Starting phenix.real_space_refine on Thu Sep 18 09:42:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bx9_45000/09_2025/9bx9_45000_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bx9_45000/09_2025/9bx9_45000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bx9_45000/09_2025/9bx9_45000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bx9_45000/09_2025/9bx9_45000.map" model { file = "/net/cci-nas-00/data/ceres_data/9bx9_45000/09_2025/9bx9_45000_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bx9_45000/09_2025/9bx9_45000_neut.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.85, per 1000 atoms: 0.24 Number of scatterers: 15954 At special positions: 0 Unit cell: (93.002, 127.75, 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: 1.51 Conformation dependent library (CDL) restraints added in 706.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.59 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: 4.076A 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: 3.638A 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: 6.055A 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: 4.274A 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: 3.950A 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: 3.722A 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: 4.622A 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: 3.566A 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: 3.515A 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: 3.567A 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: 4.874A 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: 6.313A 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: 7.059A 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: 6.457A 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: 6.792A 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: 3.02 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4959 1.34 - 1.46: 2935 1.46 - 1.58: 8229 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 1.601 -0.061 1.25e-02 6.40e+03 2.36e+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 1.02e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.574 -0.032 1.08e-02 8.57e+03 8.54e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.569 -0.032 1.17e-02 7.31e+03 7.32e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.573 -0.033 1.25e-02 6.40e+03 6.88e+00 ... (remaining 16293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21498 2.09 - 4.18: 469 4.18 - 6.27: 33 6.27 - 8.36: 2 8.36 - 10.45: 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 110.54 116.58 -6.04 1.36e+00 5.41e-01 1.97e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.14 -4.43 1.15e+00 7.56e-01 1.48e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.83 -4.33 1.23e+00 6.61e-01 1.24e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.69 -3.98 1.15e+00 7.56e-01 1.20e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.52 3.67 1.06e+00 8.90e-01 1.20e+01 ... (remaining 21999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.31: 9427 34.31 - 68.62: 332 68.62 - 102.93: 47 102.93 - 137.23: 0 137.23 - 171.54: 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 301.68 130.14 171.54 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 301.68 135.73 165.95 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 -134.35 12.35 0 2.50e+00 1.60e-01 2.44e+01 ... (remaining 9805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2130 0.094 - 0.188: 179 0.188 - 0.282: 34 0.282 - 0.376: 3 0.376 - 0.470: 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 5.52e+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 4.55e+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 2.16 0.35 2.00e-01 2.50e+01 2.99e+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 5.53e-02 4.89e+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 2.76e+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 " -0.018 2.00e-02 2.50e+03 1.13e-02 2.22e+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 " -0.010 2.00e-02 2.50e+03 ... (remaining 2809 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 131 2.51 - 3.11: 11864 3.11 - 3.70: 26403 3.70 - 4.30: 41201 4.30 - 4.90: 64928 Nonbonded interactions: 144527 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.911 2.320 nonbonded pdb=" O1B TTP A 801 " pdb="MG MG A 802 " model vdw 1.918 2.170 nonbonded pdb=" O2A TTP B 801 " pdb="MG MG B 802 " model vdw 1.928 2.170 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 ... (remaining 144522 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 16.110 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 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 0.833 16299 Z= 0.724 Angle : 0.707 10.446 22004 Z= 0.453 Chirality : 0.059 0.470 2348 Planarity : 0.003 0.055 2812 Dihedral : 17.179 171.542 6120 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 17.14 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 0.021 0.002 TYR D 179 PHE 0.021 0.002 PHE C 168 TRP 0.008 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 0.70709 (22004) hydrogen bonds : bond 0.16168 ( 896) hydrogen bonds : angle 6.35121 ( 2616) Misc. bond : bond 0.83310 ( 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 718 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 694 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.7273 (p0) cc_final: 0.6877 (p0) REVERT: A 30 LYS cc_start: 0.8021 (tptt) cc_final: 0.7771 (tppt) REVERT: A 119 GLU cc_start: 0.7911 (mp0) cc_final: 0.7527 (mp0) REVERT: A 157 LEU cc_start: 0.9234 (tp) cc_final: 0.8950 (tt) REVERT: A 177 ASP cc_start: 0.8784 (t0) cc_final: 0.8268 (t0) REVERT: A 179 LEU cc_start: 0.9223 (tp) cc_final: 0.8934 (tp) REVERT: A 188 ILE cc_start: 0.9187 (mt) cc_final: 0.8972 (mt) REVERT: A 232 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8385 (m-40) REVERT: A 240 MET cc_start: 0.5912 (tpt) cc_final: 0.5632 (tpt) REVERT: A 262 LEU cc_start: 0.8711 (mt) cc_final: 0.8291 (mt) REVERT: A 362 ASP cc_start: 0.6953 (m-30) cc_final: 0.6564 (m-30) REVERT: A 379 SER cc_start: 0.9068 (t) cc_final: 0.8362 (t) REVERT: A 447 ASN cc_start: 0.8098 (m-40) cc_final: 0.7889 (m-40) REVERT: A 458 MET cc_start: 0.8982 (mmm) cc_final: 0.8567 (mmt) REVERT: A 494 MET cc_start: 0.7915 (mtp) cc_final: 0.7678 (mtp) REVERT: A 584 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8550 (tp) REVERT: A 591 THR cc_start: 0.9175 (p) cc_final: 0.8844 (m) REVERT: A 597 ILE cc_start: 0.9307 (pt) cc_final: 0.9059 (pt) REVERT: A 598 MET cc_start: 0.7733 (mtm) cc_final: 0.7475 (mtm) REVERT: A 654 PHE cc_start: 0.8807 (t80) cc_final: 0.8465 (t80) REVERT: B 104 TYR cc_start: 0.7947 (m-80) cc_final: 0.7482 (m-80) REVERT: B 172 LEU cc_start: 0.9169 (mp) cc_final: 0.8672 (mp) REVERT: B 177 ASP cc_start: 0.8208 (t0) cc_final: 0.7740 (t0) REVERT: B 362 ASP cc_start: 0.7489 (m-30) cc_final: 0.6736 (m-30) REVERT: B 425 ILE cc_start: 0.8789 (mt) cc_final: 0.8575 (mt) REVERT: B 494 MET cc_start: 0.7901 (mtp) cc_final: 0.7694 (mtm) REVERT: B 496 ASN cc_start: 0.9058 (t0) cc_final: 0.8828 (t0) REVERT: B 501 GLN cc_start: 0.8121 (tt0) cc_final: 0.7812 (tt0) REVERT: B 550 MET cc_start: 0.8658 (ttm) cc_final: 0.8132 (mtm) REVERT: B 612 TYR cc_start: 0.7092 (m-80) cc_final: 0.6643 (m-80) REVERT: C 137 MET cc_start: -0.1844 (mtp) cc_final: -0.3139 (mmm) REVERT: C 287 LEU cc_start: -0.0458 (OUTLIER) cc_final: -0.1105 (tp) REVERT: D 137 MET cc_start: -0.1438 (mtp) cc_final: -0.3367 (mmt) REVERT: D 282 ILE cc_start: -0.0509 (OUTLIER) cc_final: -0.1113 (mt) outliers start: 24 outliers final: 5 residues processed: 712 average time/residue: 0.1459 time to fit residues: 151.0010 Evaluate side-chains 456 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 447 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 14 ASN A 320 ASN A 370 ASN A 645 GLN A 668 ASN B 14 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 418 ASN B 646 GLN C 19 GLN C 28 GLN C 91 ASN C 216 GLN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 146 GLN D 233 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.165942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.100208 restraints weight = 29644.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.103571 restraints weight = 13999.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.105742 restraints weight = 8593.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.107144 restraints weight = 6175.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.108059 restraints weight = 4907.755| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16299 Z= 0.277 Angle : 0.662 10.587 22004 Z= 0.358 Chirality : 0.044 0.212 2348 Planarity : 0.004 0.051 2812 Dihedral : 9.491 167.480 2232 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.38 % Allowed : 15.23 % Favored : 81.39 % 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: 1.71 (0.19), residues: 1928 helix: 1.62 (0.15), residues: 1128 sheet: 0.15 (0.40), residues: 136 loop : 0.71 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 293 TYR 0.018 0.002 TYR C 22 PHE 0.029 0.002 PHE A 261 TRP 0.019 0.003 TRP D 124 HIS 0.007 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00612 (16298) covalent geometry : angle 0.66239 (22004) hydrogen bonds : bond 0.04754 ( 896) hydrogen bonds : angle 5.08036 ( 2616) Misc. bond : bond 0.00007 ( 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 521 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 463 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: A 119 GLU cc_start: 0.8845 (mp0) cc_final: 0.8532 (mp0) REVERT: A 148 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8441 (mt-10) REVERT: A 174 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8067 (mm-30) REVERT: A 177 ASP cc_start: 0.8984 (t0) cc_final: 0.8662 (t0) REVERT: A 250 TYR cc_start: 0.8873 (m-80) cc_final: 0.8122 (m-80) REVERT: A 362 ASP cc_start: 0.7773 (m-30) cc_final: 0.7132 (m-30) REVERT: A 379 SER cc_start: 0.8867 (t) cc_final: 0.8167 (t) REVERT: A 493 MET cc_start: 0.9219 (tmm) cc_final: 0.8688 (tmm) REVERT: A 494 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8903 (mtp) REVERT: A 584 ILE cc_start: 0.9477 (tp) cc_final: 0.9238 (tp) REVERT: A 686 ARG cc_start: 0.8078 (mmt-90) cc_final: 0.7712 (mtt90) REVERT: B 104 TYR cc_start: 0.8904 (m-80) cc_final: 0.8154 (m-80) REVERT: B 109 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8469 (m-40) REVERT: B 177 ASP cc_start: 0.8336 (t0) cc_final: 0.7877 (t0) REVERT: B 181 ASP cc_start: 0.8769 (m-30) cc_final: 0.8527 (m-30) REVERT: B 276 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8632 (mmtm) REVERT: B 286 ASP cc_start: 0.7849 (m-30) cc_final: 0.7551 (m-30) REVERT: B 334 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8942 (pttm) REVERT: B 362 ASP cc_start: 0.8419 (m-30) cc_final: 0.8071 (m-30) REVERT: B 586 TYR cc_start: 0.8770 (m-80) cc_final: 0.8537 (m-80) REVERT: B 612 TYR cc_start: 0.8417 (m-80) cc_final: 0.7773 (m-80) REVERT: B 640 MET cc_start: 0.9018 (tpp) cc_final: 0.8642 (tpp) REVERT: C 137 MET cc_start: -0.4959 (mtp) cc_final: -0.5431 (mmm) REVERT: C 205 VAL cc_start: 0.4232 (t) cc_final: 0.3651 (m) REVERT: C 235 LEU cc_start: 0.7735 (mt) cc_final: 0.7519 (mt) REVERT: C 287 LEU cc_start: 0.0101 (OUTLIER) cc_final: -0.0582 (tp) REVERT: D 110 MET cc_start: 0.5161 (mtt) cc_final: 0.4717 (tmm) REVERT: D 185 MET cc_start: 0.6114 (mmm) cc_final: 0.5718 (mmm) outliers start: 58 outliers final: 35 residues processed: 498 average time/residue: 0.1345 time to fit residues: 100.3464 Evaluate side-chains 420 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 380 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 433 THR 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 494 MET Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 181 optimal weight: 30.0000 chunk 149 optimal weight: 6.9990 chunk 125 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 156 optimal weight: 9.9990 chunk 168 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 239 GLN A 370 ASN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN B 646 GLN ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 25 ASN C 84 HIS D 71 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.168003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.101903 restraints weight = 29856.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.105485 restraints weight = 13853.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107697 restraints weight = 8402.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.109085 restraints weight = 5982.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.109986 restraints weight = 4677.932| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16299 Z= 0.155 Angle : 0.582 6.570 22004 Z= 0.310 Chirality : 0.041 0.156 2348 Planarity : 0.003 0.048 2812 Dihedral : 8.997 156.253 2225 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.86 % Allowed : 18.09 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.75 (0.19), residues: 1928 helix: 1.69 (0.15), residues: 1130 sheet: 0.37 (0.40), residues: 134 loop : 0.60 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 331 TYR 0.020 0.001 TYR C 22 PHE 0.022 0.001 PHE A 261 TRP 0.024 0.002 TRP D 124 HIS 0.005 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00345 (16298) covalent geometry : angle 0.58158 (22004) hydrogen bonds : bond 0.04195 ( 896) hydrogen bonds : angle 4.87614 ( 2616) Misc. bond : bond 0.00016 ( 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 500 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 451 time to evaluate : 0.638 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: A 30 LYS cc_start: 0.9323 (tppt) cc_final: 0.8978 (tppt) REVERT: A 119 GLU cc_start: 0.8843 (mp0) cc_final: 0.8524 (mp0) REVERT: A 157 LEU cc_start: 0.9350 (tp) cc_final: 0.9117 (tp) REVERT: A 174 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8092 (mm-30) REVERT: A 177 ASP cc_start: 0.8909 (t0) cc_final: 0.8573 (t0) REVERT: A 232 ASN cc_start: 0.9104 (OUTLIER) cc_final: 0.8658 (m-40) REVERT: A 250 TYR cc_start: 0.8904 (m-80) cc_final: 0.8177 (m-80) REVERT: A 362 ASP cc_start: 0.7884 (m-30) cc_final: 0.7425 (m-30) REVERT: A 379 SER cc_start: 0.9033 (t) cc_final: 0.8347 (t) REVERT: A 437 THR cc_start: 0.9608 (m) cc_final: 0.9253 (p) REVERT: A 493 MET cc_start: 0.9255 (tmm) cc_final: 0.8610 (tmm) REVERT: A 686 ARG cc_start: 0.8085 (mmt-90) cc_final: 0.7805 (mtt90) REVERT: B 8 LYS cc_start: 0.8727 (tppt) cc_final: 0.8512 (tppt) REVERT: B 135 GLU cc_start: 0.8303 (mp0) cc_final: 0.8024 (mp0) REVERT: B 147 GLN cc_start: 0.9217 (mt0) cc_final: 0.8855 (mm-40) REVERT: B 276 LYS cc_start: 0.8805 (mtmm) cc_final: 0.8598 (mmtm) REVERT: B 286 ASP cc_start: 0.7800 (m-30) cc_final: 0.7587 (m-30) REVERT: B 290 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7808 (tm-30) REVERT: B 334 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8931 (pttm) REVERT: B 362 ASP cc_start: 0.8348 (m-30) cc_final: 0.7965 (m-30) REVERT: B 483 GLU cc_start: 0.8773 (mp0) cc_final: 0.8218 (pm20) REVERT: B 526 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7494 (tp30) REVERT: B 586 TYR cc_start: 0.8659 (m-80) cc_final: 0.8260 (m-80) REVERT: B 634 MET cc_start: 0.9128 (mmm) cc_final: 0.8900 (mmt) REVERT: B 640 MET cc_start: 0.9017 (tpp) cc_final: 0.8594 (tpp) REVERT: C 74 MET cc_start: 0.8250 (mmm) cc_final: 0.7796 (mtm) REVERT: C 137 MET cc_start: -0.4649 (mtp) cc_final: -0.5491 (mmm) REVERT: C 235 LEU cc_start: 0.7875 (mt) cc_final: 0.7530 (mt) REVERT: C 287 LEU cc_start: 0.0363 (OUTLIER) cc_final: -0.0011 (tp) REVERT: D 110 MET cc_start: 0.5313 (mtt) cc_final: 0.4954 (tmm) REVERT: D 137 MET cc_start: -0.6356 (ptp) cc_final: -0.7355 (tpp) REVERT: D 185 MET cc_start: 0.6383 (mmm) cc_final: 0.6032 (mmm) outliers start: 49 outliers final: 32 residues processed: 473 average time/residue: 0.1342 time to fit residues: 95.0102 Evaluate side-chains 443 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 408 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 435 SER 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 598 MET Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 147 optimal weight: 20.0000 chunk 132 optimal weight: 0.6980 chunk 185 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 172 optimal weight: 30.0000 chunk 134 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN D 28 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.166827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.100906 restraints weight = 29866.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.104352 restraints weight = 13976.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.106496 restraints weight = 8516.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.107901 restraints weight = 6065.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.108790 restraints weight = 4776.900| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16299 Z= 0.176 Angle : 0.569 7.774 22004 Z= 0.306 Chirality : 0.042 0.218 2348 Planarity : 0.003 0.053 2812 Dihedral : 8.826 150.224 2224 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.21 % Allowed : 18.90 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.68 (0.19), residues: 1928 helix: 1.67 (0.15), residues: 1132 sheet: -0.07 (0.40), residues: 140 loop : 0.58 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 121 TYR 0.035 0.001 TYR D 142 PHE 0.020 0.001 PHE A 261 TRP 0.028 0.002 TRP D 124 HIS 0.004 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00393 (16298) covalent geometry : angle 0.56908 (22004) hydrogen bonds : bond 0.03934 ( 896) hydrogen bonds : angle 4.85037 ( 2616) Misc. bond : bond 0.00030 ( 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 471 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 416 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.9354 (tppt) cc_final: 0.8991 (tppt) REVERT: A 119 GLU cc_start: 0.8855 (mp0) cc_final: 0.8514 (mp0) REVERT: A 157 LEU cc_start: 0.9321 (tp) cc_final: 0.8910 (tp) REVERT: A 161 ARG cc_start: 0.7796 (ttm170) cc_final: 0.7419 (mtm180) REVERT: A 232 ASN cc_start: 0.9010 (OUTLIER) cc_final: 0.8290 (m-40) REVERT: A 250 TYR cc_start: 0.8895 (m-80) cc_final: 0.8223 (m-80) REVERT: A 334 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8563 (ptpt) REVERT: A 362 ASP cc_start: 0.7818 (m-30) cc_final: 0.7617 (m-30) REVERT: A 379 SER cc_start: 0.8991 (t) cc_final: 0.8369 (t) REVERT: A 493 MET cc_start: 0.9272 (tmm) cc_final: 0.8556 (tmm) REVERT: A 686 ARG cc_start: 0.8061 (mmt-90) cc_final: 0.7709 (mtt90) REVERT: B 135 GLU cc_start: 0.8288 (mp0) cc_final: 0.7911 (mp0) REVERT: B 286 ASP cc_start: 0.7823 (m-30) cc_final: 0.7615 (m-30) REVERT: B 348 MET cc_start: 0.8156 (tmm) cc_final: 0.7925 (tmm) REVERT: B 362 ASP cc_start: 0.8325 (m-30) cc_final: 0.8006 (m-30) REVERT: B 483 GLU cc_start: 0.8759 (mp0) cc_final: 0.8237 (pm20) REVERT: B 494 MET cc_start: 0.8878 (mtp) cc_final: 0.8559 (mtp) REVERT: B 526 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7424 (tp30) REVERT: B 590 SER cc_start: 0.9566 (p) cc_final: 0.9304 (t) REVERT: B 640 MET cc_start: 0.9004 (tpp) cc_final: 0.8598 (tpp) REVERT: C 137 MET cc_start: -0.4805 (mtp) cc_final: -0.5666 (mmm) REVERT: C 231 LEU cc_start: 0.1602 (OUTLIER) cc_final: 0.1080 (pp) REVERT: C 287 LEU cc_start: 0.0740 (OUTLIER) cc_final: 0.0184 (tp) REVERT: D 110 MET cc_start: 0.5550 (mtt) cc_final: 0.4967 (tmm) REVERT: D 137 MET cc_start: -0.6322 (ptp) cc_final: -0.7393 (tpp) REVERT: D 185 MET cc_start: 0.6700 (mmm) cc_final: 0.6446 (mmm) outliers start: 55 outliers final: 34 residues processed: 443 average time/residue: 0.1331 time to fit residues: 89.2006 Evaluate side-chains 425 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 387 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 66 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 191 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 164 optimal weight: 20.0000 chunk 189 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 145 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** D 91 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 = 0.3968 r_free = 0.3968 target = 0.166119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.100125 restraints weight = 30066.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.103613 restraints weight = 14064.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.105750 restraints weight = 8552.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.106969 restraints weight = 6044.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.107935 restraints weight = 4896.460| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16299 Z= 0.213 Angle : 0.595 9.922 22004 Z= 0.317 Chirality : 0.042 0.165 2348 Planarity : 0.004 0.056 2812 Dihedral : 8.886 148.922 2224 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.38 % Allowed : 20.19 % Favored : 76.43 % 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: 1.52 (0.19), residues: 1928 helix: 1.55 (0.15), residues: 1130 sheet: -0.50 (0.40), residues: 146 loop : 0.60 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 274 TYR 0.017 0.001 TYR D 142 PHE 0.019 0.002 PHE A 261 TRP 0.026 0.002 TRP D 124 HIS 0.004 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00476 (16298) covalent geometry : angle 0.59504 (22004) hydrogen bonds : bond 0.03973 ( 896) hydrogen bonds : angle 4.86020 ( 2616) Misc. bond : bond 0.00080 ( 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 448 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 390 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.9369 (tppt) cc_final: 0.9000 (tppt) REVERT: A 119 GLU cc_start: 0.8849 (mp0) cc_final: 0.8483 (mp0) REVERT: A 178 SER cc_start: 0.9193 (OUTLIER) cc_final: 0.8864 (p) REVERT: A 250 TYR cc_start: 0.8911 (m-80) cc_final: 0.8147 (m-80) REVERT: A 274 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7648 (tpp-160) REVERT: A 334 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8627 (ptpt) REVERT: A 379 SER cc_start: 0.8955 (t) cc_final: 0.8299 (t) REVERT: A 384 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.6836 (pm20) REVERT: A 493 MET cc_start: 0.9273 (tmm) cc_final: 0.8551 (tmm) REVERT: A 657 PHE cc_start: 0.9100 (m-80) cc_final: 0.8808 (m-80) REVERT: A 686 ARG cc_start: 0.8072 (mmt-90) cc_final: 0.7697 (mtt90) REVERT: B 104 TYR cc_start: 0.8996 (m-80) cc_final: 0.8139 (m-80) REVERT: B 111 LYS cc_start: 0.9169 (mppt) cc_final: 0.8904 (mppt) REVERT: B 135 GLU cc_start: 0.8305 (mp0) cc_final: 0.7959 (mp0) REVERT: B 148 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8529 (mt-10) REVERT: B 232 ASN cc_start: 0.9025 (OUTLIER) cc_final: 0.8781 (m-40) REVERT: B 276 LYS cc_start: 0.8842 (mtmm) cc_final: 0.8606 (mmtm) REVERT: B 317 MET cc_start: 0.8566 (mtt) cc_final: 0.8365 (mtt) REVERT: B 362 ASP cc_start: 0.8334 (m-30) cc_final: 0.7891 (m-30) REVERT: B 415 ASN cc_start: 0.9423 (t0) cc_final: 0.9126 (t0) REVERT: B 420 MET cc_start: 0.9151 (mmm) cc_final: 0.8784 (mmm) REVERT: B 526 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7462 (tp30) REVERT: B 588 GLN cc_start: 0.9238 (mm-40) cc_final: 0.8926 (mt0) REVERT: B 640 MET cc_start: 0.8983 (tpp) cc_final: 0.8548 (tpp) REVERT: C 95 MET cc_start: 0.8648 (tmm) cc_final: 0.8085 (ptt) REVERT: C 129 LYS cc_start: 0.7688 (tptp) cc_final: 0.6648 (ptmt) REVERT: C 231 LEU cc_start: 0.1643 (OUTLIER) cc_final: 0.1139 (pp) REVERT: C 287 LEU cc_start: 0.0748 (OUTLIER) cc_final: 0.0263 (tp) REVERT: D 110 MET cc_start: 0.5529 (mtt) cc_final: 0.5102 (tmm) REVERT: D 137 MET cc_start: -0.6283 (ptp) cc_final: -0.6555 (mmt) REVERT: D 185 MET cc_start: 0.6642 (mmm) cc_final: 0.6057 (mmm) outliers start: 58 outliers final: 40 residues processed: 420 average time/residue: 0.1397 time to fit residues: 87.1781 Evaluate side-chains 419 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 372 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 92 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.170363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.104867 restraints weight = 29688.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108386 restraints weight = 13704.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110556 restraints weight = 8199.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.111798 restraints weight = 5805.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.112764 restraints weight = 4568.493| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16299 Z= 0.131 Angle : 0.562 10.749 22004 Z= 0.296 Chirality : 0.041 0.165 2348 Planarity : 0.003 0.056 2812 Dihedral : 8.616 143.320 2224 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.57 % Allowed : 20.71 % Favored : 76.72 % 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: 1.50 (0.19), residues: 1928 helix: 1.59 (0.15), residues: 1131 sheet: -0.42 (0.39), residues: 144 loop : 0.44 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 225 TYR 0.016 0.001 TYR D 142 PHE 0.018 0.001 PHE A 261 TRP 0.024 0.001 TRP D 124 HIS 0.004 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00291 (16298) covalent geometry : angle 0.56206 (22004) hydrogen bonds : bond 0.03677 ( 896) hydrogen bonds : angle 4.76685 ( 2616) Misc. bond : bond 0.00014 ( 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 469 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 425 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.9324 (tppt) cc_final: 0.8987 (tppt) REVERT: A 119 GLU cc_start: 0.8756 (mp0) cc_final: 0.8424 (mp0) REVERT: A 178 SER cc_start: 0.9193 (OUTLIER) cc_final: 0.8856 (p) REVERT: A 250 TYR cc_start: 0.8792 (m-80) cc_final: 0.8174 (m-80) REVERT: A 274 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7700 (tpp-160) REVERT: A 334 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8591 (ptpt) REVERT: A 379 SER cc_start: 0.9083 (t) cc_final: 0.8357 (t) REVERT: A 384 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.6710 (pm20) REVERT: A 446 ARG cc_start: 0.7890 (mtp85) cc_final: 0.7665 (mmm160) REVERT: A 493 MET cc_start: 0.9285 (tmm) cc_final: 0.8609 (tmm) REVERT: A 586 TYR cc_start: 0.8816 (m-10) cc_final: 0.8522 (m-10) REVERT: A 640 MET cc_start: 0.9237 (tpp) cc_final: 0.8896 (tpp) REVERT: B 104 TYR cc_start: 0.8939 (m-80) cc_final: 0.8121 (m-80) REVERT: B 111 LYS cc_start: 0.9073 (mppt) cc_final: 0.8866 (mppt) REVERT: B 148 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8481 (mt-10) REVERT: B 274 ARG cc_start: 0.7818 (tpp80) cc_final: 0.7496 (ttm-80) REVERT: B 317 MET cc_start: 0.8595 (mtt) cc_final: 0.8373 (mtt) REVERT: B 483 GLU cc_start: 0.8747 (mp0) cc_final: 0.8283 (pm20) REVERT: B 526 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7376 (tp30) REVERT: B 588 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8830 (mt0) REVERT: B 640 MET cc_start: 0.8999 (tpp) cc_final: 0.8544 (tpp) REVERT: B 668 ASN cc_start: 0.9046 (m-40) cc_final: 0.8803 (m-40) REVERT: C 129 LYS cc_start: 0.7662 (tptp) cc_final: 0.6654 (ptmt) REVERT: C 197 ASP cc_start: 0.6828 (OUTLIER) cc_final: 0.6328 (p0) REVERT: C 231 LEU cc_start: 0.1832 (OUTLIER) cc_final: 0.1423 (pp) REVERT: C 287 LEU cc_start: 0.0690 (OUTLIER) cc_final: 0.0272 (tp) REVERT: D 72 THR cc_start: 0.7341 (OUTLIER) cc_final: 0.6542 (t) REVERT: D 110 MET cc_start: 0.5473 (mtt) cc_final: 0.5059 (tmm) REVERT: D 132 GLN cc_start: 0.2933 (OUTLIER) cc_final: 0.2705 (mp-120) REVERT: D 137 MET cc_start: -0.5879 (ptp) cc_final: -0.6650 (mmt) REVERT: D 185 MET cc_start: 0.6340 (mmm) cc_final: 0.6049 (mmm) outliers start: 44 outliers final: 25 residues processed: 451 average time/residue: 0.1370 time to fit residues: 92.2559 Evaluate side-chains 406 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 372 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 2 optimal weight: 3.9990 chunk 165 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 147 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.168731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.103850 restraints weight = 29667.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.107345 restraints weight = 13873.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.109446 restraints weight = 8338.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.110819 restraints weight = 5846.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.111698 restraints weight = 4579.847| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16299 Z= 0.176 Angle : 0.608 11.720 22004 Z= 0.316 Chirality : 0.043 0.189 2348 Planarity : 0.004 0.053 2812 Dihedral : 8.640 145.315 2220 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.51 % Allowed : 20.77 % Favored : 76.72 % 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: 1.46 (0.19), residues: 1928 helix: 1.57 (0.15), residues: 1121 sheet: -0.42 (0.40), residues: 144 loop : 0.41 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 274 TYR 0.025 0.001 TYR D 105 PHE 0.019 0.001 PHE A 492 TRP 0.016 0.002 TRP D 124 HIS 0.014 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00398 (16298) covalent geometry : angle 0.60784 (22004) hydrogen bonds : bond 0.03772 ( 896) hydrogen bonds : angle 4.79403 ( 2616) Misc. bond : bond 0.00045 ( 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 424 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 381 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.9353 (tppt) cc_final: 0.9014 (tppt) REVERT: A 119 GLU cc_start: 0.8777 (mp0) cc_final: 0.8390 (mp0) REVERT: A 161 ARG cc_start: 0.7716 (ttm170) cc_final: 0.7278 (mtm180) REVERT: A 178 SER cc_start: 0.9174 (OUTLIER) cc_final: 0.8838 (p) REVERT: A 240 MET cc_start: 0.6969 (tpp) cc_final: 0.6758 (tpp) REVERT: A 250 TYR cc_start: 0.8855 (m-80) cc_final: 0.8256 (m-80) REVERT: A 274 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7777 (tpp-160) REVERT: A 379 SER cc_start: 0.9035 (t) cc_final: 0.8412 (t) REVERT: A 384 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.6560 (pm20) REVERT: A 493 MET cc_start: 0.9307 (tmm) cc_final: 0.8576 (tmm) REVERT: A 586 TYR cc_start: 0.8836 (m-10) cc_final: 0.8580 (m-10) REVERT: A 657 PHE cc_start: 0.9000 (m-80) cc_final: 0.8772 (m-80) REVERT: B 104 TYR cc_start: 0.8962 (m-80) cc_final: 0.8193 (m-80) REVERT: B 148 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8488 (mt-10) REVERT: B 274 ARG cc_start: 0.7650 (tpp80) cc_final: 0.7253 (ttm-80) REVERT: B 406 ASP cc_start: 0.7978 (m-30) cc_final: 0.7571 (t0) REVERT: B 483 GLU cc_start: 0.8765 (mp0) cc_final: 0.8439 (pm20) REVERT: B 526 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7136 (tp30) REVERT: B 529 ASP cc_start: 0.7998 (m-30) cc_final: 0.6917 (m-30) REVERT: B 588 GLN cc_start: 0.9192 (mm-40) cc_final: 0.8905 (mt0) REVERT: B 640 MET cc_start: 0.8965 (tpp) cc_final: 0.8549 (tpp) REVERT: C 231 LEU cc_start: 0.1469 (OUTLIER) cc_final: 0.1088 (pp) REVERT: C 287 LEU cc_start: 0.0466 (OUTLIER) cc_final: 0.0097 (tp) REVERT: D 110 MET cc_start: 0.5356 (mtt) cc_final: 0.4935 (tmm) REVERT: D 132 GLN cc_start: 0.3435 (OUTLIER) cc_final: 0.3127 (mp10) REVERT: D 137 MET cc_start: -0.5897 (ptp) cc_final: -0.6710 (mmt) outliers start: 43 outliers final: 31 residues processed: 408 average time/residue: 0.1347 time to fit residues: 82.5114 Evaluate side-chains 401 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 364 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 138 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 184 optimal weight: 0.9980 chunk 167 optimal weight: 20.0000 chunk 154 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 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 = 0.3985 r_free = 0.3985 target = 0.168563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.104890 restraints weight = 29934.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.108493 restraints weight = 13770.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110423 restraints weight = 8251.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.111793 restraints weight = 5716.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.112702 restraints weight = 4511.843| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 16299 Z= 0.165 Angle : 0.611 13.151 22004 Z= 0.318 Chirality : 0.042 0.258 2348 Planarity : 0.003 0.052 2812 Dihedral : 8.514 140.845 2219 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.63 % Allowed : 21.30 % Favored : 76.08 % 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: 1.39 (0.19), residues: 1928 helix: 1.54 (0.15), residues: 1120 sheet: -0.45 (0.41), residues: 144 loop : 0.35 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 225 TYR 0.040 0.001 TYR C 204 PHE 0.019 0.001 PHE A 492 TRP 0.015 0.002 TRP D 124 HIS 0.011 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00372 (16298) covalent geometry : angle 0.61109 (22004) hydrogen bonds : bond 0.03758 ( 896) hydrogen bonds : angle 4.85974 ( 2616) Misc. bond : bond 0.00057 ( 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 423 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 378 time to evaluate : 0.646 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: A 119 GLU cc_start: 0.8748 (mp0) cc_final: 0.8357 (mp0) REVERT: A 178 SER cc_start: 0.9192 (OUTLIER) cc_final: 0.8831 (p) REVERT: A 240 MET cc_start: 0.6976 (tpp) cc_final: 0.6717 (tpp) REVERT: A 250 TYR cc_start: 0.8805 (m-80) cc_final: 0.8211 (m-80) REVERT: A 274 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7812 (tpp-160) REVERT: A 290 GLU cc_start: 0.8419 (pp20) cc_final: 0.8214 (pp20) REVERT: A 334 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8578 (ptpt) REVERT: A 379 SER cc_start: 0.9065 (t) cc_final: 0.8434 (t) REVERT: A 384 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.6481 (pm20) REVERT: A 406 ASP cc_start: 0.8087 (m-30) cc_final: 0.7743 (t0) REVERT: A 433 THR cc_start: 0.9678 (m) cc_final: 0.9382 (p) REVERT: A 493 MET cc_start: 0.9295 (tmm) cc_final: 0.8577 (tmm) REVERT: A 586 TYR cc_start: 0.8833 (m-10) cc_final: 0.8587 (m-10) REVERT: B 104 TYR cc_start: 0.8967 (m-80) cc_final: 0.8199 (m-80) REVERT: B 148 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8464 (mt-10) REVERT: B 172 LEU cc_start: 0.9124 (mt) cc_final: 0.7965 (mt) REVERT: B 274 ARG cc_start: 0.7729 (tpp80) cc_final: 0.7318 (ttm-80) REVERT: B 406 ASP cc_start: 0.7961 (m-30) cc_final: 0.7538 (t0) REVERT: B 526 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7153 (tp30) REVERT: B 529 ASP cc_start: 0.8003 (m-30) cc_final: 0.6908 (m-30) REVERT: B 588 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8928 (mt0) REVERT: B 640 MET cc_start: 0.8974 (tpp) cc_final: 0.8556 (tpp) REVERT: C 20 MET cc_start: 0.7432 (ppp) cc_final: 0.7226 (ppp) REVERT: C 231 LEU cc_start: 0.1504 (OUTLIER) cc_final: 0.1076 (pp) REVERT: C 287 LEU cc_start: 0.0417 (OUTLIER) cc_final: 0.0055 (tp) REVERT: D 110 MET cc_start: 0.5283 (mtt) cc_final: 0.4847 (tmm) REVERT: D 132 GLN cc_start: 0.3572 (OUTLIER) cc_final: 0.3217 (mp-120) outliers start: 45 outliers final: 31 residues processed: 407 average time/residue: 0.1349 time to fit residues: 82.6046 Evaluate side-chains 400 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 362 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 76 optimal weight: 0.0870 chunk 68 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.170592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.105944 restraints weight = 30084.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.110355 restraints weight = 14952.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.111391 restraints weight = 8764.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112960 restraints weight = 6719.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.113647 restraints weight = 5041.607| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 16299 Z= 0.140 Angle : 0.622 11.620 22004 Z= 0.323 Chirality : 0.043 0.311 2348 Planarity : 0.004 0.051 2812 Dihedral : 8.402 137.749 2219 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.10 % Allowed : 22.29 % Favored : 75.61 % 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: 1.34 (0.19), residues: 1928 helix: 1.48 (0.15), residues: 1128 sheet: -0.23 (0.42), residues: 138 loop : 0.27 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 225 TYR 0.029 0.001 TYR D 142 PHE 0.019 0.001 PHE A 492 TRP 0.024 0.002 TRP D 124 HIS 0.009 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00314 (16298) covalent geometry : angle 0.62196 (22004) hydrogen bonds : bond 0.03691 ( 896) hydrogen bonds : angle 4.87564 ( 2616) Misc. bond : bond 0.00657 ( 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 419 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 383 time to evaluate : 0.648 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: A 119 GLU cc_start: 0.8696 (mp0) cc_final: 0.8324 (mp0) REVERT: A 161 ARG cc_start: 0.7885 (ttm170) cc_final: 0.7416 (mtm180) REVERT: A 173 LEU cc_start: 0.9620 (mt) cc_final: 0.9367 (mt) REVERT: A 178 SER cc_start: 0.9217 (OUTLIER) cc_final: 0.8869 (p) REVERT: A 250 TYR cc_start: 0.8756 (m-80) cc_final: 0.8215 (m-80) REVERT: A 274 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7823 (tpp-160) REVERT: A 334 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8596 (ptpt) REVERT: A 379 SER cc_start: 0.9118 (t) cc_final: 0.8431 (t) REVERT: A 384 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.6544 (pm20) REVERT: A 393 SER cc_start: 0.9057 (t) cc_final: 0.8574 (p) REVERT: A 406 ASP cc_start: 0.8018 (m-30) cc_final: 0.7772 (t0) REVERT: A 433 THR cc_start: 0.9647 (m) cc_final: 0.9363 (p) REVERT: A 493 MET cc_start: 0.9273 (tmm) cc_final: 0.8586 (tmm) REVERT: A 586 TYR cc_start: 0.8760 (m-10) cc_final: 0.8526 (m-10) REVERT: A 588 GLN cc_start: 0.9353 (tp40) cc_final: 0.9142 (tp40) REVERT: B 104 TYR cc_start: 0.8959 (m-80) cc_final: 0.8163 (m-80) REVERT: B 274 ARG cc_start: 0.7856 (tpp80) cc_final: 0.7470 (ttm-80) REVERT: B 406 ASP cc_start: 0.7931 (m-30) cc_final: 0.7538 (t0) REVERT: B 483 GLU cc_start: 0.8763 (mp0) cc_final: 0.8417 (pm20) REVERT: B 529 ASP cc_start: 0.7943 (m-30) cc_final: 0.6801 (m-30) REVERT: B 640 MET cc_start: 0.8944 (tpp) cc_final: 0.8514 (tpp) REVERT: C 231 LEU cc_start: 0.1431 (OUTLIER) cc_final: 0.1078 (pp) REVERT: C 287 LEU cc_start: 0.0434 (OUTLIER) cc_final: 0.0178 (tp) REVERT: D 110 MET cc_start: 0.5326 (mtt) cc_final: 0.4958 (tmm) outliers start: 36 outliers final: 29 residues processed: 406 average time/residue: 0.1382 time to fit residues: 83.5025 Evaluate side-chains 401 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 366 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 51 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 191 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 chunk 57 optimal weight: 0.3980 chunk 121 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.171552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.108183 restraints weight = 30047.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.112636 restraints weight = 14937.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.113745 restraints weight = 8122.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.115233 restraints weight = 6729.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.115910 restraints weight = 4892.263| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.5704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 16299 Z= 0.134 Angle : 0.649 11.196 22004 Z= 0.333 Chirality : 0.043 0.337 2348 Planarity : 0.004 0.053 2812 Dihedral : 8.222 136.159 2219 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.75 % Allowed : 22.81 % Favored : 75.44 % 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: 1.35 (0.19), residues: 1928 helix: 1.48 (0.15), residues: 1126 sheet: -0.17 (0.43), residues: 138 loop : 0.27 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 225 TYR 0.026 0.001 TYR D 142 PHE 0.018 0.001 PHE A 654 TRP 0.021 0.002 TRP D 124 HIS 0.008 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00303 (16298) covalent geometry : angle 0.64885 (22004) hydrogen bonds : bond 0.03670 ( 896) hydrogen bonds : angle 4.87962 ( 2616) Misc. bond : bond 0.00401 ( 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 410 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 380 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.8359 (mmm) cc_final: 0.8125 (mmm) REVERT: A 119 GLU cc_start: 0.8696 (mp0) cc_final: 0.8322 (mp0) REVERT: A 161 ARG cc_start: 0.7880 (ttm170) cc_final: 0.7378 (mtm180) REVERT: A 173 LEU cc_start: 0.9622 (mt) cc_final: 0.9348 (mt) REVERT: A 178 SER cc_start: 0.9196 (OUTLIER) cc_final: 0.8837 (p) REVERT: A 250 TYR cc_start: 0.8747 (m-80) cc_final: 0.8249 (m-80) REVERT: A 274 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7817 (tpp-160) REVERT: A 334 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8586 (ptpt) REVERT: A 379 SER cc_start: 0.9147 (t) cc_final: 0.8500 (t) REVERT: A 384 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.6543 (pm20) REVERT: A 393 SER cc_start: 0.9054 (t) cc_final: 0.8546 (p) REVERT: A 406 ASP cc_start: 0.8028 (m-30) cc_final: 0.7799 (t0) REVERT: A 433 THR cc_start: 0.9623 (m) cc_final: 0.9337 (p) REVERT: A 436 LEU cc_start: 0.9352 (mm) cc_final: 0.9147 (mm) REVERT: A 493 MET cc_start: 0.9283 (tmm) cc_final: 0.8664 (tmm) REVERT: B 104 TYR cc_start: 0.8938 (m-80) cc_final: 0.8242 (m-80) REVERT: B 274 ARG cc_start: 0.7918 (tpp80) cc_final: 0.7561 (ttm-80) REVERT: B 406 ASP cc_start: 0.7931 (m-30) cc_final: 0.7563 (t0) REVERT: B 483 GLU cc_start: 0.8789 (mp0) cc_final: 0.8422 (pm20) REVERT: B 640 MET cc_start: 0.8978 (tpp) cc_final: 0.8560 (tpp) REVERT: C 231 LEU cc_start: 0.1429 (OUTLIER) cc_final: 0.1072 (pp) REVERT: D 110 MET cc_start: 0.5308 (mtt) cc_final: 0.4918 (tmm) REVERT: D 132 GLN cc_start: 0.4076 (OUTLIER) cc_final: 0.3721 (mp10) outliers start: 30 outliers final: 20 residues processed: 400 average time/residue: 0.1390 time to fit residues: 82.8673 Evaluate side-chains 388 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 362 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 316 LYS 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: 5.9990 chunk 151 optimal weight: 0.0770 chunk 162 optimal weight: 0.0770 chunk 146 optimal weight: 30.0000 chunk 96 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 147 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.171567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.110478 restraints weight = 29685.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.115335 restraints weight = 14728.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.115913 restraints weight = 7640.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.117144 restraints weight = 6341.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.119312 restraints weight = 4654.365| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.5909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 16299 Z= 0.128 Angle : 0.643 11.891 22004 Z= 0.330 Chirality : 0.043 0.328 2348 Planarity : 0.004 0.048 2812 Dihedral : 7.961 133.740 2217 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.58 % Allowed : 23.10 % Favored : 75.32 % 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: 1.33 (0.19), residues: 1928 helix: 1.53 (0.15), residues: 1116 sheet: -0.20 (0.42), residues: 140 loop : 0.16 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 225 TYR 0.025 0.001 TYR D 105 PHE 0.022 0.001 PHE B 657 TRP 0.026 0.002 TRP C 44 HIS 0.008 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00284 (16298) covalent geometry : angle 0.64294 (22004) hydrogen bonds : bond 0.03621 ( 896) hydrogen bonds : angle 4.86395 ( 2616) Misc. bond : bond 0.00329 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3695.92 seconds wall clock time: 64 minutes 49.30 seconds (3889.30 seconds total)