Starting phenix.real_space_refine on Sat May 17 14:52:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bx9_45000/05_2025/9bx9_45000_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bx9_45000/05_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_45000/05_2025/9bx9_45000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bx9_45000/05_2025/9bx9_45000.map" model { file = "/net/cci-nas-00/data/ceres_data/9bx9_45000/05_2025/9bx9_45000_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bx9_45000/05_2025/9bx9_45000_neut.cif" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 12 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10190 2.51 5 N 2598 2.21 5 O 3066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15954 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 9.86, per 1000 atoms: 0.62 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: 4.43 Conformation dependent library (CDL) restraints added in 2.2 seconds 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3688 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 10 sheets defined 64.3% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 27 through 41 removed outlier: 3.554A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.076A 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: 5.45 Time building geometry restraints manager: 4.97 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 38.170 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.150 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.18), residues: 1928 helix: 1.05 (0.15), residues: 1133 sheet: 0.46 (0.39), residues: 146 loop : 0.45 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 PHE 0.021 0.002 PHE C 168 TYR 0.021 0.002 TYR D 179 ARG 0.004 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.16168 ( 896) hydrogen bonds : angle 6.35121 ( 2616) covalent geometry : bond 0.00542 (16298) covalent geometry : angle 0.70709 (22004) 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 : 1.719 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: 0.6878 (p0) REVERT: A 30 LYS cc_start: 0.8021 (tptt) cc_final: 0.7772 (tppt) REVERT: A 119 GLU cc_start: 0.7911 (mp0) cc_final: 0.7525 (mp0) REVERT: A 157 LEU cc_start: 0.9234 (tp) cc_final: 0.8952 (tt) REVERT: A 177 ASP cc_start: 0.8784 (t0) cc_final: 0.8271 (t0) REVERT: A 179 LEU cc_start: 0.9223 (tp) cc_final: 0.8935 (tp) REVERT: A 188 ILE cc_start: 0.9187 (mt) cc_final: 0.8973 (mt) REVERT: A 232 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8381 (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: 0.6566 (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: 0.7888 (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: 0.7677 (mtp) REVERT: A 584 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8551 (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: 0.7476 (mtm) REVERT: A 654 PHE cc_start: 0.8807 (t80) cc_final: 0.8466 (t80) REVERT: B 104 TYR cc_start: 0.7947 (m-80) cc_final: 0.7481 (m-80) REVERT: B 172 LEU cc_start: 0.9169 (mp) cc_final: 0.8677 (mp) REVERT: B 177 ASP cc_start: 0.8208 (t0) cc_final: 0.7740 (t0) REVERT: B 194 LYS cc_start: 0.8863 (tttt) cc_final: 0.8662 (ttpt) REVERT: B 286 ASP cc_start: 0.6882 (m-30) cc_final: 0.6681 (m-30) REVERT: B 362 ASP cc_start: 0.7489 (m-30) cc_final: 0.6733 (m-30) REVERT: B 425 ILE cc_start: 0.8789 (mt) cc_final: 0.8578 (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: 0.8827 (t0) REVERT: B 550 MET cc_start: 0.8658 (ttm) cc_final: 0.8130 (mtm) REVERT: B 612 TYR cc_start: 0.7092 (m-80) cc_final: 0.6820 (m-80) REVERT: C 137 MET cc_start: -0.1844 (mtp) cc_final: -0.3145 (mmm) REVERT: C 287 LEU cc_start: -0.0458 (OUTLIER) cc_final: -0.1103 (tp) REVERT: D 137 MET cc_start: -0.1438 (mtp) cc_final: -0.3363 (mmt) REVERT: D 282 ILE cc_start: -0.0509 (OUTLIER) cc_final: -0.1124 (mt) outliers start: 24 outliers final: 5 residues processed: 712 average time/residue: 0.2905 time to fit residues: 296.8021 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 : 1.742 ------------------------------------------------------------------------------- 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 162 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 112 optimal weight: 0.0370 chunk 174 optimal weight: 3.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 645 GLN B 646 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.175196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.108426 restraints weight = 28638.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.112261 restraints weight = 13305.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114664 restraints weight = 8097.323| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16299 Z= 0.146 Angle : 0.613 10.439 22004 Z= 0.330 Chirality : 0.042 0.191 2348 Planarity : 0.004 0.053 2812 Dihedral : 9.113 162.477 2232 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.28 % Allowed : 15.81 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.18), residues: 1928 helix: 1.66 (0.15), residues: 1127 sheet: 0.98 (0.40), residues: 114 loop : 0.57 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 124 HIS 0.004 0.001 HIS A 568 PHE 0.031 0.002 PHE A 261 TYR 0.020 0.001 TYR C 22 ARG 0.008 0.001 ARG B 293 Details of bonding type rmsd hydrogen bonds : bond 0.04613 ( 896) hydrogen bonds : angle 5.07494 ( 2616) covalent geometry : bond 0.00318 (16298) covalent geometry : angle 0.61333 (22004) Misc. bond : bond 0.00028 ( 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 542 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 503 time to evaluate : 1.839 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 27 ASP cc_start: 0.8195 (p0) cc_final: 0.7944 (p0) REVERT: A 119 GLU cc_start: 0.8765 (mp0) cc_final: 0.8431 (mp0) REVERT: A 147 GLN cc_start: 0.9268 (mt0) cc_final: 0.9062 (mt0) REVERT: A 177 ASP cc_start: 0.8870 (t0) cc_final: 0.8508 (t0) REVERT: A 179 LEU cc_start: 0.9516 (tp) cc_final: 0.9307 (tp) REVERT: A 232 ASN cc_start: 0.8937 (OUTLIER) cc_final: 0.8149 (m-40) REVERT: A 250 TYR cc_start: 0.8751 (m-80) cc_final: 0.8294 (m-80) REVERT: A 334 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8572 (ptpt) REVERT: A 362 ASP cc_start: 0.7772 (m-30) cc_final: 0.7493 (m-30) REVERT: A 379 SER cc_start: 0.9173 (t) cc_final: 0.8587 (t) REVERT: A 640 MET cc_start: 0.9198 (tpp) cc_final: 0.8931 (tpp) REVERT: A 654 PHE cc_start: 0.9116 (t80) cc_final: 0.8741 (t80) REVERT: A 657 PHE cc_start: 0.9051 (m-80) cc_final: 0.8678 (m-80) REVERT: A 686 ARG cc_start: 0.7957 (mmt-90) cc_final: 0.7742 (mtt90) REVERT: B 109 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8357 (m110) REVERT: B 119 GLU cc_start: 0.8678 (mp0) cc_final: 0.8420 (mp0) REVERT: B 135 GLU cc_start: 0.8421 (mp0) cc_final: 0.8117 (mp0) REVERT: B 158 ASN cc_start: 0.9006 (m-40) cc_final: 0.8775 (m110) REVERT: B 177 ASP cc_start: 0.8258 (t0) cc_final: 0.7822 (t0) REVERT: B 181 ASP cc_start: 0.8665 (m-30) cc_final: 0.8449 (m-30) REVERT: B 286 ASP cc_start: 0.8070 (m-30) cc_final: 0.7415 (m-30) REVERT: B 290 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7638 (tm-30) REVERT: B 334 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8769 (pttm) REVERT: B 362 ASP cc_start: 0.8112 (m-30) cc_final: 0.7256 (m-30) REVERT: B 483 GLU cc_start: 0.8813 (mp0) cc_final: 0.8380 (pm20) REVERT: B 586 TYR cc_start: 0.8555 (m-80) cc_final: 0.8315 (m-80) REVERT: B 604 ARG cc_start: 0.8671 (mmp80) cc_final: 0.8410 (mmp80) REVERT: B 612 TYR cc_start: 0.8047 (m-80) cc_final: 0.7297 (m-80) REVERT: B 640 MET cc_start: 0.9105 (tpp) cc_final: 0.8767 (tpp) REVERT: B 668 ASN cc_start: 0.9221 (m-40) cc_final: 0.8931 (m-40) REVERT: C 258 LYS cc_start: 0.7403 (pttm) cc_final: 0.6153 (tptt) REVERT: C 283 ASN cc_start: 0.4492 (t0) cc_final: 0.4103 (t0) REVERT: C 287 LEU cc_start: 0.0250 (OUTLIER) cc_final: -0.0363 (tp) REVERT: D 74 MET cc_start: 0.3581 (tpp) cc_final: 0.3241 (tpp) REVERT: D 76 ILE cc_start: 0.6281 (OUTLIER) cc_final: 0.5814 (tt) REVERT: D 110 MET cc_start: 0.5121 (mtt) cc_final: 0.4686 (tmm) REVERT: D 185 MET cc_start: 0.6257 (mmm) cc_final: 0.5952 (mmm) outliers start: 39 outliers final: 20 residues processed: 521 average time/residue: 0.2778 time to fit residues: 214.6141 Evaluate side-chains 458 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 432 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 590 SER 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 334 LYS 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 599 GLU 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 262 TYR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 76 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 191 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 175 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 136 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 121 optimal weight: 0.4980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 370 ASN B 62 GLN B 150 GLN B 646 GLN C 19 GLN C 84 HIS ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN D 119 ASN D 233 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.169146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.104144 restraints weight = 29285.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.107600 restraints weight = 13673.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.109852 restraints weight = 8347.774| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 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 = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16299 Z= 0.161 Angle : 0.578 10.085 22004 Z= 0.307 Chirality : 0.041 0.259 2348 Planarity : 0.004 0.048 2812 Dihedral : 8.859 161.946 2222 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.27 % Allowed : 17.09 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.19), residues: 1928 helix: 1.73 (0.15), residues: 1129 sheet: 0.85 (0.41), residues: 118 loop : 0.48 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 124 HIS 0.005 0.001 HIS A 255 PHE 0.019 0.001 PHE A 74 TYR 0.032 0.001 TYR D 142 ARG 0.005 0.001 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.04075 ( 896) hydrogen bonds : angle 4.89440 ( 2616) covalent geometry : bond 0.00361 (16298) covalent geometry : angle 0.57797 (22004) Misc. bond : bond 0.00026 ( 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 518 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 462 time to evaluate : 1.744 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 27 ASP cc_start: 0.8244 (p0) cc_final: 0.8039 (p0) REVERT: A 30 LYS cc_start: 0.9341 (tppt) cc_final: 0.8991 (tppt) REVERT: A 119 GLU cc_start: 0.8709 (mp0) cc_final: 0.8472 (mp0) REVERT: A 177 ASP cc_start: 0.8941 (t0) cc_final: 0.8610 (t0) REVERT: A 179 LEU cc_start: 0.9555 (tp) cc_final: 0.9344 (tp) REVERT: A 232 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8153 (m-40) REVERT: A 250 TYR cc_start: 0.8928 (m-80) cc_final: 0.8235 (m-80) REVERT: A 334 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8661 (ptpt) REVERT: A 362 ASP cc_start: 0.7904 (m-30) cc_final: 0.7541 (m-30) REVERT: A 379 SER cc_start: 0.9144 (t) cc_final: 0.8505 (t) REVERT: A 493 MET cc_start: 0.9297 (tmm) cc_final: 0.9055 (tmm) REVERT: A 604 ARG cc_start: 0.8509 (mmp80) cc_final: 0.8308 (mmp80) REVERT: A 686 ARG cc_start: 0.8032 (mmt-90) cc_final: 0.7800 (mtt90) REVERT: B 119 GLU cc_start: 0.8671 (mp0) cc_final: 0.8412 (mp0) REVERT: B 135 GLU cc_start: 0.8373 (mp0) cc_final: 0.8056 (mp0) REVERT: B 147 GLN cc_start: 0.9132 (mt0) cc_final: 0.8666 (mm-40) REVERT: B 276 LYS cc_start: 0.8818 (mtmm) cc_final: 0.8547 (mmtm) REVERT: B 286 ASP cc_start: 0.8104 (m-30) cc_final: 0.7449 (m-30) REVERT: B 334 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8806 (pttm) REVERT: B 362 ASP cc_start: 0.8086 (m-30) cc_final: 0.7262 (m-30) REVERT: B 526 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7380 (tp30) REVERT: B 586 TYR cc_start: 0.8629 (m-80) cc_final: 0.8245 (m-80) REVERT: B 590 SER cc_start: 0.9497 (p) cc_final: 0.9246 (t) REVERT: B 604 ARG cc_start: 0.8554 (mmp80) cc_final: 0.8334 (mmp80) REVERT: B 612 TYR cc_start: 0.8297 (m-80) cc_final: 0.7887 (m-80) REVERT: B 640 MET cc_start: 0.9051 (tpp) cc_final: 0.8669 (tpp) REVERT: B 668 ASN cc_start: 0.9177 (m-40) cc_final: 0.8860 (m-40) REVERT: C 74 MET cc_start: 0.8169 (mmm) cc_final: 0.7872 (mtm) REVERT: C 134 LYS cc_start: 0.2935 (ttpt) cc_final: 0.2549 (ttpt) REVERT: C 137 MET cc_start: -0.4390 (mtp) cc_final: -0.5626 (mmm) REVERT: C 258 LYS cc_start: 0.7360 (pttm) cc_final: 0.6086 (tptt) REVERT: C 287 LEU cc_start: 0.0338 (OUTLIER) cc_final: -0.0200 (tp) REVERT: D 110 MET cc_start: 0.5276 (mtt) cc_final: 0.5001 (tmm) REVERT: D 137 MET cc_start: -0.6271 (ptp) cc_final: -0.6565 (mmt) REVERT: D 185 MET cc_start: 0.6377 (mmm) cc_final: 0.5995 (mmm) outliers start: 56 outliers final: 34 residues processed: 487 average time/residue: 0.2629 time to fit residues: 190.7784 Evaluate side-chains 464 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 426 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 367 VAL 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 615 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 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 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 25 ASN Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 153 optimal weight: 20.0000 chunk 136 optimal weight: 7.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN D 107 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.169030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.103380 restraints weight = 29562.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.106892 restraints weight = 13800.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109146 restraints weight = 8414.321| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16299 Z= 0.154 Angle : 0.569 7.890 22004 Z= 0.301 Chirality : 0.041 0.155 2348 Planarity : 0.003 0.051 2812 Dihedral : 8.683 160.476 2221 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.68 % Allowed : 18.67 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.19), residues: 1928 helix: 1.68 (0.15), residues: 1131 sheet: -0.12 (0.39), residues: 140 loop : 0.53 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 124 HIS 0.004 0.001 HIS A 255 PHE 0.021 0.001 PHE A 261 TYR 0.017 0.001 TYR D 142 ARG 0.007 0.000 ARG B 274 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 896) hydrogen bonds : angle 4.81882 ( 2616) covalent geometry : bond 0.00345 (16298) covalent geometry : angle 0.56884 (22004) Misc. bond : bond 0.00025 ( 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 492 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 446 time to evaluate : 1.776 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: 0.9359 (tppt) cc_final: 0.8995 (tppt) REVERT: A 58 LEU cc_start: 0.9632 (mt) cc_final: 0.9409 (mt) REVERT: A 119 GLU cc_start: 0.8837 (mp0) cc_final: 0.8506 (mp0) REVERT: A 178 SER cc_start: 0.9075 (OUTLIER) cc_final: 0.8679 (p) REVERT: A 179 LEU cc_start: 0.9544 (tp) cc_final: 0.9333 (tp) REVERT: A 250 TYR cc_start: 0.8962 (m-80) cc_final: 0.8289 (m-80) REVERT: A 379 SER cc_start: 0.9086 (t) cc_final: 0.8447 (t) REVERT: A 433 THR cc_start: 0.9704 (m) cc_final: 0.9370 (p) REVERT: A 493 MET cc_start: 0.9269 (tmm) cc_final: 0.8997 (tmm) REVERT: A 654 PHE cc_start: 0.9206 (t80) cc_final: 0.8956 (t80) REVERT: A 686 ARG cc_start: 0.8074 (mmt-90) cc_final: 0.7787 (mtt90) REVERT: B 119 GLU cc_start: 0.8698 (mp0) cc_final: 0.8442 (mp0) REVERT: B 135 GLU cc_start: 0.8326 (mp0) cc_final: 0.8065 (mp0) REVERT: B 147 GLN cc_start: 0.9169 (mt0) cc_final: 0.8755 (mm-40) REVERT: B 276 LYS cc_start: 0.8698 (mtmm) cc_final: 0.8484 (mmtm) REVERT: B 286 ASP cc_start: 0.8083 (m-30) cc_final: 0.7487 (m-30) REVERT: B 334 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8880 (pttm) REVERT: B 348 MET cc_start: 0.8198 (tmm) cc_final: 0.7942 (tmm) REVERT: B 362 ASP cc_start: 0.8057 (m-30) cc_final: 0.7292 (m-30) REVERT: B 483 GLU cc_start: 0.8834 (mp0) cc_final: 0.8470 (pm20) REVERT: B 550 MET cc_start: 0.8995 (mtm) cc_final: 0.8794 (mtt) REVERT: B 612 TYR cc_start: 0.8380 (m-80) cc_final: 0.7937 (m-80) REVERT: B 640 MET cc_start: 0.9076 (tpp) cc_final: 0.8661 (tpp) REVERT: C 74 MET cc_start: 0.8240 (mmm) cc_final: 0.7965 (mtm) REVERT: C 134 LYS cc_start: 0.2971 (ttpt) cc_final: 0.2595 (ttpt) REVERT: C 137 MET cc_start: -0.4414 (mtp) cc_final: -0.5748 (mmm) REVERT: C 258 LYS cc_start: 0.7375 (pttm) cc_final: 0.6138 (tptt) REVERT: D 110 MET cc_start: 0.5335 (mtt) cc_final: 0.5017 (tmm) outliers start: 46 outliers final: 29 residues processed: 465 average time/residue: 0.2680 time to fit residues: 184.2218 Evaluate side-chains 424 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 393 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 410 ASN 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 615 MET 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 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 584 ILE 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 200 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 262 TYR 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 25 ASN Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 109 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 188 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 165 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 119 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 D 28 GLN D 107 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN D 233 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.167768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.103054 restraints weight = 30131.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.106470 restraints weight = 13868.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.108679 restraints weight = 8398.531| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16299 Z= 0.161 Angle : 0.568 10.201 22004 Z= 0.302 Chirality : 0.041 0.181 2348 Planarity : 0.004 0.054 2812 Dihedral : 8.498 158.934 2217 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.74 % Allowed : 19.72 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.19), residues: 1928 helix: 1.67 (0.15), residues: 1132 sheet: -0.49 (0.38), residues: 144 loop : 0.43 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 124 HIS 0.004 0.001 HIS A 255 PHE 0.016 0.001 PHE C 92 TYR 0.018 0.001 TYR D 142 ARG 0.007 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 896) hydrogen bonds : angle 4.79889 ( 2616) covalent geometry : bond 0.00360 (16298) covalent geometry : angle 0.56799 (22004) Misc. bond : bond 0.00056 ( 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 488 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 441 time to evaluate : 1.760 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 119 GLU cc_start: 0.8817 (mp0) cc_final: 0.8459 (mp0) REVERT: A 174 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8170 (mm-30) REVERT: A 250 TYR cc_start: 0.8939 (m-80) cc_final: 0.8300 (m-80) REVERT: A 334 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8749 (ptpt) REVERT: A 379 SER cc_start: 0.9111 (t) cc_final: 0.8430 (t) REVERT: A 433 THR cc_start: 0.9697 (m) cc_final: 0.9368 (p) REVERT: A 493 MET cc_start: 0.9254 (tmm) cc_final: 0.8636 (tmm) REVERT: A 586 TYR cc_start: 0.8814 (m-10) cc_final: 0.8509 (m-10) REVERT: A 640 MET cc_start: 0.9304 (tpp) cc_final: 0.9065 (tpp) REVERT: A 654 PHE cc_start: 0.9225 (t80) cc_final: 0.9004 (t80) REVERT: B 147 GLN cc_start: 0.9251 (mt0) cc_final: 0.8948 (mm-40) REVERT: B 157 LEU cc_start: 0.9336 (tp) cc_final: 0.9090 (tp) REVERT: B 276 LYS cc_start: 0.8782 (mtmm) cc_final: 0.8550 (mmtm) REVERT: B 286 ASP cc_start: 0.8083 (m-30) cc_final: 0.7516 (m-30) REVERT: B 362 ASP cc_start: 0.8104 (m-30) cc_final: 0.7308 (m-30) REVERT: B 612 TYR cc_start: 0.8400 (m-80) cc_final: 0.8103 (m-80) REVERT: B 640 MET cc_start: 0.9061 (tpp) cc_final: 0.8621 (tpp) REVERT: B 662 MET cc_start: 0.7386 (ppp) cc_final: 0.6595 (ppp) REVERT: B 668 ASN cc_start: 0.9074 (m-40) cc_final: 0.8827 (m-40) REVERT: C 74 MET cc_start: 0.8216 (mmm) cc_final: 0.7897 (mtm) REVERT: C 129 LYS cc_start: 0.7712 (tptp) cc_final: 0.6658 (ptmt) REVERT: C 134 LYS cc_start: 0.3093 (ttpt) cc_final: 0.2724 (ttpt) REVERT: C 137 MET cc_start: -0.4458 (mtp) cc_final: -0.5761 (mmm) REVERT: C 197 ASP cc_start: 0.6692 (OUTLIER) cc_final: 0.6358 (p0) REVERT: C 258 LYS cc_start: 0.7258 (pttm) cc_final: 0.6050 (tptt) REVERT: C 287 LEU cc_start: 0.0611 (OUTLIER) cc_final: 0.0298 (tp) REVERT: D 110 MET cc_start: 0.5595 (mtt) cc_final: 0.5206 (tmm) REVERT: D 132 GLN cc_start: 0.1716 (OUTLIER) cc_final: 0.1490 (mp10) outliers start: 47 outliers final: 35 residues processed: 464 average time/residue: 0.2771 time to fit residues: 193.0024 Evaluate side-chains 431 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 392 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 413 SER 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 599 GLU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR 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 565 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 599 GLU 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 200 ILE Chi-restraints excluded: chain C residue 213 TYR 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 25 ASN Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 132 GLN 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 143 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 182 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 D 128 ASN D 233 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.168269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.103113 restraints weight = 29680.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.106499 restraints weight = 13814.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.108747 restraints weight = 8469.017| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16299 Z= 0.148 Angle : 0.582 7.632 22004 Z= 0.303 Chirality : 0.041 0.165 2348 Planarity : 0.004 0.055 2812 Dihedral : 8.385 150.381 2217 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.74 % Allowed : 21.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.18), residues: 1928 helix: 1.67 (0.15), residues: 1135 sheet: -0.58 (0.38), residues: 144 loop : 0.38 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 124 HIS 0.004 0.001 HIS A 255 PHE 0.020 0.001 PHE A 261 TYR 0.019 0.001 TYR D 242 ARG 0.006 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 896) hydrogen bonds : angle 4.77391 ( 2616) covalent geometry : bond 0.00333 (16298) covalent geometry : angle 0.58158 (22004) Misc. bond : bond 0.00061 ( 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 478 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 431 time to evaluate : 1.744 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 65 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7592 (mt-10) REVERT: A 119 GLU cc_start: 0.8820 (mp0) cc_final: 0.8460 (mp0) REVERT: A 157 LEU cc_start: 0.9503 (tt) cc_final: 0.9256 (tp) REVERT: A 161 ARG cc_start: 0.7561 (ttm110) cc_final: 0.6773 (mtt180) REVERT: A 173 LEU cc_start: 0.9642 (mt) cc_final: 0.9336 (mt) REVERT: A 178 SER cc_start: 0.9099 (OUTLIER) cc_final: 0.8847 (p) REVERT: A 250 TYR cc_start: 0.8921 (m-80) cc_final: 0.8228 (m-80) REVERT: A 334 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8725 (ptpt) REVERT: A 379 SER cc_start: 0.9113 (t) cc_final: 0.8345 (t) REVERT: A 406 ASP cc_start: 0.8103 (m-30) cc_final: 0.7851 (t0) REVERT: A 433 THR cc_start: 0.9691 (m) cc_final: 0.9363 (p) REVERT: A 493 MET cc_start: 0.9255 (tmm) cc_final: 0.8634 (tmm) REVERT: A 586 TYR cc_start: 0.8832 (m-10) cc_final: 0.8495 (m-10) REVERT: A 654 PHE cc_start: 0.9264 (t80) cc_final: 0.9042 (t80) REVERT: B 147 GLN cc_start: 0.9256 (mt0) cc_final: 0.8937 (mm-40) REVERT: B 157 LEU cc_start: 0.9357 (tp) cc_final: 0.9150 (tp) REVERT: B 274 ARG cc_start: 0.7887 (tpp80) cc_final: 0.7567 (ttm-80) REVERT: B 286 ASP cc_start: 0.8070 (m-30) cc_final: 0.7509 (m-30) REVERT: B 317 MET cc_start: 0.8867 (mtp) cc_final: 0.8538 (mtt) REVERT: B 362 ASP cc_start: 0.8116 (m-30) cc_final: 0.7329 (m-30) REVERT: B 415 ASN cc_start: 0.9354 (t0) cc_final: 0.9122 (t0) REVERT: B 483 GLU cc_start: 0.8810 (mp0) cc_final: 0.8384 (pm20) REVERT: B 612 TYR cc_start: 0.8359 (m-80) cc_final: 0.8086 (m-80) REVERT: B 640 MET cc_start: 0.9058 (tpp) cc_final: 0.8631 (tpp) REVERT: B 662 MET cc_start: 0.7551 (ppp) cc_final: 0.6535 (ppp) REVERT: B 668 ASN cc_start: 0.9048 (m-40) cc_final: 0.8797 (m-40) REVERT: C 23 ASN cc_start: 0.7805 (OUTLIER) cc_final: 0.7605 (p0) REVERT: C 74 MET cc_start: 0.8238 (mmm) cc_final: 0.7920 (mtm) REVERT: C 95 MET cc_start: 0.8559 (tmm) cc_final: 0.8216 (ptt) REVERT: C 129 LYS cc_start: 0.7722 (tptp) cc_final: 0.6693 (ptmt) REVERT: C 197 ASP cc_start: 0.6930 (OUTLIER) cc_final: 0.6602 (p0) REVERT: C 258 LYS cc_start: 0.7387 (pttm) cc_final: 0.6218 (tptt) REVERT: C 287 LEU cc_start: 0.0589 (OUTLIER) cc_final: 0.0092 (tp) REVERT: D 110 MET cc_start: 0.5545 (mtt) cc_final: 0.5161 (tmm) outliers start: 47 outliers final: 32 residues processed: 457 average time/residue: 0.2753 time to fit residues: 187.5589 Evaluate side-chains 426 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 389 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 413 SER 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 615 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 414 LEU 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 565 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 23 ASN 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 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 25 ASN Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 128 ASN 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 7 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 26 optimal weight: 0.0370 chunk 84 optimal weight: 0.9980 chunk 185 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- 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 668 ASN B 150 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN D 233 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.169291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.104599 restraints weight = 29834.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.108103 restraints weight = 13831.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.110329 restraints weight = 8388.525| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16299 Z= 0.132 Angle : 0.580 8.783 22004 Z= 0.300 Chirality : 0.041 0.168 2348 Planarity : 0.003 0.056 2812 Dihedral : 8.235 144.578 2217 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.33 % Allowed : 21.65 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.18), residues: 1928 helix: 1.67 (0.15), residues: 1134 sheet: -0.60 (0.39), residues: 144 loop : 0.33 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 124 HIS 0.004 0.001 HIS A 255 PHE 0.020 0.001 PHE C 92 TYR 0.020 0.001 TYR C 204 ARG 0.006 0.000 ARG B 274 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 896) hydrogen bonds : angle 4.75300 ( 2616) covalent geometry : bond 0.00297 (16298) covalent geometry : angle 0.57962 (22004) Misc. bond : bond 0.00034 ( 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 476 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 436 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.9334 (tppt) cc_final: 0.8931 (tppt) REVERT: A 52 LYS cc_start: 0.9116 (ttmt) cc_final: 0.8845 (tppt) REVERT: A 65 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7518 (mt-10) REVERT: A 119 GLU cc_start: 0.8775 (mp0) cc_final: 0.8427 (mp0) REVERT: A 161 ARG cc_start: 0.7481 (ttm110) cc_final: 0.7239 (ttm110) REVERT: A 178 SER cc_start: 0.9102 (OUTLIER) cc_final: 0.8840 (p) REVERT: A 250 TYR cc_start: 0.8832 (m-80) cc_final: 0.8224 (m-80) REVERT: A 334 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8758 (ptpt) REVERT: A 379 SER cc_start: 0.9131 (t) cc_final: 0.8423 (t) REVERT: A 384 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.6729 (pm20) REVERT: A 433 THR cc_start: 0.9672 (m) cc_final: 0.9341 (p) REVERT: A 467 ASN cc_start: 0.9445 (t0) cc_final: 0.9005 (m-40) REVERT: A 493 MET cc_start: 0.9231 (tmm) cc_final: 0.8608 (tmm) REVERT: A 586 TYR cc_start: 0.8815 (m-10) cc_final: 0.8579 (m-10) REVERT: A 655 THR cc_start: 0.9094 (m) cc_final: 0.8746 (t) REVERT: B 116 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8024 (mt-10) REVERT: B 147 GLN cc_start: 0.9186 (mt0) cc_final: 0.8929 (mm-40) REVERT: B 286 ASP cc_start: 0.7985 (m-30) cc_final: 0.7520 (m-30) REVERT: B 317 MET cc_start: 0.8890 (mtp) cc_final: 0.8544 (mtt) REVERT: B 362 ASP cc_start: 0.8100 (m-30) cc_final: 0.7329 (m-30) REVERT: B 483 GLU cc_start: 0.8799 (mp0) cc_final: 0.8487 (pm20) REVERT: B 526 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7506 (mm-30) REVERT: B 612 TYR cc_start: 0.8303 (m-80) cc_final: 0.8084 (m-80) REVERT: B 640 MET cc_start: 0.9063 (tpp) cc_final: 0.8624 (tpp) REVERT: B 668 ASN cc_start: 0.8989 (m-40) cc_final: 0.8743 (m-40) REVERT: C 20 MET cc_start: 0.6622 (ppp) cc_final: 0.6344 (ppp) REVERT: C 23 ASN cc_start: 0.7864 (OUTLIER) cc_final: 0.7621 (p0) REVERT: C 74 MET cc_start: 0.8234 (mmm) cc_final: 0.7898 (mtm) REVERT: C 95 MET cc_start: 0.8585 (tmm) cc_final: 0.8265 (ptt) REVERT: C 129 LYS cc_start: 0.7770 (tptp) cc_final: 0.6724 (ptmt) REVERT: C 197 ASP cc_start: 0.6901 (OUTLIER) cc_final: 0.6571 (p0) REVERT: C 258 LYS cc_start: 0.7353 (pttm) cc_final: 0.6215 (tptt) REVERT: C 287 LEU cc_start: 0.0465 (OUTLIER) cc_final: -0.0073 (tp) REVERT: D 110 MET cc_start: 0.5414 (mtt) cc_final: 0.5048 (tmm) outliers start: 40 outliers final: 29 residues processed: 461 average time/residue: 0.2765 time to fit residues: 189.3240 Evaluate side-chains 430 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 395 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 178 SER 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 413 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 414 LEU 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 565 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain C residue 23 ASN 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 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 25 ASN Chi-restraints excluded: chain D residue 115 THR 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 146 optimal weight: 20.0000 chunk 80 optimal weight: 0.8980 chunk 174 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 181 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 25 GLN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN D 233 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.169940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.105651 restraints weight = 29743.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109264 restraints weight = 13759.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.111398 restraints weight = 8249.620| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.5260 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= 0.153 Angle : 0.615 14.919 22004 Z= 0.317 Chirality : 0.042 0.221 2348 Planarity : 0.004 0.056 2812 Dihedral : 8.224 144.052 2217 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.22 % Allowed : 22.40 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.18), residues: 1928 helix: 1.55 (0.15), residues: 1134 sheet: -0.49 (0.40), residues: 138 loop : 0.28 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 124 HIS 0.004 0.001 HIS B 551 PHE 0.019 0.001 PHE A 261 TYR 0.023 0.001 TYR D 142 ARG 0.006 0.001 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.03679 ( 896) hydrogen bonds : angle 4.82867 ( 2616) covalent geometry : bond 0.00348 (16298) covalent geometry : angle 0.61517 (22004) Misc. bond : bond 0.00050 ( 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 433 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 395 time to evaluate : 1.903 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: 0.9328 (tppt) cc_final: 0.9073 (tmmt) REVERT: A 52 LYS cc_start: 0.9105 (ttmt) cc_final: 0.8857 (tppt) REVERT: A 119 GLU cc_start: 0.8785 (mp0) cc_final: 0.8422 (mp0) REVERT: A 178 SER cc_start: 0.9126 (OUTLIER) cc_final: 0.8885 (p) REVERT: A 238 ASP cc_start: 0.7613 (m-30) cc_final: 0.7363 (m-30) REVERT: A 250 TYR cc_start: 0.8776 (m-80) cc_final: 0.8187 (m-80) REVERT: A 334 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8732 (ptpt) REVERT: A 379 SER cc_start: 0.9101 (t) cc_final: 0.8405 (t) REVERT: A 384 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.6745 (pm20) REVERT: A 406 ASP cc_start: 0.8077 (m-30) cc_final: 0.7819 (t0) REVERT: A 433 THR cc_start: 0.9644 (m) cc_final: 0.9357 (p) REVERT: A 493 MET cc_start: 0.9243 (tmm) cc_final: 0.8598 (tmm) REVERT: A 586 TYR cc_start: 0.8801 (m-10) cc_final: 0.8576 (m-10) REVERT: B 78 LYS cc_start: 0.9216 (ptpt) cc_final: 0.8992 (ptpt) REVERT: B 104 TYR cc_start: 0.8950 (m-80) cc_final: 0.8197 (m-80) REVERT: B 232 ASN cc_start: 0.9031 (t0) cc_final: 0.8550 (m-40) REVERT: B 274 ARG cc_start: 0.7583 (tpp80) cc_final: 0.7288 (ttm-80) REVERT: B 286 ASP cc_start: 0.8022 (m-30) cc_final: 0.7514 (m-30) REVERT: B 350 ARG cc_start: 0.9015 (mtp85) cc_final: 0.7929 (mtp85) REVERT: B 362 ASP cc_start: 0.8095 (m-30) cc_final: 0.7359 (m-30) REVERT: B 526 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7787 (mm-30) REVERT: B 612 TYR cc_start: 0.8319 (m-80) cc_final: 0.8115 (m-80) REVERT: B 640 MET cc_start: 0.9025 (tpp) cc_final: 0.8582 (tpp) REVERT: B 668 ASN cc_start: 0.8969 (m-40) cc_final: 0.8739 (m-40) REVERT: C 20 MET cc_start: 0.7318 (ppp) cc_final: 0.7070 (ppp) REVERT: C 74 MET cc_start: 0.8258 (mmm) cc_final: 0.7853 (mtm) REVERT: C 287 LEU cc_start: 0.0448 (OUTLIER) cc_final: 0.0027 (tp) REVERT: D 110 MET cc_start: 0.5490 (mtt) cc_final: 0.5125 (tmm) outliers start: 38 outliers final: 29 residues processed: 420 average time/residue: 0.2700 time to fit residues: 169.2717 Evaluate side-chains 405 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 372 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 178 SER 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 413 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 660 ASP 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 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 25 ASN Chi-restraints excluded: chain D residue 115 THR 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 140 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 162 optimal weight: 20.0000 chunk 168 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 122 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.167829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.103506 restraints weight = 29959.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.107024 restraints weight = 13846.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109066 restraints weight = 8445.140| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.5373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 16299 Z= 0.185 Angle : 0.635 10.172 22004 Z= 0.331 Chirality : 0.043 0.291 2348 Planarity : 0.004 0.053 2812 Dihedral : 8.265 146.407 2217 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.16 % Allowed : 22.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.18), residues: 1928 helix: 1.51 (0.15), residues: 1121 sheet: -0.86 (0.39), residues: 144 loop : 0.30 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 124 HIS 0.012 0.001 HIS C 101 PHE 0.018 0.001 PHE A 261 TYR 0.028 0.001 TYR D 142 ARG 0.009 0.001 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 896) hydrogen bonds : angle 4.91952 ( 2616) covalent geometry : bond 0.00421 (16298) covalent geometry : angle 0.63534 (22004) Misc. bond : bond 0.00072 ( 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 416 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 379 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8843 (mp0) cc_final: 0.8430 (mp0) REVERT: A 178 SER cc_start: 0.9073 (OUTLIER) cc_final: 0.8806 (p) REVERT: A 250 TYR cc_start: 0.8816 (m-80) cc_final: 0.8177 (m-80) REVERT: A 334 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8752 (ptpt) REVERT: A 379 SER cc_start: 0.9037 (t) cc_final: 0.8338 (t) REVERT: A 384 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.6653 (pm20) REVERT: A 406 ASP cc_start: 0.8048 (m-30) cc_final: 0.7808 (t0) REVERT: A 433 THR cc_start: 0.9666 (m) cc_final: 0.9369 (p) REVERT: A 493 MET cc_start: 0.9245 (tmm) cc_final: 0.8598 (tmm) REVERT: A 586 TYR cc_start: 0.8800 (m-10) cc_final: 0.8571 (m-10) REVERT: A 655 THR cc_start: 0.9158 (m) cc_final: 0.8863 (t) REVERT: A 657 PHE cc_start: 0.8911 (m-80) cc_final: 0.8434 (m-80) REVERT: B 17 MET cc_start: 0.8189 (mmm) cc_final: 0.7870 (mmm) REVERT: B 104 TYR cc_start: 0.9056 (m-80) cc_final: 0.8283 (m-80) REVERT: B 111 LYS cc_start: 0.9007 (mppt) cc_final: 0.8792 (mppt) REVERT: B 227 MET cc_start: 0.9210 (mtp) cc_final: 0.8856 (ttm) REVERT: B 232 ASN cc_start: 0.9041 (t0) cc_final: 0.8551 (m-40) REVERT: B 286 ASP cc_start: 0.8048 (m-30) cc_final: 0.7540 (m-30) REVERT: B 317 MET cc_start: 0.8989 (mtp) cc_final: 0.8657 (mtt) REVERT: B 350 ARG cc_start: 0.9043 (mtp85) cc_final: 0.7919 (mtp85) REVERT: B 362 ASP cc_start: 0.8165 (m-30) cc_final: 0.7302 (m-30) REVERT: B 406 ASP cc_start: 0.8099 (m-30) cc_final: 0.7685 (t0) REVERT: B 483 GLU cc_start: 0.8843 (mp0) cc_final: 0.8499 (mp0) REVERT: B 526 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7905 (mm-30) REVERT: B 550 MET cc_start: 0.8710 (mtp) cc_final: 0.8484 (mtt) REVERT: B 612 TYR cc_start: 0.8345 (m-80) cc_final: 0.8074 (m-80) REVERT: B 640 MET cc_start: 0.9030 (tpp) cc_final: 0.8621 (tpp) REVERT: B 668 ASN cc_start: 0.9002 (m-40) cc_final: 0.8773 (m-40) REVERT: C 74 MET cc_start: 0.8297 (mmm) cc_final: 0.7881 (mtm) REVERT: C 137 MET cc_start: -0.4591 (mtp) cc_final: -0.5127 (mtp) REVERT: C 287 LEU cc_start: 0.0588 (OUTLIER) cc_final: 0.0141 (tp) REVERT: D 37 LEU cc_start: 0.5107 (pp) cc_final: 0.4753 (pp) REVERT: D 110 MET cc_start: 0.5610 (mtt) cc_final: 0.5098 (tmm) outliers start: 37 outliers final: 29 residues processed: 404 average time/residue: 0.2680 time to fit residues: 160.6259 Evaluate side-chains 403 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 370 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 178 SER 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 413 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 660 ASP 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 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 25 ASN Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 281 ASP 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 8 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 165 optimal weight: 10.0000 chunk 180 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 190 optimal weight: 20.0000 chunk 129 optimal weight: 6.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN ** 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 = 0.3949 r_free = 0.3949 target = 0.164232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.099832 restraints weight = 30343.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.103313 restraints weight = 14295.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.105229 restraints weight = 8668.418| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 16299 Z= 0.275 Angle : 0.695 10.016 22004 Z= 0.365 Chirality : 0.046 0.332 2348 Planarity : 0.004 0.052 2812 Dihedral : 8.747 152.872 2217 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.16 % Allowed : 22.46 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.19), residues: 1928 helix: 1.39 (0.15), residues: 1118 sheet: -1.13 (0.39), residues: 150 loop : 0.27 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP D 124 HIS 0.010 0.001 HIS C 101 PHE 0.018 0.002 PHE B 261 TYR 0.018 0.002 TYR C 204 ARG 0.014 0.001 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 896) hydrogen bonds : angle 5.06140 ( 2616) covalent geometry : bond 0.00617 (16298) covalent geometry : angle 0.69530 (22004) Misc. bond : bond 0.00045 ( 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 407 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 370 time to evaluate : 1.986 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 65 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7567 (mt-10) REVERT: A 119 GLU cc_start: 0.8924 (mp0) cc_final: 0.8526 (mp0) REVERT: A 173 LEU cc_start: 0.9541 (mt) cc_final: 0.9271 (mt) REVERT: A 178 SER cc_start: 0.9134 (OUTLIER) cc_final: 0.8889 (p) REVERT: A 250 TYR cc_start: 0.8839 (m-80) cc_final: 0.8159 (m-80) REVERT: A 379 SER cc_start: 0.8926 (t) cc_final: 0.8253 (t) REVERT: A 384 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.6678 (pm20) REVERT: A 406 ASP cc_start: 0.8023 (m-30) cc_final: 0.7791 (t0) REVERT: A 433 THR cc_start: 0.9678 (m) cc_final: 0.9400 (p) REVERT: A 493 MET cc_start: 0.9257 (tmm) cc_final: 0.8583 (tmm) REVERT: A 586 TYR cc_start: 0.8821 (m-10) cc_final: 0.8553 (m-10) REVERT: A 634 MET cc_start: 0.8992 (mmt) cc_final: 0.8760 (mmt) REVERT: A 655 THR cc_start: 0.9197 (m) cc_final: 0.8996 (t) REVERT: A 657 PHE cc_start: 0.8863 (m-80) cc_final: 0.8427 (m-80) REVERT: B 104 TYR cc_start: 0.9121 (m-80) cc_final: 0.8336 (m-80) REVERT: B 286 ASP cc_start: 0.8025 (m-30) cc_final: 0.7483 (m-30) REVERT: B 317 MET cc_start: 0.8998 (mtp) cc_final: 0.8575 (mtt) REVERT: B 362 ASP cc_start: 0.8193 (m-30) cc_final: 0.7363 (m-30) REVERT: B 463 LEU cc_start: 0.9634 (tp) cc_final: 0.9359 (tp) REVERT: B 526 GLU cc_start: 0.8239 (mm-30) cc_final: 0.8009 (mm-30) REVERT: B 612 TYR cc_start: 0.8430 (m-80) cc_final: 0.8213 (m-80) REVERT: B 668 ASN cc_start: 0.9081 (m-40) cc_final: 0.8816 (m-40) REVERT: C 74 MET cc_start: 0.8449 (mmm) cc_final: 0.7993 (mtm) REVERT: C 137 MET cc_start: -0.4677 (mtp) cc_final: -0.5210 (mtp) REVERT: C 287 LEU cc_start: 0.0476 (OUTLIER) cc_final: 0.0059 (tp) REVERT: D 110 MET cc_start: 0.5494 (mtt) cc_final: 0.5005 (tmm) outliers start: 37 outliers final: 32 residues processed: 392 average time/residue: 0.2810 time to fit residues: 165.1428 Evaluate side-chains 387 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 352 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 414 LEU 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 565 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 660 ASP 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 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 25 ASN Chi-restraints excluded: chain D residue 56 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 281 ASP 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 74 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 186 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.169166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.105243 restraints weight = 29988.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.108846 restraints weight = 13865.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.110991 restraints weight = 8240.109| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 16299 Z= 0.138 Angle : 0.668 17.298 22004 Z= 0.341 Chirality : 0.043 0.327 2348 Planarity : 0.004 0.051 2812 Dihedral : 8.290 143.294 2217 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.87 % Allowed : 22.64 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.19), residues: 1928 helix: 1.41 (0.15), residues: 1131 sheet: -0.80 (0.40), residues: 140 loop : 0.16 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 124 HIS 0.009 0.001 HIS C 101 PHE 0.018 0.001 PHE A 261 TYR 0.016 0.001 TYR B 522 ARG 0.015 0.001 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 896) hydrogen bonds : angle 4.95915 ( 2616) covalent geometry : bond 0.00312 (16298) covalent geometry : angle 0.66764 (22004) Misc. bond : bond 0.00029 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6197.24 seconds wall clock time: 109 minutes 9.79 seconds (6549.79 seconds total)