9304 (t80) cc_final: 0.8816 (t80) REVERT: C 93 MET cc_start: 0.8491 (mtt) cc_final: 0.8284 (mtt) REVERT: C 95 MET cc_start: 0.8759 (tmm) cc_final: 0.8135 (tmm) REVERT: C 96 MET cc_start: 0.8311 (mmm) cc_final: 0.7436 (mmm) REVERT: C 109 PHE cc_start: 0.8447 (m-10) cc_final: 0.8103 (m-80) REVERT: C 124 TRP cc_start: 0.8010 (t60) cc_final: 0.7242 (t60) REVERT: C 162 TYR cc_start: 0.8856 (m-10) cc_final: 0.8190 (m-10) REVERT: C 178 PHE cc_start: 0.7971 (m-10) cc_final: 0.7468 (m-10) REVERT: C 185 MET cc_start: 0.3542 (mpp) cc_final: 0.3044 (mmm) REVERT: C 271 LEU cc_start: 0.8490 (mt) cc_final: 0.8235 (mt) REVERT: D 20 MET cc_start: 0.9432 (mmm) cc_final: 0.8982 (ptm) REVERT: D 21 PHE cc_start: 0.8452 (m-80) cc_final: 0.8223 (m-10) REVERT: D 55 TYR cc_start: 0.7554 (t80) cc_final: 0.7148 (t80) REVERT: D 56 MET cc_start: 0.9127 (mmp) cc_final: 0.8586 (ptp) REVERT: D 79 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8178 (pp20) REVERT: D 148 ASP cc_start: 0.7676 (m-30) cc_final: 0.7464 (m-30) REVERT: D 154 PHE cc_start: 0.8204 (t80) cc_final: 0.7900 (t80) REVERT: D 174 TYR cc_start: 0.8739 (t80) cc_final: 0.8462 (t80) REVERT: D 213 TYR cc_start: 0.6828 (t80) cc_final: 0.6406 (t80) REVERT: D 240 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6633 (pp) REVERT: D 260 ILE cc_start: 0.8089 (pt) cc_final: 0.7835 (pt) REVERT: D 261 ARG cc_start: 0.7387 (ttm170) cc_final: 0.6575 (ptm160) REVERT: D 273 PHE cc_start: 0.6450 (m-80) cc_final: 0.5974 (t80) outliers start: 63 outliers final: 44 residues processed: 578 average time/residue: 0.1187 time to fit residues: 102.3565 Evaluate side-chains 548 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 497 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 238 ASP 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 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 109 ASN Chi-restraints excluded: chain B residue 121 ARG 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 266 LYS Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 602 GLU 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 226 GLU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 286 VAL 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 59 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 250 VAL 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 66 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 164 optimal weight: 8.9990 chunk 189 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 145 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.133160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.091556 restraints weight = 32665.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.094850 restraints weight = 15337.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.096855 restraints weight = 9062.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.098177 restraints weight = 6380.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.099059 restraints weight = 4991.784| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 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 = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16299 Z= 0.156 Angle : 0.639 10.161 22004 Z= 0.329 Chirality : 0.043 0.183 2348 Planarity : 0.003 0.045 2812 Dihedral : 8.323 139.167 2217 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.85 % Allowed : 21.88 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.19), residues: 1928 helix: 1.26 (0.15), residues: 1141 sheet: 0.18 (0.41), residues: 126 loop : 0.48 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 161 TYR 0.039 0.002 TYR D 142 PHE 0.049 0.002 PHE D 227 TRP 0.028 0.002 TRP C 30 HIS 0.008 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00345 (16298) covalent geometry : angle 0.63923 (22004) hydrogen bonds : bond 0.04038 ( 896) hydrogen bonds : angle 4.99034 ( 2616) Misc. bond : bond 0.00009 ( 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 587 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 521 time to evaluate : 0.658 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 115 LEU cc_start: 0.9017 (mp) cc_final: 0.8371 (mt) REVERT: A 135 GLU cc_start: 0.8620 (mp0) cc_final: 0.8415 (mp0) REVERT: A 139 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8391 (mm-30) REVERT: A 161 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7601 (mtt-85) REVERT: A 164 ARG cc_start: 0.7989 (ptt90) cc_final: 0.7594 (ptt90) REVERT: A 174 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7684 (mm-30) REVERT: A 181 ASP cc_start: 0.8695 (m-30) cc_final: 0.8461 (m-30) REVERT: A 191 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8039 (mm-40) REVERT: A 214 LYS cc_start: 0.8379 (mmtm) cc_final: 0.8080 (mmtm) REVERT: A 256 ARG cc_start: 0.8928 (tpt90) cc_final: 0.8421 (tpt90) REVERT: A 286 ASP cc_start: 0.8126 (m-30) cc_final: 0.7921 (m-30) REVERT: A 334 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8296 (ptpt) REVERT: A 348 MET cc_start: 0.8852 (ttp) cc_final: 0.8561 (tmm) REVERT: A 362 ASP cc_start: 0.8428 (m-30) cc_final: 0.7514 (m-30) REVERT: A 393 SER cc_start: 0.8790 (m) cc_final: 0.8099 (p) REVERT: A 415 ASN cc_start: 0.8953 (t0) cc_final: 0.8708 (t0) REVERT: A 599 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8034 (pt0) REVERT: A 602 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7469 (tp30) REVERT: A 604 ARG cc_start: 0.8519 (mtp85) cc_final: 0.8239 (mmp80) REVERT: B 52 LYS cc_start: 0.9184 (tppt) cc_final: 0.8708 (tppt) REVERT: B 56 ASP cc_start: 0.9022 (m-30) cc_final: 0.8712 (m-30) REVERT: B 78 LYS cc_start: 0.9172 (pttm) cc_final: 0.8826 (pttm) REVERT: B 95 MET cc_start: 0.9186 (tpp) cc_final: 0.8917 (tpp) REVERT: B 102 ASN cc_start: 0.9280 (m-40) cc_final: 0.8866 (m110) REVERT: B 104 TYR cc_start: 0.8928 (m-80) cc_final: 0.8500 (m-80) REVERT: B 172 LEU cc_start: 0.8932 (mp) cc_final: 0.8694 (mp) REVERT: B 179 LEU cc_start: 0.9543 (tp) cc_final: 0.9128 (tt) REVERT: B 181 ASP cc_start: 0.8699 (m-30) cc_final: 0.8250 (m-30) REVERT: B 184 ARG cc_start: 0.9131 (tpp-160) cc_final: 0.8839 (tpp80) REVERT: B 238 ASP cc_start: 0.7979 (t0) cc_final: 0.7258 (t70) REVERT: B 274 ARG cc_start: 0.6576 (ttp-110) cc_final: 0.6001 (ttp-110) REVERT: B 334 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8865 (ptpt) REVERT: B 362 ASP cc_start: 0.8291 (m-30) cc_final: 0.7984 (m-30) REVERT: B 381 LEU cc_start: 0.9338 (tt) cc_final: 0.9136 (tp) REVERT: B 466 MET cc_start: 0.8888 (ptt) cc_final: 0.8348 (ptp) REVERT: B 515 ASP cc_start: 0.9097 (m-30) cc_final: 0.8845 (m-30) REVERT: B 550 MET cc_start: 0.8206 (ttm) cc_final: 0.7993 (mtp) REVERT: B 570 MET cc_start: 0.8527 (mtp) cc_final: 0.8230 (mtp) REVERT: B 578 ILE cc_start: 0.9127 (mt) cc_final: 0.8899 (mt) REVERT: B 588 GLN cc_start: 0.8854 (mm-40) cc_final: 0.7799 (mm-40) REVERT: B 599 GLU cc_start: 0.8541 (pt0) cc_final: 0.7619 (pm20) REVERT: B 602 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7600 (tp30) REVERT: B 610 LYS cc_start: 0.8442 (mmmm) cc_final: 0.8171 (mmmt) REVERT: B 639 ASP cc_start: 0.8483 (m-30) cc_final: 0.8040 (m-30) REVERT: C 26 VAL cc_start: 0.9345 (m) cc_final: 0.9091 (m) REVERT: C 30 TRP cc_start: 0.7049 (p-90) cc_final: 0.6015 (p-90) REVERT: C 89 VAL cc_start: 0.8448 (t) cc_final: 0.8057 (t) REVERT: C 92 PHE cc_start: 0.9335 (t80) cc_final: 0.8786 (t80) REVERT: C 93 MET cc_start: 0.8672 (mtt) cc_final: 0.8459 (mtt) REVERT: C 95 MET cc_start: 0.8834 (tmm) cc_final: 0.8065 (tmm) REVERT: C 96 MET cc_start: 0.8269 (mmm) cc_final: 0.7643 (mmm) REVERT: C 109 PHE cc_start: 0.8347 (m-10) cc_final: 0.7619 (m-80) REVERT: C 162 TYR cc_start: 0.8820 (m-10) cc_final: 0.8163 (m-10) REVERT: C 270 ASN cc_start: 0.8921 (m-40) cc_final: 0.8441 (m-40) REVERT: D 20 MET cc_start: 0.9461 (mmm) cc_final: 0.9086 (ptm) REVERT: D 25 ASN cc_start: 0.9478 (m-40) cc_final: 0.9230 (m110) REVERT: D 56 MET cc_start: 0.9139 (mmp) cc_final: 0.8564 (ptp) REVERT: D 93 MET cc_start: 0.6076 (ptm) cc_final: 0.5688 (ptm) REVERT: D 148 ASP cc_start: 0.7774 (m-30) cc_final: 0.7507 (m-30) REVERT: D 157 MET cc_start: 0.6996 (ppp) cc_final: 0.6673 (ppp) REVERT: D 174 TYR cc_start: 0.8812 (t80) cc_final: 0.8556 (t80) REVERT: D 185 MET cc_start: 0.5788 (ppp) cc_final: 0.5566 (ppp) REVERT: D 261 ARG cc_start: 0.7440 (ttm170) cc_final: 0.6584 (ptm160) REVERT: D 273 PHE cc_start: 0.6349 (m-80) cc_final: 0.5956 (m-10) outliers start: 66 outliers final: 39 residues processed: 556 average time/residue: 0.1202 time to fit residues: 99.6065 Evaluate side-chains 533 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 488 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 161 ARG 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 443 THR 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 B residue 96 SER Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN 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 396 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 495 VAL 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 C residue 64 LEU Chi-restraints excluded: chain C residue 115 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 285 ILE 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 184 LEU 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 92 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 438 HIS C 216 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.131435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.090421 restraints weight = 32570.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.093605 restraints weight = 15263.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.095586 restraints weight = 9067.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.096924 restraints weight = 6365.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.097689 restraints weight = 4979.224| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 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 = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.5512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16299 Z= 0.191 Angle : 0.666 14.973 22004 Z= 0.340 Chirality : 0.044 0.233 2348 Planarity : 0.004 0.050 2812 Dihedral : 8.327 139.197 2217 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.97 % Allowed : 22.58 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.19), residues: 1928 helix: 1.20 (0.15), residues: 1134 sheet: 0.07 (0.43), residues: 126 loop : 0.42 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 261 TYR 0.040 0.002 TYR D 142 PHE 0.030 0.002 PHE D 172 TRP 0.020 0.002 TRP C 30 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00428 (16298) covalent geometry : angle 0.66564 (22004) hydrogen bonds : bond 0.04054 ( 896) hydrogen bonds : angle 5.05130 ( 2616) Misc. bond : bond 0.00002 ( 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 569 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 501 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8469 (mp0) cc_final: 0.7965 (mp0) REVERT: A 135 GLU cc_start: 0.8616 (mp0) cc_final: 0.8387 (mp0) REVERT: A 139 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8403 (mm-30) REVERT: A 174 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7801 (mm-30) REVERT: A 181 ASP cc_start: 0.8720 (m-30) cc_final: 0.8410 (m-30) REVERT: A 214 LYS cc_start: 0.8353 (mmtm) cc_final: 0.8047 (mmtm) REVERT: A 256 ARG cc_start: 0.8934 (tpt90) cc_final: 0.8481 (tpt90) REVERT: A 286 ASP cc_start: 0.8130 (m-30) cc_final: 0.7886 (m-30) REVERT: A 317 MET cc_start: 0.8485 (mtt) cc_final: 0.8190 (mtt) REVERT: A 334 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.8353 (ptpt) REVERT: A 348 MET cc_start: 0.8867 (ttp) cc_final: 0.8576 (tmm) REVERT: A 362 ASP cc_start: 0.8451 (m-30) cc_final: 0.7484 (m-30) REVERT: A 393 SER cc_start: 0.8752 (m) cc_final: 0.8344 (p) REVERT: A 415 ASN cc_start: 0.9048 (t0) cc_final: 0.8829 (t0) REVERT: A 446 ARG cc_start: 0.7787 (mmp80) cc_final: 0.7184 (mmp-170) REVERT: A 509 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8372 (tm-30) REVERT: A 599 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8128 (pt0) REVERT: A 602 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7564 (tp30) REVERT: A 604 ARG cc_start: 0.8495 (mtp85) cc_final: 0.8236 (mmp80) REVERT: A 686 ARG cc_start: 0.7565 (mtp85) cc_final: 0.7342 (mtp85) REVERT: B 102 ASN cc_start: 0.9269 (m-40) cc_final: 0.8858 (m110) REVERT: B 104 TYR cc_start: 0.8988 (m-80) cc_final: 0.8633 (m-80) REVERT: B 172 LEU cc_start: 0.8958 (mp) cc_final: 0.8724 (mp) REVERT: B 179 LEU cc_start: 0.9531 (tp) cc_final: 0.9050 (tt) REVERT: B 184 ARG cc_start: 0.9129 (tpp-160) cc_final: 0.8850 (tpp80) REVERT: B 238 ASP cc_start: 0.7911 (t0) cc_final: 0.7167 (t70) REVERT: B 274 ARG cc_start: 0.6636 (ttp-110) cc_final: 0.6083 (ttp-110) REVERT: B 334 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8808 (ptpt) REVERT: B 381 LEU cc_start: 0.9350 (tt) cc_final: 0.9142 (tp) REVERT: B 466 MET cc_start: 0.8943 (ptt) cc_final: 0.8522 (ptp) REVERT: B 515 ASP cc_start: 0.9098 (m-30) cc_final: 0.8826 (m-30) REVERT: B 570 MET cc_start: 0.8524 (mtp) cc_final: 0.8229 (mtp) REVERT: B 578 ILE cc_start: 0.9139 (mt) cc_final: 0.8895 (mt) REVERT: B 586 TYR cc_start: 0.9151 (m-80) cc_final: 0.8572 (m-80) REVERT: B 588 GLN cc_start: 0.8868 (mm-40) cc_final: 0.7825 (mm-40) REVERT: B 599 GLU cc_start: 0.8540 (pt0) cc_final: 0.7557 (pm20) REVERT: B 602 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7514 (tp30) REVERT: B 604 ARG cc_start: 0.8911 (mmm160) cc_final: 0.8260 (mmm160) REVERT: B 639 ASP cc_start: 0.8485 (m-30) cc_final: 0.8025 (m-30) REVERT: C 17 PHE cc_start: 0.7641 (p90) cc_final: 0.7420 (p90) REVERT: C 89 VAL cc_start: 0.8543 (t) cc_final: 0.8226 (t) REVERT: C 93 MET cc_start: 0.8927 (mtt) cc_final: 0.8655 (mtt) REVERT: C 105 TYR cc_start: 0.6406 (p90) cc_final: 0.6049 (p90) REVERT: C 122 PHE cc_start: 0.9287 (t80) cc_final: 0.9041 (t80) REVERT: C 162 TYR cc_start: 0.8810 (m-10) cc_final: 0.8157 (m-10) REVERT: D 21 PHE cc_start: 0.8449 (m-10) cc_final: 0.8236 (m-80) REVERT: D 25 ASN cc_start: 0.9496 (m-40) cc_final: 0.9218 (m110) REVERT: D 51 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8269 (mm-30) REVERT: D 56 MET cc_start: 0.9234 (mmp) cc_final: 0.8492 (ptp) REVERT: D 109 PHE cc_start: 0.8215 (m-80) cc_final: 0.7760 (m-80) REVERT: D 148 ASP cc_start: 0.7735 (m-30) cc_final: 0.7447 (m-30) REVERT: D 174 TYR cc_start: 0.8837 (t80) cc_final: 0.8521 (t80) REVERT: D 185 MET cc_start: 0.6000 (ppp) cc_final: 0.5696 (ppp) REVERT: D 236 TYR cc_start: 0.6497 (t80) cc_final: 0.6270 (t80) REVERT: D 261 ARG cc_start: 0.7451 (ttm170) cc_final: 0.6583 (ptm160) outliers start: 68 outliers final: 52 residues processed: 534 average time/residue: 0.1206 time to fit residues: 96.3115 Evaluate side-chains 529 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 472 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 232 ASN 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 443 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 499 SER 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 223 VAL Chi-restraints excluded: chain B residue 232 ASN 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 396 ASP Chi-restraints excluded: chain B residue 410 ASN 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 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 602 GLU 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 259 PHE 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 312 VAL 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 59 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 2 optimal weight: 5.9990 chunk 165 optimal weight: 0.0980 chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 147 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 474 GLN C 210 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.131836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.091008 restraints weight = 32294.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.094194 restraints weight = 15191.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.096208 restraints weight = 9011.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.097543 restraints weight = 6318.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.098439 restraints weight = 4937.732| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 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 = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16299 Z= 0.169 Angle : 0.672 13.097 22004 Z= 0.345 Chirality : 0.044 0.189 2348 Planarity : 0.004 0.052 2812 Dihedral : 8.309 140.115 2217 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.97 % Allowed : 23.16 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.19), residues: 1928 helix: 1.14 (0.15), residues: 1129 sheet: -0.06 (0.43), residues: 126 loop : 0.43 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 261 TYR 0.041 0.002 TYR D 142 PHE 0.030 0.002 PHE D 172 TRP 0.035 0.002 TRP C 30 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00381 (16298) covalent geometry : angle 0.67240 (22004) hydrogen bonds : bond 0.04014 ( 896) hydrogen bonds : angle 5.07814 ( 2616) Misc. bond : bond 0.00006 ( 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 568 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 500 time to evaluate : 0.566 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: A 11 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8444 (mt0) REVERT: A 115 LEU cc_start: 0.9022 (mp) cc_final: 0.8429 (mt) REVERT: A 119 GLU cc_start: 0.8461 (mp0) cc_final: 0.7970 (mp0) REVERT: A 139 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8415 (mm-30) REVERT: A 174 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7805 (mm-30) REVERT: A 181 ASP cc_start: 0.8692 (m-30) cc_final: 0.8392 (m-30) REVERT: A 191 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8263 (mm-40) REVERT: A 214 LYS cc_start: 0.8363 (mmtm) cc_final: 0.8042 (mmtm) REVERT: A 256 ARG cc_start: 0.8920 (tpt90) cc_final: 0.8432 (tpt90) REVERT: A 286 ASP cc_start: 0.8117 (m-30) cc_final: 0.7891 (m-30) REVERT: A 334 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.8378 (ptpt) REVERT: A 348 MET cc_start: 0.8878 (ttp) cc_final: 0.8573 (tmm) REVERT: A 362 ASP cc_start: 0.8443 (m-30) cc_final: 0.7457 (m-30) REVERT: A 393 SER cc_start: 0.8764 (m) cc_final: 0.8128 (p) REVERT: A 415 ASN cc_start: 0.9087 (t0) cc_final: 0.8876 (t0) REVERT: A 446 ARG cc_start: 0.7795 (mmp80) cc_final: 0.7180 (mmp-170) REVERT: A 509 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8364 (tm-30) REVERT: A 599 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8165 (pt0) REVERT: A 602 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7535 (tp30) REVERT: A 604 ARG cc_start: 0.8527 (mtp85) cc_final: 0.8290 (mmp80) REVERT: A 686 ARG cc_start: 0.7560 (mtp85) cc_final: 0.7347 (mtp85) REVERT: B 78 LYS cc_start: 0.9123 (pttm) cc_final: 0.8698 (pttm) REVERT: B 102 ASN cc_start: 0.9265 (m-40) cc_final: 0.8893 (m110) REVERT: B 104 TYR cc_start: 0.8959 (m-80) cc_final: 0.8573 (m-80) REVERT: B 172 LEU cc_start: 0.8955 (mp) cc_final: 0.8699 (mp) REVERT: B 181 ASP cc_start: 0.8682 (m-30) cc_final: 0.8287 (m-30) REVERT: B 184 ARG cc_start: 0.9102 (tpp-160) cc_final: 0.8717 (tpp80) REVERT: B 238 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7172 (t70) REVERT: B 274 ARG cc_start: 0.6898 (ttp-110) cc_final: 0.6345 (ttp-110) REVERT: B 334 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8843 (ptpt) REVERT: B 357 TYR cc_start: 0.8916 (m-10) cc_final: 0.8417 (m-10) REVERT: B 466 MET cc_start: 0.8988 (ptt) cc_final: 0.8349 (ptp) REVERT: B 515 ASP cc_start: 0.9095 (m-30) cc_final: 0.8821 (m-30) REVERT: B 570 MET cc_start: 0.8523 (mtp) cc_final: 0.8248 (mtp) REVERT: B 578 ILE cc_start: 0.9139 (mt) cc_final: 0.8901 (mt) REVERT: B 586 TYR cc_start: 0.9146 (m-80) cc_final: 0.8626 (m-80) REVERT: B 588 GLN cc_start: 0.8859 (mm-40) cc_final: 0.7806 (mm-40) REVERT: B 599 GLU cc_start: 0.8542 (pt0) cc_final: 0.7193 (pm20) REVERT: B 639 ASP cc_start: 0.8494 (m-30) cc_final: 0.8010 (m-30) REVERT: C 24 GLN cc_start: 0.9575 (mm-40) cc_final: 0.9329 (mm-40) REVERT: C 74 MET cc_start: 0.6872 (mtt) cc_final: 0.6316 (mtm) REVERT: C 89 VAL cc_start: 0.8603 (t) cc_final: 0.8094 (t) REVERT: C 93 MET cc_start: 0.8960 (mtt) cc_final: 0.8565 (mtt) REVERT: C 122 PHE cc_start: 0.9204 (t80) cc_final: 0.8964 (t80) REVERT: C 124 TRP cc_start: 0.7672 (t60) cc_final: 0.6737 (t60) REVERT: C 162 TYR cc_start: 0.8766 (m-10) cc_final: 0.8171 (m-10) REVERT: C 226 GLU cc_start: 0.9225 (mm-30) cc_final: 0.8689 (pp20) REVERT: D 20 MET cc_start: 0.9484 (mmm) cc_final: 0.9152 (ptm) REVERT: D 25 ASN cc_start: 0.9501 (m-40) cc_final: 0.9198 (m110) REVERT: D 51 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8371 (mm-30) REVERT: D 56 MET cc_start: 0.9230 (mmp) cc_final: 0.8459 (ptp) REVERT: D 109 PHE cc_start: 0.8368 (m-80) cc_final: 0.7890 (m-80) REVERT: D 134 LYS cc_start: 0.8174 (pttt) cc_final: 0.7324 (pttp) REVERT: D 157 MET cc_start: 0.6728 (ppp) cc_final: 0.6405 (ppp) REVERT: D 174 TYR cc_start: 0.8880 (t80) cc_final: 0.8530 (t80) REVERT: D 239 GLU cc_start: 0.7061 (pp20) cc_final: 0.6798 (pp20) REVERT: D 261 ARG cc_start: 0.7521 (ttm170) cc_final: 0.6686 (ptm160) outliers start: 68 outliers final: 51 residues processed: 537 average time/residue: 0.1218 time to fit residues: 97.4022 Evaluate side-chains 537 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 480 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 60 GLU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 232 ASN 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 443 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 499 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 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 238 ASP 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 396 ASP Chi-restraints excluded: chain B residue 410 ASN 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 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 163 LEU 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 312 VAL 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 161 VAL Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 138 optimal weight: 0.0170 chunk 8 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 174 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 overall best weight: 1.5222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.131954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.091441 restraints weight = 32519.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.094603 restraints weight = 15176.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.096585 restraints weight = 8958.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.097896 restraints weight = 6271.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.098726 restraints weight = 4911.272| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 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 = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.5887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16299 Z= 0.171 Angle : 0.698 12.632 22004 Z= 0.358 Chirality : 0.044 0.199 2348 Planarity : 0.004 0.055 2812 Dihedral : 8.303 139.886 2216 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.03 % Allowed : 24.85 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.19), residues: 1928 helix: 1.10 (0.15), residues: 1129 sheet: -0.16 (0.43), residues: 126 loop : 0.37 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 261 TYR 0.038 0.002 TYR D 142 PHE 0.024 0.001 PHE C 109 TRP 0.045 0.002 TRP C 30 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00387 (16298) covalent geometry : angle 0.69814 (22004) hydrogen bonds : bond 0.03984 ( 896) hydrogen bonds : angle 5.13532 ( 2616) Misc. bond : bond 0.00010 ( 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 544 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 492 time to evaluate : 0.566 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: 0.8844 (OUTLIER) cc_final: 0.8517 (mt0) REVERT: A 95 MET cc_start: 0.9032 (tpp) cc_final: 0.8832 (tpp) REVERT: A 115 LEU cc_start: 0.9017 (mp) cc_final: 0.8495 (mt) REVERT: A 119 GLU cc_start: 0.8469 (mp0) cc_final: 0.8003 (mp0) REVERT: A 174 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7832 (mm-30) REVERT: A 181 ASP cc_start: 0.8719 (m-30) cc_final: 0.8383 (m-30) REVERT: A 191 GLN cc_start: 0.8487 (mm-40) cc_final: 0.8156 (mm-40) REVERT: A 214 LYS cc_start: 0.8354 (mmtm) cc_final: 0.8016 (mmtm) REVERT: A 256 ARG cc_start: 0.8948 (tpt90) cc_final: 0.8461 (tpt90) REVERT: A 286 ASP cc_start: 0.8097 (m-30) cc_final: 0.7882 (m-30) REVERT: A 334 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.8401 (ptpt) REVERT: A 348 MET cc_start: 0.8893 (ttp) cc_final: 0.8583 (tmm) REVERT: A 362 ASP cc_start: 0.8448 (m-30) cc_final: 0.7500 (m-30) REVERT: A 393 SER cc_start: 0.8755 (m) cc_final: 0.8376 (p) REVERT: A 446 ARG cc_start: 0.7805 (mmp80) cc_final: 0.7202 (mmp-170) REVERT: A 483 GLU cc_start: 0.8896 (mp0) cc_final: 0.8500 (pm20) REVERT: A 509 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8365 (tm-30) REVERT: A 604 ARG cc_start: 0.8506 (mtp85) cc_final: 0.8305 (mmp80) REVERT: A 637 VAL cc_start: 0.9377 (t) cc_final: 0.9053 (p) REVERT: B 78 LYS cc_start: 0.9145 (pttm) cc_final: 0.8772 (pttm) REVERT: B 102 ASN cc_start: 0.9245 (m-40) cc_final: 0.8899 (m110) REVERT: B 104 TYR cc_start: 0.8955 (m-80) cc_final: 0.8632 (m-80) REVERT: B 172 LEU cc_start: 0.8949 (mp) cc_final: 0.8420 (mp) REVERT: B 179 LEU cc_start: 0.9473 (tp) cc_final: 0.9077 (tt) REVERT: B 181 ASP cc_start: 0.8609 (m-30) cc_final: 0.8164 (m-30) REVERT: B 184 ARG cc_start: 0.9105 (tpp-160) cc_final: 0.8864 (tpp80) REVERT: B 238 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7178 (t70) REVERT: B 274 ARG cc_start: 0.7053 (ttp-110) cc_final: 0.6461 (ttp-110) REVERT: B 318 ASP cc_start: 0.8466 (t0) cc_final: 0.8121 (p0) REVERT: B 334 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8849 (ptpt) REVERT: B 362 ASP cc_start: 0.8389 (m-30) cc_final: 0.8100 (m-30) REVERT: B 466 MET cc_start: 0.8937 (ptt) cc_final: 0.8242 (ptp) REVERT: B 515 ASP cc_start: 0.9091 (m-30) cc_final: 0.8800 (m-30) REVERT: B 570 MET cc_start: 0.8541 (mtp) cc_final: 0.8271 (mtp) REVERT: B 578 ILE cc_start: 0.9159 (mt) cc_final: 0.8923 (mt) REVERT: B 586 TYR cc_start: 0.9136 (m-80) cc_final: 0.8677 (m-80) REVERT: B 588 GLN cc_start: 0.8850 (mm-40) cc_final: 0.7863 (mm-40) REVERT: B 639 ASP cc_start: 0.8476 (m-30) cc_final: 0.8015 (m-30) REVERT: B 686 ARG cc_start: 0.8098 (mmt180) cc_final: 0.7827 (mmt180) REVERT: C 17 PHE cc_start: 0.7625 (p90) cc_final: 0.6456 (p90) REVERT: C 24 GLN cc_start: 0.9557 (mm-40) cc_final: 0.9312 (mm-40) REVERT: C 74 MET cc_start: 0.6847 (mtt) cc_final: 0.6309 (mtm) REVERT: C 89 VAL cc_start: 0.8552 (t) cc_final: 0.8006 (t) REVERT: C 93 MET cc_start: 0.9095 (mtt) cc_final: 0.8665 (mtt) REVERT: C 122 PHE cc_start: 0.9143 (t80) cc_final: 0.8852 (t80) REVERT: C 226 GLU cc_start: 0.9251 (mm-30) cc_final: 0.8685 (pp20) REVERT: D 20 MET cc_start: 0.9480 (mmm) cc_final: 0.9195 (ptm) REVERT: D 25 ASN cc_start: 0.9530 (m-40) cc_final: 0.9222 (m110) REVERT: D 51 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8379 (mm-30) REVERT: D 56 MET cc_start: 0.9202 (mmp) cc_final: 0.8444 (ptp) REVERT: D 79 GLU cc_start: 0.8440 (tm-30) cc_final: 0.7416 (mm-30) REVERT: D 109 PHE cc_start: 0.8373 (m-80) cc_final: 0.7840 (m-80) REVERT: D 134 LYS cc_start: 0.8161 (pttt) cc_final: 0.7326 (pttp) REVERT: D 157 MET cc_start: 0.6734 (ppp) cc_final: 0.6423 (ppp) REVERT: D 174 TYR cc_start: 0.8880 (t80) cc_final: 0.8464 (t80) REVERT: D 179 TYR cc_start: 0.8322 (t80) cc_final: 0.8075 (t80) REVERT: D 261 ARG cc_start: 0.7595 (ttm170) cc_final: 0.6765 (ptm160) outliers start: 52 outliers final: 42 residues processed: 521 average time/residue: 0.1276 time to fit residues: 99.3057 Evaluate side-chains 528 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 482 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 232 ASN 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 443 THR 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 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 253 ILE 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 396 ASP Chi-restraints excluded: chain B residue 410 ASN 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 C residue 163 LEU 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 59 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 143 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 12 optimal weight: 0.0570 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.134712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.094696 restraints weight = 32153.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.097931 restraints weight = 14858.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.100015 restraints weight = 8770.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.101400 restraints weight = 6034.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.102233 restraints weight = 4682.887| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 16299 Z= 0.138 Angle : 0.691 12.176 22004 Z= 0.354 Chirality : 0.044 0.214 2348 Planarity : 0.003 0.053 2812 Dihedral : 8.160 135.378 2216 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.45 % Allowed : 25.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.19), residues: 1928 helix: 0.99 (0.15), residues: 1145 sheet: -0.32 (0.43), residues: 128 loop : 0.31 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 261 TYR 0.039 0.001 TYR D 142 PHE 0.025 0.001 PHE D 172 TRP 0.046 0.002 TRP C 30 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00315 (16298) covalent geometry : angle 0.69127 (22004) hydrogen bonds : bond 0.03923 ( 896) hydrogen bonds : angle 5.12567 ( 2616) Misc. bond : bond 0.00011 ( 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 546 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 504 time to evaluate : 0.560 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: 0.8824 (OUTLIER) cc_final: 0.8479 (mt0) REVERT: A 37 PHE cc_start: 0.8266 (m-10) cc_final: 0.7557 (m-10) REVERT: A 95 MET cc_start: 0.9022 (tpp) cc_final: 0.8821 (tpp) REVERT: A 106 LEU cc_start: 0.9390 (tp) cc_final: 0.9174 (tp) REVERT: A 119 GLU cc_start: 0.8454 (mp0) cc_final: 0.8008 (mp0) REVERT: A 174 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7874 (mm-30) REVERT: A 181 ASP cc_start: 0.8715 (m-30) cc_final: 0.8389 (m-30) REVERT: A 214 LYS cc_start: 0.8253 (mmtm) cc_final: 0.7872 (mmtm) REVERT: A 256 ARG cc_start: 0.8926 (tpt90) cc_final: 0.8381 (tpt90) REVERT: A 286 ASP cc_start: 0.8068 (m-30) cc_final: 0.7838 (m-30) REVERT: A 334 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.8359 (ptpt) REVERT: A 348 MET cc_start: 0.8892 (ttp) cc_final: 0.8574 (tmm) REVERT: A 350 ARG cc_start: 0.8955 (mtp85) cc_final: 0.8252 (mtp85) REVERT: A 362 ASP cc_start: 0.8402 (m-30) cc_final: 0.7425 (m-30) REVERT: A 393 SER cc_start: 0.8747 (m) cc_final: 0.8193 (p) REVERT: A 483 GLU cc_start: 0.8901 (mp0) cc_final: 0.8507 (pm20) REVERT: A 509 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8348 (tm-30) REVERT: A 599 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7992 (pt0) REVERT: B 8 LYS cc_start: 0.8935 (tppt) cc_final: 0.8620 (tppt) REVERT: B 78 LYS cc_start: 0.9137 (pttm) cc_final: 0.8716 (pttm) REVERT: B 102 ASN cc_start: 0.9254 (m-40) cc_final: 0.8920 (m110) REVERT: B 119 GLU cc_start: 0.9053 (mp0) cc_final: 0.8751 (mp0) REVERT: B 172 LEU cc_start: 0.8881 (mp) cc_final: 0.8657 (mp) REVERT: B 179 LEU cc_start: 0.9450 (tp) cc_final: 0.9144 (tt) REVERT: B 181 ASP cc_start: 0.8521 (m-30) cc_final: 0.8098 (m-30) REVERT: B 184 ARG cc_start: 0.9122 (tpp-160) cc_final: 0.8913 (tpp80) REVERT: B 235 ARG cc_start: 0.8680 (ttp-110) cc_final: 0.8338 (ttm110) REVERT: B 238 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7213 (t70) REVERT: B 250 TYR cc_start: 0.9184 (m-80) cc_final: 0.8869 (m-80) REVERT: B 274 ARG cc_start: 0.7039 (ttp-110) cc_final: 0.6486 (ttp-110) REVERT: B 317 MET cc_start: 0.8185 (mtm) cc_final: 0.7761 (mtt) REVERT: B 318 ASP cc_start: 0.8442 (t0) cc_final: 0.8163 (p0) REVERT: B 334 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8883 (ptpt) REVERT: B 415 ASN cc_start: 0.9101 (t0) cc_final: 0.8809 (t0) REVERT: B 466 MET cc_start: 0.8890 (ptt) cc_final: 0.8356 (ptp) REVERT: B 515 ASP cc_start: 0.9040 (m-30) cc_final: 0.8757 (m-30) REVERT: B 570 MET cc_start: 0.8490 (mtp) cc_final: 0.8253 (mtp) REVERT: B 578 ILE cc_start: 0.9167 (mt) cc_final: 0.8955 (mt) REVERT: B 586 TYR cc_start: 0.9092 (m-80) cc_final: 0.8797 (m-80) REVERT: B 588 GLN cc_start: 0.8800 (mm-40) cc_final: 0.7991 (mm-40) REVERT: B 639 ASP cc_start: 0.8506 (m-30) cc_final: 0.8069 (m-30) REVERT: C 74 MET cc_start: 0.6805 (mtt) cc_final: 0.6191 (mtm) REVERT: C 89 VAL cc_start: 0.8761 (t) cc_final: 0.8224 (t) REVERT: C 93 MET cc_start: 0.9064 (mtt) cc_final: 0.8741 (mtt) REVERT: C 122 PHE cc_start: 0.9124 (t80) cc_final: 0.8842 (t80) REVERT: C 124 TRP cc_start: 0.7640 (t60) cc_final: 0.6865 (t60) REVERT: C 226 GLU cc_start: 0.9252 (mm-30) cc_final: 0.8665 (pp20) REVERT: C 268 LEU cc_start: 0.8504 (tp) cc_final: 0.8203 (pp) REVERT: D 20 MET cc_start: 0.9480 (mmm) cc_final: 0.9199 (ptm) REVERT: D 25 ASN cc_start: 0.9513 (m-40) cc_final: 0.9204 (m110) REVERT: D 51 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8402 (mm-30) REVERT: D 56 MET cc_start: 0.9201 (mmp) cc_final: 0.8439 (ptp) REVERT: D 79 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7290 (mm-30) REVERT: D 109 PHE cc_start: 0.8356 (m-80) cc_final: 0.7874 (m-80) REVERT: D 154 PHE cc_start: 0.7829 (t80) cc_final: 0.7382 (t80) REVERT: D 157 MET cc_start: 0.6633 (ppp) cc_final: 0.6319 (ppp) REVERT: D 174 TYR cc_start: 0.8941 (t80) cc_final: 0.8505 (t80) REVERT: D 179 TYR cc_start: 0.8299 (t80) cc_final: 0.7983 (t80) REVERT: D 213 TYR cc_start: 0.6826 (t80) cc_final: 0.6393 (t80) REVERT: D 261 ARG cc_start: 0.7596 (ttm170) cc_final: 0.6635 (ptm160) REVERT: D 273 PHE cc_start: 0.6548 (m-80) cc_final: 0.5875 (m-10) outliers start: 42 outliers final: 35 residues processed: 528 average time/residue: 0.1235 time to fit residues: 97.5612 Evaluate side-chains 517 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 477 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 232 ASN 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 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 232 ASN Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 334 LYS 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 446 ARG Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP 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 59 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 51 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 191 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 174 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.132462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.092320 restraints weight = 32561.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.095402 restraints weight = 15187.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.097449 restraints weight = 9055.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.098791 restraints weight = 6300.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.099619 restraints weight = 4907.708| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 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 = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.6188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16299 Z= 0.183 Angle : 0.721 13.029 22004 Z= 0.371 Chirality : 0.046 0.267 2348 Planarity : 0.004 0.056 2812 Dihedral : 8.267 138.984 2216 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.80 % Allowed : 26.14 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.19), residues: 1928 helix: 0.95 (0.15), residues: 1140 sheet: -0.84 (0.40), residues: 148 loop : 0.37 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 261 TYR 0.037 0.002 TYR D 142 PHE 0.049 0.002 PHE D 227 TRP 0.044 0.002 TRP C 30 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00418 (16298) covalent geometry : angle 0.72110 (22004) hydrogen bonds : bond 0.04040 ( 896) hydrogen bonds : angle 5.20233 ( 2616) Misc. bond : bond 0.00012 ( 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 521 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 473 time to evaluate : 0.560 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 11 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8528 (mt0) REVERT: A 95 MET cc_start: 0.9068 (tpp) cc_final: 0.8865 (tpp) REVERT: A 106 LEU cc_start: 0.9443 (tp) cc_final: 0.9217 (tp) REVERT: A 119 GLU cc_start: 0.8495 (mp0) cc_final: 0.8011 (mp0) REVERT: A 181 ASP cc_start: 0.8735 (m-30) cc_final: 0.8430 (m-30) REVERT: A 214 LYS cc_start: 0.8333 (mmtm) cc_final: 0.7981 (mmtm) REVERT: A 256 ARG cc_start: 0.8978 (tpt90) cc_final: 0.8494 (tpt90) REVERT: A 286 ASP cc_start: 0.8101 (m-30) cc_final: 0.7829 (m-30) REVERT: A 317 MET cc_start: 0.8213 (mtt) cc_final: 0.7952 (mtt) REVERT: A 334 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.8424 (ptpt) REVERT: A 348 MET cc_start: 0.8914 (ttp) cc_final: 0.8618 (tmm) REVERT: A 350 ARG cc_start: 0.9007 (mtp85) cc_final: 0.8139 (mtp85) REVERT: A 362 ASP cc_start: 0.8408 (m-30) cc_final: 0.7417 (m-30) REVERT: A 393 SER cc_start: 0.8739 (m) cc_final: 0.8164 (p) REVERT: A 446 ARG cc_start: 0.7824 (mmp80) cc_final: 0.7213 (mmp-170) REVERT: A 453 ARG cc_start: 0.9220 (OUTLIER) cc_final: 0.8976 (ttt-90) REVERT: A 483 GLU cc_start: 0.8945 (mp0) cc_final: 0.8527 (pm20) REVERT: A 509 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8350 (tm-30) REVERT: A 570 MET cc_start: 0.8478 (mtp) cc_final: 0.8137 (mtm) REVERT: A 598 MET cc_start: 0.7954 (mtp) cc_final: 0.5820 (mtp) REVERT: A 599 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8325 (pt0) REVERT: A 637 VAL cc_start: 0.9438 (t) cc_final: 0.9164 (p) REVERT: A 686 ARG cc_start: 0.7616 (mtp85) cc_final: 0.6892 (mtp180) REVERT: B 78 LYS cc_start: 0.9151 (pttm) cc_final: 0.8735 (pttm) REVERT: B 95 MET cc_start: 0.9188 (tpp) cc_final: 0.8915 (tpp) REVERT: B 102 ASN cc_start: 0.9188 (m-40) cc_final: 0.8853 (m110) REVERT: B 172 LEU cc_start: 0.8875 (mp) cc_final: 0.8662 (mp) REVERT: B 179 LEU cc_start: 0.9467 (tp) cc_final: 0.9147 (tt) REVERT: B 184 ARG cc_start: 0.9132 (tpp-160) cc_final: 0.8905 (tpp80) REVERT: B 235 ARG cc_start: 0.8693 (ttp-110) cc_final: 0.8242 (mtm-85) REVERT: B 238 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7173 (t70) REVERT: B 250 TYR cc_start: 0.9210 (m-80) cc_final: 0.8879 (m-80) REVERT: B 274 ARG cc_start: 0.7072 (ttp-110) cc_final: 0.6482 (ttp-110) REVERT: B 317 MET cc_start: 0.8284 (mtm) cc_final: 0.7916 (mtt) REVERT: B 318 ASP cc_start: 0.8482 (t0) cc_final: 0.8152 (p0) REVERT: B 334 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8831 (ptpt) REVERT: B 466 MET cc_start: 0.8792 (ptt) cc_final: 0.8352 (ptp) REVERT: B 515 ASP cc_start: 0.9075 (m-30) cc_final: 0.8779 (m-30) REVERT: B 570 MET cc_start: 0.8517 (mtp) cc_final: 0.8239 (mtp) REVERT: B 578 ILE cc_start: 0.9168 (mt) cc_final: 0.8953 (mt) REVERT: B 586 TYR cc_start: 0.9076 (m-80) cc_final: 0.8807 (m-80) REVERT: B 588 GLN cc_start: 0.8833 (mm-40) cc_final: 0.7896 (mm-40) REVERT: B 599 GLU cc_start: 0.8622 (pm20) cc_final: 0.8386 (pm20) REVERT: B 602 GLU cc_start: 0.8598 (tp30) cc_final: 0.8022 (tp30) REVERT: B 610 LYS cc_start: 0.9019 (tppp) cc_final: 0.8771 (tppt) REVERT: B 639 ASP cc_start: 0.8500 (m-30) cc_final: 0.8008 (m-30) REVERT: B 686 ARG cc_start: 0.8064 (mmt180) cc_final: 0.7809 (mmt180) REVERT: C 74 MET cc_start: 0.7111 (mtt) cc_final: 0.6478 (mtm) REVERT: C 89 VAL cc_start: 0.8687 (t) cc_final: 0.8172 (t) REVERT: C 93 MET cc_start: 0.9104 (mtt) cc_final: 0.8715 (mtt) REVERT: C 122 PHE cc_start: 0.9103 (t80) cc_final: 0.8785 (t80) REVERT: C 158 VAL cc_start: 0.9571 (t) cc_final: 0.8879 (m) REVERT: C 162 TYR cc_start: 0.8830 (m-10) cc_final: 0.8322 (m-10) REVERT: C 204 TYR cc_start: 0.9187 (t80) cc_final: 0.8944 (t80) REVERT: C 226 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8628 (pp20) REVERT: D 20 MET cc_start: 0.9472 (mmm) cc_final: 0.9213 (ptm) REVERT: D 25 ASN cc_start: 0.9518 (m-40) cc_final: 0.9223 (m110) REVERT: D 51 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8461 (mm-30) REVERT: D 56 MET cc_start: 0.9219 (mmp) cc_final: 0.8474 (ptp) REVERT: D 79 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7284 (mm-30) REVERT: D 109 PHE cc_start: 0.8448 (m-80) cc_final: 0.7938 (m-80) REVERT: D 174 TYR cc_start: 0.8900 (t80) cc_final: 0.8528 (t80) REVERT: D 179 TYR cc_start: 0.8378 (t80) cc_final: 0.7994 (t80) REVERT: D 261 ARG cc_start: 0.7434 (ttm170) cc_final: 0.6910 (ptm160) REVERT: D 273 PHE cc_start: 0.6649 (m-80) cc_final: 0.6138 (m-10) REVERT: D 277 PHE cc_start: 0.4301 (m-80) cc_final: 0.3952 (m-80) outliers start: 48 outliers final: 35 residues processed: 501 average time/residue: 0.1238 time to fit residues: 92.1754 Evaluate side-chains 508 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 467 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 232 ASN 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 439 VAL 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 232 ASN Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 334 LYS 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 446 ARG Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 230 ASP 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 246 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 97 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 151 optimal weight: 20.0000 chunk 162 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 120 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.135066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.094868 restraints weight = 32704.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.098129 restraints weight = 15131.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.100233 restraints weight = 8885.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.101664 restraints weight = 6138.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.102494 restraints weight = 4776.338| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.6362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16299 Z= 0.155 Angle : 0.725 12.607 22004 Z= 0.370 Chirality : 0.046 0.270 2348 Planarity : 0.004 0.055 2812 Dihedral : 8.120 136.567 2216 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.98 % Allowed : 27.25 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.19), residues: 1928 helix: 0.87 (0.15), residues: 1157 sheet: -0.41 (0.42), residues: 128 loop : 0.14 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 261 TYR 0.041 0.002 TYR A 571 PHE 0.024 0.002 PHE D 172 TRP 0.050 0.002 TRP C 30 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00354 (16298) covalent geometry : angle 0.72453 (22004) hydrogen bonds : bond 0.04041 ( 896) hydrogen bonds : angle 5.21511 ( 2616) Misc. bond : bond 0.00005 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3285.58 seconds wall clock time: 57 minutes 43.96 seconds (3463.96 seconds total)