Starting phenix.real_space_refine on Sat May 17 14:56:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bwx_44985/05_2025/9bwx_44985_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bwx_44985/05_2025/9bwx_44985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bwx_44985/05_2025/9bwx_44985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bwx_44985/05_2025/9bwx_44985.map" model { file = "/net/cci-nas-00/data/ceres_data/9bwx_44985/05_2025/9bwx_44985_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bwx_44985/05_2025/9bwx_44985_neut.cif" } resolution = 2.91 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): 0.04s 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: 9.57, per 1000 atoms: 0.60 Number of scatterers: 15954 At special positions: 0 Unit cell: (93.002, 134.904, 133.882, 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: 3.87 Conformation dependent library (CDL) restraints added in 2.1 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: 1.97 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: 6.056A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.520A 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: 3.547A pdb=" N GLU B 31 " --> pdb=" O ASP B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.949A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.960A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.722A 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: 5.842A 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: 4.173A pdb=" N VAL B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 424 through 443 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 474 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.565A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 589 removed outlier: 4.403A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 677 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.514A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.889A pdb=" N GLY A 462 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASN A 410 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLY A 464 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 6.313A 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: 4.314A 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: 5.889A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 removed outlier: 6.456A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.656A 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: 5.99 Time building geometry restraints manager: 4.32 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: 4956 1.34 - 1.46: 2920 1.46 - 1.58: 8247 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 2.37e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.039 1.20e-02 6.94e+03 1.05e+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 8.76e+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 7.60e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.574 -0.033 1.25e-02 6.40e+03 7.18e+00 ... (remaining 16293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21496 2.09 - 4.17: 471 4.17 - 6.26: 33 6.26 - 8.35: 2 8.35 - 10.43: 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 110.54 116.62 -6.08 1.36e+00 5.41e-01 2.00e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.12 -4.41 1.15e+00 7.56e-01 1.47e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.25 -3.97 1.09e+00 8.42e-01 1.33e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.80 -4.30 1.23e+00 6.61e-01 1.22e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.68 -3.97 1.15e+00 7.56e-01 1.19e+01 ... (remaining 21999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.31: 9429 34.31 - 68.63: 329 68.63 - 102.94: 48 102.94 - 137.25: 0 137.25 - 171.56: 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 301.68 130.12 171.56 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 301.68 135.69 165.99 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 -134.29 12.29 0 2.50e+00 1.60e-01 2.42e+01 ... (remaining 9805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2126 0.093 - 0.187: 183 0.187 - 0.280: 34 0.280 - 0.374: 3 0.374 - 0.467: 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 5.45e+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 4.67e+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 3.00e+00 ... (remaining 2345 not shown) Planarity restraints: 2812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 6 " 0.036 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO B 7 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 7 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 7 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.017 2.00e-02 2.50e+03 1.11e-02 2.17e+00 pdb=" CG PHE D 92 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.009 2.00e-02 2.50e+03 ... (remaining 2809 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 131 2.51 - 3.11: 11880 3.11 - 3.70: 26437 3.70 - 4.30: 41184 4.30 - 4.90: 64920 Nonbonded interactions: 144552 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" O1B TTP A 801 " pdb="MG MG A 802 " model vdw 1.919 2.170 nonbonded pdb=" O2A TTP B 801 " pdb="MG MG B 802 " model vdw 1.928 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 144547 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 38.400 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 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 10.433 22004 Z= 0.453 Chirality : 0.059 0.467 2348 Planarity : 0.003 0.055 2812 Dihedral : 17.179 171.563 6120 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.34 % Allowed : 14.12 % 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: 1.04 (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 227 TYR 0.021 0.002 TYR D 179 ARG 0.004 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.16170 ( 896) hydrogen bonds : angle 6.35243 ( 2616) covalent geometry : bond 0.00542 (16298) covalent geometry : angle 0.70717 (22004) Misc. bond : bond 0.83345 ( 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 434 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 411 time to evaluate : 1.792 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 184 ARG cc_start: 0.8631 (tpp-160) cc_final: 0.8417 (tpp-160) REVERT: B 274 ARG cc_start: 0.8031 (ptm160) cc_final: 0.7762 (ptp-110) outliers start: 23 outliers final: 6 residues processed: 427 average time/residue: 1.3603 time to fit residues: 636.1137 Evaluate side-chains 285 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 279 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 127 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 150 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 112 optimal weight: 0.2980 chunk 174 optimal weight: 8.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 232 ASN A 668 ASN B 11 GLN B 14 ASN B 49 HIS B 418 ASN D 80 HIS D 186 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.186463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.096175 restraints weight = 20592.293| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.41 r_work: 0.2823 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16299 Z= 0.189 Angle : 0.582 12.132 22004 Z= 0.312 Chirality : 0.042 0.186 2348 Planarity : 0.004 0.053 2812 Dihedral : 9.076 166.124 2228 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.03 % Allowed : 16.57 % Favored : 80.40 % 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: 1.83 (0.19), residues: 1928 helix: 1.74 (0.15), residues: 1125 sheet: 0.47 (0.41), residues: 132 loop : 0.65 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 9 HIS 0.004 0.001 HIS A 255 PHE 0.021 0.002 PHE B 624 TYR 0.022 0.001 TYR D 105 ARG 0.007 0.001 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.04452 ( 896) hydrogen bonds : angle 4.93360 ( 2616) covalent geometry : bond 0.00421 (16298) covalent geometry : angle 0.58234 (22004) Misc. bond : bond 0.00038 ( 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 362 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 310 time to evaluate : 1.492 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 79 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8122 (mm-30) REVERT: A 184 ARG cc_start: 0.9181 (tpp-160) cc_final: 0.8854 (tpp-160) REVERT: A 194 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8964 (tttm) REVERT: A 227 MET cc_start: 0.9575 (mtp) cc_final: 0.9369 (mtp) REVERT: A 232 ASN cc_start: 0.9097 (OUTLIER) cc_final: 0.8576 (m-40) REVERT: A 274 ARG cc_start: 0.8561 (ttt90) cc_final: 0.8296 (ttt90) REVERT: A 276 LYS cc_start: 0.9205 (mtpp) cc_final: 0.8944 (mmpt) REVERT: A 296 LYS cc_start: 0.8763 (mttt) cc_final: 0.8195 (mmmt) REVERT: A 570 MET cc_start: 0.9515 (mtp) cc_final: 0.9307 (ttm) REVERT: A 602 GLU cc_start: 0.8966 (tt0) cc_final: 0.8296 (tt0) REVERT: A 604 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8510 (mmt90) REVERT: B 11 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8277 (mt0) REVERT: B 15 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8511 (mm-30) REVERT: B 52 LYS cc_start: 0.9404 (OUTLIER) cc_final: 0.9131 (tptm) REVERT: B 56 ASP cc_start: 0.9162 (m-30) cc_final: 0.8844 (m-30) REVERT: B 112 LYS cc_start: 0.9336 (mtpp) cc_final: 0.9099 (mtmm) REVERT: B 120 ASP cc_start: 0.8982 (m-30) cc_final: 0.8728 (m-30) REVERT: B 235 ARG cc_start: 0.9049 (mtm-85) cc_final: 0.8806 (mtm-85) REVERT: B 274 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.7387 (ptp90) REVERT: B 341 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8992 (mmmm) REVERT: B 343 LEU cc_start: 0.9372 (mt) cc_final: 0.9142 (mt) REVERT: B 402 GLU cc_start: 0.8963 (tp30) cc_final: 0.8678 (mp0) REVERT: B 604 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.8908 (mmp80) REVERT: B 610 LYS cc_start: 0.8984 (mtpp) cc_final: 0.8702 (mtpp) REVERT: B 659 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8297 (mtpp) REVERT: C 56 MET cc_start: -0.0644 (mmp) cc_final: -0.1131 (tpt) outliers start: 52 outliers final: 11 residues processed: 340 average time/residue: 1.3281 time to fit residues: 496.5034 Evaluate side-chains 280 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 260 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 313 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 191 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 175 optimal weight: 30.0000 chunk 56 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 136 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 232 ASN A 668 ASN B 109 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.183283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.093545 restraints weight = 20847.551| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.38 r_work: 0.2801 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16299 Z= 0.221 Angle : 0.563 10.875 22004 Z= 0.299 Chirality : 0.042 0.188 2348 Planarity : 0.004 0.055 2812 Dihedral : 8.912 164.972 2219 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.27 % Allowed : 17.04 % Favored : 79.70 % 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: 1.73 (0.19), residues: 1928 helix: 1.66 (0.15), residues: 1135 sheet: 0.14 (0.41), residues: 132 loop : 0.65 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 9 HIS 0.004 0.001 HIS C 101 PHE 0.017 0.001 PHE B 261 TYR 0.019 0.001 TYR C 46 ARG 0.009 0.001 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.04076 ( 896) hydrogen bonds : angle 4.81871 ( 2616) covalent geometry : bond 0.00501 (16298) covalent geometry : angle 0.56314 (22004) Misc. bond : bond 0.00115 ( 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 320 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 264 time to evaluate : 1.785 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 79 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8148 (mm-30) REVERT: A 184 ARG cc_start: 0.9212 (tpp-160) cc_final: 0.8887 (tpp-160) REVERT: A 194 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.9005 (tttm) REVERT: A 227 MET cc_start: 0.9613 (mtp) cc_final: 0.9407 (mtp) REVERT: A 274 ARG cc_start: 0.8694 (ttt90) cc_final: 0.8204 (ttt90) REVERT: A 276 LYS cc_start: 0.9172 (mtpp) cc_final: 0.8748 (mmpt) REVERT: A 296 LYS cc_start: 0.8876 (mttt) cc_final: 0.8270 (mmmt) REVERT: A 316 GLU cc_start: 0.8601 (tp30) cc_final: 0.8375 (tp30) REVERT: A 444 ASP cc_start: 0.8645 (t70) cc_final: 0.8232 (p0) REVERT: A 570 MET cc_start: 0.9511 (mtp) cc_final: 0.9291 (ttm) REVERT: A 602 GLU cc_start: 0.8928 (tt0) cc_final: 0.8655 (tt0) REVERT: B 15 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8519 (mm-30) REVERT: B 31 GLU cc_start: 0.9364 (mt-10) cc_final: 0.9093 (mt-10) REVERT: B 52 LYS cc_start: 0.9420 (OUTLIER) cc_final: 0.9085 (tptm) REVERT: B 56 ASP cc_start: 0.9076 (m-30) cc_final: 0.8768 (m-30) REVERT: B 274 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7078 (ptp90) REVERT: B 276 LYS cc_start: 0.9002 (ptpp) cc_final: 0.8741 (mmtm) REVERT: B 341 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.9005 (mmmm) REVERT: B 343 LEU cc_start: 0.9419 (mt) cc_final: 0.9170 (mt) REVERT: B 603 GLU cc_start: 0.8434 (tm-30) cc_final: 0.7956 (mm-30) REVERT: B 604 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.8921 (mmp80) REVERT: B 610 LYS cc_start: 0.9011 (mtpp) cc_final: 0.8368 (tttp) REVERT: B 659 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8237 (mtpp) REVERT: B 686 ARG cc_start: 0.8441 (mtp85) cc_final: 0.8215 (mtp85) REVERT: D 103 LYS cc_start: 0.5286 (tptm) cc_final: 0.4897 (pptt) outliers start: 56 outliers final: 23 residues processed: 294 average time/residue: 1.5252 time to fit residues: 495.8864 Evaluate side-chains 275 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 246 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 646 GLN Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 8 LYS Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 313 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 153 optimal weight: 40.0000 chunk 136 optimal weight: 8.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 668 ASN B 11 GLN B 232 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.185638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.097120 restraints weight = 20812.681| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.40 r_work: 0.2853 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16299 Z= 0.139 Angle : 0.528 11.562 22004 Z= 0.280 Chirality : 0.040 0.155 2348 Planarity : 0.003 0.047 2812 Dihedral : 8.623 163.915 2219 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.80 % Allowed : 18.09 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.72 (0.19), residues: 1928 helix: 1.68 (0.15), residues: 1136 sheet: -0.01 (0.42), residues: 132 loop : 0.60 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 9 HIS 0.004 0.001 HIS B 438 PHE 0.015 0.001 PHE A 100 TYR 0.035 0.001 TYR D 105 ARG 0.009 0.001 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.03686 ( 896) hydrogen bonds : angle 4.64307 ( 2616) covalent geometry : bond 0.00308 (16298) covalent geometry : angle 0.52840 (22004) Misc. bond : bond 0.00124 ( 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 327 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 279 time to evaluate : 1.764 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 184 ARG cc_start: 0.9163 (tpp-160) cc_final: 0.8801 (tpp-160) REVERT: A 274 ARG cc_start: 0.8756 (ttt90) cc_final: 0.8246 (ttt90) REVERT: A 276 LYS cc_start: 0.9154 (mtpp) cc_final: 0.8735 (mmpt) REVERT: A 296 LYS cc_start: 0.8856 (mttt) cc_final: 0.8242 (mmmt) REVERT: A 316 GLU cc_start: 0.8593 (tp30) cc_final: 0.8330 (tp30) REVERT: A 444 ASP cc_start: 0.8633 (t70) cc_final: 0.8130 (p0) REVERT: A 602 GLU cc_start: 0.8903 (tt0) cc_final: 0.8687 (tt0) REVERT: B 11 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8004 (mt0) REVERT: B 15 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8469 (mp0) REVERT: B 52 LYS cc_start: 0.9429 (OUTLIER) cc_final: 0.9080 (tptm) REVERT: B 56 ASP cc_start: 0.9047 (m-30) cc_final: 0.8723 (m-30) REVERT: B 79 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8019 (mm-30) REVERT: B 120 ASP cc_start: 0.8934 (m-30) cc_final: 0.8731 (m-30) REVERT: B 170 CYS cc_start: 0.8586 (p) cc_final: 0.8246 (m) REVERT: B 274 ARG cc_start: 0.8651 (ptm160) cc_final: 0.7336 (ptp90) REVERT: B 335 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8278 (mt-10) REVERT: B 341 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8997 (mmmm) REVERT: B 343 LEU cc_start: 0.9399 (mt) cc_final: 0.9145 (mt) REVERT: B 362 ASP cc_start: 0.8680 (m-30) cc_final: 0.8282 (m-30) REVERT: B 402 GLU cc_start: 0.8997 (tp30) cc_final: 0.8754 (mp0) REVERT: B 603 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7781 (tm-30) REVERT: B 604 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.8939 (mmp80) REVERT: B 610 LYS cc_start: 0.9032 (mtpp) cc_final: 0.8781 (ttmm) REVERT: B 659 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8243 (mtpp) REVERT: C 56 MET cc_start: -0.0633 (mmp) cc_final: -0.1180 (tpt) outliers start: 48 outliers final: 22 residues processed: 304 average time/residue: 1.3169 time to fit residues: 440.0596 Evaluate side-chains 279 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 252 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 147 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 109 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 188 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 165 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN B 232 ASN D 24 GLN D 28 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.182067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.093325 restraints weight = 21240.851| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.38 r_work: 0.2773 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2608 r_free = 0.2608 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2608 r_free = 0.2608 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16299 Z= 0.285 Angle : 0.582 11.531 22004 Z= 0.306 Chirality : 0.043 0.147 2348 Planarity : 0.004 0.049 2812 Dihedral : 8.889 167.755 2217 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.33 % Allowed : 18.26 % Favored : 78.41 % 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: 1.63 (0.19), residues: 1928 helix: 1.59 (0.15), residues: 1135 sheet: -0.12 (0.43), residues: 128 loop : 0.63 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 9 HIS 0.004 0.001 HIS A 255 PHE 0.017 0.002 PHE A 492 TYR 0.014 0.001 TYR D 142 ARG 0.010 0.001 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 896) hydrogen bonds : angle 4.73606 ( 2616) covalent geometry : bond 0.00650 (16298) covalent geometry : angle 0.58201 (22004) Misc. bond : bond 0.00119 ( 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 310 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 253 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8449 (mm-30) REVERT: A 184 ARG cc_start: 0.9177 (tpp-160) cc_final: 0.8888 (tpp-160) REVERT: A 274 ARG cc_start: 0.8629 (ttt90) cc_final: 0.8304 (ttt90) REVERT: A 316 GLU cc_start: 0.8590 (tp30) cc_final: 0.8330 (tp30) REVERT: A 444 ASP cc_start: 0.8641 (t70) cc_final: 0.8254 (p0) REVERT: A 589 SER cc_start: 0.9598 (OUTLIER) cc_final: 0.9306 (t) REVERT: A 604 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8187 (mmt-90) REVERT: B 52 LYS cc_start: 0.9409 (OUTLIER) cc_final: 0.9075 (tptm) REVERT: B 56 ASP cc_start: 0.9104 (m-30) cc_final: 0.8760 (m-30) REVERT: B 112 LYS cc_start: 0.9395 (mtpp) cc_final: 0.9077 (mtmm) REVERT: B 274 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7300 (ptp90) REVERT: B 341 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8997 (mmmm) REVERT: B 402 GLU cc_start: 0.9002 (tp30) cc_final: 0.8651 (mp0) REVERT: B 603 GLU cc_start: 0.8466 (tm-30) cc_final: 0.7983 (tm-30) REVERT: B 610 LYS cc_start: 0.9052 (mtpp) cc_final: 0.8589 (mtpp) REVERT: B 659 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8257 (mtpp) REVERT: B 686 ARG cc_start: 0.8387 (mtp85) cc_final: 0.7993 (mtp85) outliers start: 57 outliers final: 28 residues processed: 287 average time/residue: 1.3634 time to fit residues: 429.0598 Evaluate side-chains 262 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 228 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 174 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 143 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 108 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 182 optimal weight: 50.0000 chunk 56 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN B 11 GLN B 62 GLN B 232 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.185105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.096557 restraints weight = 20843.458| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.37 r_work: 0.2852 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16299 Z= 0.137 Angle : 0.547 12.854 22004 Z= 0.283 Chirality : 0.040 0.153 2348 Planarity : 0.003 0.050 2812 Dihedral : 8.487 163.745 2217 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.45 % Allowed : 20.07 % Favored : 77.48 % 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: 1.67 (0.19), residues: 1928 helix: 1.71 (0.15), residues: 1130 sheet: -0.44 (0.41), residues: 136 loop : 0.57 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 9 HIS 0.004 0.001 HIS B 438 PHE 0.016 0.001 PHE A 492 TYR 0.039 0.001 TYR D 105 ARG 0.011 0.001 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 896) hydrogen bonds : angle 4.58515 ( 2616) covalent geometry : bond 0.00307 (16298) covalent geometry : angle 0.54734 (22004) Misc. bond : bond 0.00483 ( 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 296 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 254 time to evaluate : 1.752 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 79 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8406 (mm-30) REVERT: A 112 LYS cc_start: 0.9306 (mtpp) cc_final: 0.8980 (ptpp) REVERT: A 184 ARG cc_start: 0.9125 (tpp-160) cc_final: 0.8814 (tpp-160) REVERT: A 274 ARG cc_start: 0.8663 (ttt90) cc_final: 0.8391 (ttm110) REVERT: A 276 LYS cc_start: 0.9122 (mtpp) cc_final: 0.8761 (mmpt) REVERT: A 316 GLU cc_start: 0.8599 (tp30) cc_final: 0.8383 (tp30) REVERT: A 402 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8394 (mt-10) REVERT: A 586 TYR cc_start: 0.9431 (m-80) cc_final: 0.9223 (m-80) REVERT: A 589 SER cc_start: 0.9633 (OUTLIER) cc_final: 0.9343 (t) REVERT: A 602 GLU cc_start: 0.8917 (tt0) cc_final: 0.8552 (tt0) REVERT: B 11 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8254 (mt0) REVERT: B 15 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8540 (mm-30) REVERT: B 52 LYS cc_start: 0.9427 (OUTLIER) cc_final: 0.9086 (tptm) REVERT: B 56 ASP cc_start: 0.9062 (m-30) cc_final: 0.8723 (m-30) REVERT: B 79 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8004 (mm-30) REVERT: B 112 LYS cc_start: 0.9341 (mtpp) cc_final: 0.8988 (mtmm) REVERT: B 170 CYS cc_start: 0.8585 (p) cc_final: 0.8282 (m) REVERT: B 228 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8700 (mtmm) REVERT: B 246 SER cc_start: 0.8256 (OUTLIER) cc_final: 0.7672 (p) REVERT: B 274 ARG cc_start: 0.8558 (ptm160) cc_final: 0.7369 (ptp90) REVERT: B 335 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8252 (mt-10) REVERT: B 341 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8974 (mmmm) REVERT: B 343 LEU cc_start: 0.9328 (mt) cc_final: 0.9077 (mt) REVERT: B 362 ASP cc_start: 0.8686 (m-30) cc_final: 0.8282 (m-30) REVERT: B 402 GLU cc_start: 0.9016 (tp30) cc_final: 0.8721 (mp0) REVERT: B 603 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7953 (tm-30) REVERT: B 610 LYS cc_start: 0.9075 (mtpp) cc_final: 0.8673 (mtpp) REVERT: B 659 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8293 (mtpp) REVERT: C 56 MET cc_start: -0.0505 (mmp) cc_final: -0.1146 (tpt) REVERT: D 46 TYR cc_start: 0.8548 (m-10) cc_final: 0.8266 (p90) REVERT: D 269 MET cc_start: 0.6085 (OUTLIER) cc_final: 0.5737 (mmp) outliers start: 42 outliers final: 21 residues processed: 277 average time/residue: 1.3793 time to fit residues: 419.4010 Evaluate side-chains 267 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 238 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 7 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 26 optimal weight: 0.0970 chunk 84 optimal weight: 0.9990 chunk 185 optimal weight: 20.0000 chunk 34 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN B 11 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 ASN C 216 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.186086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.098614 restraints weight = 20991.321| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.35 r_work: 0.2878 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16299 Z= 0.127 Angle : 0.539 12.865 22004 Z= 0.279 Chirality : 0.040 0.189 2348 Planarity : 0.003 0.054 2812 Dihedral : 8.162 162.118 2216 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.51 % Allowed : 20.30 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.71 (0.19), residues: 1928 helix: 1.74 (0.15), residues: 1130 sheet: -0.45 (0.39), residues: 148 loop : 0.62 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 9 HIS 0.004 0.001 HIS B 438 PHE 0.016 0.001 PHE A 492 TYR 0.027 0.001 TYR D 105 ARG 0.012 0.001 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.03406 ( 896) hydrogen bonds : angle 4.49294 ( 2616) covalent geometry : bond 0.00283 (16298) covalent geometry : angle 0.53932 (22004) Misc. bond : bond 0.00583 ( 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 301 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 258 time to evaluate : 1.699 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 79 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8370 (mm-30) REVERT: A 112 LYS cc_start: 0.9276 (mtpp) cc_final: 0.8986 (ptpp) REVERT: A 274 ARG cc_start: 0.8699 (ttt90) cc_final: 0.8099 (ttm170) REVERT: A 276 LYS cc_start: 0.9074 (mtpp) cc_final: 0.8715 (mmtt) REVERT: A 316 GLU cc_start: 0.8568 (tp30) cc_final: 0.8360 (tp30) REVERT: A 402 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8358 (mt-10) REVERT: A 446 ARG cc_start: 0.8030 (mmp-170) cc_final: 0.7799 (mmp-170) REVERT: A 589 SER cc_start: 0.9629 (t) cc_final: 0.9356 (t) REVERT: A 602 GLU cc_start: 0.8913 (tt0) cc_final: 0.8163 (tt0) REVERT: A 604 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8497 (mmt90) REVERT: B 11 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8310 (mt0) REVERT: B 15 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8531 (mm-30) REVERT: B 52 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.9025 (tptm) REVERT: B 56 ASP cc_start: 0.9042 (m-30) cc_final: 0.8710 (m-30) REVERT: B 79 GLU cc_start: 0.8487 (mm-30) cc_final: 0.7981 (mm-30) REVERT: B 112 LYS cc_start: 0.9338 (mtpp) cc_final: 0.8955 (mtmm) REVERT: B 170 CYS cc_start: 0.8524 (p) cc_final: 0.8264 (m) REVERT: B 246 SER cc_start: 0.8248 (OUTLIER) cc_final: 0.7669 (p) REVERT: B 274 ARG cc_start: 0.8507 (ptm160) cc_final: 0.7282 (ptp90) REVERT: B 335 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8328 (mt-10) REVERT: B 341 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8922 (mmmm) REVERT: B 343 LEU cc_start: 0.9307 (mt) cc_final: 0.9059 (mt) REVERT: B 362 ASP cc_start: 0.8628 (m-30) cc_final: 0.8220 (m-30) REVERT: B 526 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8433 (mp0) REVERT: B 603 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7935 (tm-30) REVERT: B 610 LYS cc_start: 0.9085 (mtpp) cc_final: 0.8609 (mtpp) REVERT: C 56 MET cc_start: -0.0465 (mmp) cc_final: -0.1053 (tpt) REVERT: D 105 TYR cc_start: 0.2384 (OUTLIER) cc_final: 0.1669 (p90) REVERT: D 269 MET cc_start: 0.6141 (OUTLIER) cc_final: 0.5819 (mmp) outliers start: 43 outliers final: 20 residues processed: 281 average time/residue: 1.3721 time to fit residues: 424.2849 Evaluate side-chains 270 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 243 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 146 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 174 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 96 optimal weight: 0.3980 chunk 31 optimal weight: 4.9990 chunk 181 optimal weight: 30.0000 chunk 9 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 131 ASN B 232 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 HIS ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.184237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.096915 restraints weight = 20817.046| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.33 r_work: 0.2852 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16299 Z= 0.167 Angle : 0.558 14.901 22004 Z= 0.291 Chirality : 0.040 0.188 2348 Planarity : 0.003 0.054 2812 Dihedral : 8.152 162.576 2216 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.28 % Allowed : 21.41 % Favored : 76.31 % 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: 1.68 (0.19), residues: 1928 helix: 1.69 (0.15), residues: 1134 sheet: -0.55 (0.39), residues: 144 loop : 0.66 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 9 HIS 0.004 0.001 HIS B 438 PHE 0.020 0.001 PHE A 492 TYR 0.031 0.001 TYR C 46 ARG 0.008 0.001 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.03464 ( 896) hydrogen bonds : angle 4.51297 ( 2616) covalent geometry : bond 0.00379 (16298) covalent geometry : angle 0.55810 (22004) Misc. bond : bond 0.00105 ( 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 291 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 252 time to evaluate : 1.867 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: 0.9238 (ttmm) cc_final: 0.8816 (tptt) REVERT: A 79 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8378 (mm-30) REVERT: A 112 LYS cc_start: 0.9273 (mtpp) cc_final: 0.8999 (ptpp) REVERT: A 274 ARG cc_start: 0.8756 (ttt90) cc_final: 0.8462 (ttm-80) REVERT: A 276 LYS cc_start: 0.9097 (mtpp) cc_final: 0.8718 (mmtt) REVERT: A 296 LYS cc_start: 0.8779 (mttt) cc_final: 0.8158 (mmmt) REVERT: A 316 GLU cc_start: 0.8602 (tp30) cc_final: 0.8399 (tp30) REVERT: A 402 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8413 (mt-10) REVERT: A 446 ARG cc_start: 0.8115 (mmp-170) cc_final: 0.7844 (mmp-170) REVERT: A 589 SER cc_start: 0.9629 (t) cc_final: 0.9377 (t) REVERT: A 602 GLU cc_start: 0.8894 (tt0) cc_final: 0.8117 (tt0) REVERT: A 604 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8481 (mmt90) REVERT: B 15 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8570 (mm-30) REVERT: B 52 LYS cc_start: 0.9421 (OUTLIER) cc_final: 0.9038 (tptm) REVERT: B 56 ASP cc_start: 0.9036 (m-30) cc_final: 0.8716 (m-30) REVERT: B 79 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8000 (mm-30) REVERT: B 112 LYS cc_start: 0.9313 (mtpp) cc_final: 0.9057 (mtpm) REVERT: B 170 CYS cc_start: 0.8595 (p) cc_final: 0.8291 (m) REVERT: B 274 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7378 (ptp90) REVERT: B 335 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8190 (mt-10) REVERT: B 341 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8946 (mmmm) REVERT: B 343 LEU cc_start: 0.9351 (mt) cc_final: 0.9111 (mt) REVERT: B 362 ASP cc_start: 0.8669 (m-30) cc_final: 0.8302 (m-30) REVERT: B 402 GLU cc_start: 0.8975 (tp30) cc_final: 0.8734 (mp0) REVERT: B 526 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8457 (mp0) REVERT: B 603 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7901 (tm-30) REVERT: B 610 LYS cc_start: 0.9064 (mtpp) cc_final: 0.8606 (mtpp) REVERT: C 56 MET cc_start: -0.0665 (mmp) cc_final: -0.1229 (tpt) REVERT: C 319 ASP cc_start: 0.9211 (m-30) cc_final: 0.8943 (m-30) REVERT: D 46 TYR cc_start: 0.8463 (m-10) cc_final: 0.8075 (p90) REVERT: D 105 TYR cc_start: 0.2279 (OUTLIER) cc_final: 0.1425 (p90) REVERT: D 269 MET cc_start: 0.6111 (OUTLIER) cc_final: 0.5780 (mmp) outliers start: 39 outliers final: 26 residues processed: 276 average time/residue: 1.3270 time to fit residues: 403.3802 Evaluate side-chains 278 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 246 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 140 optimal weight: 50.0000 chunk 110 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 162 optimal weight: 50.0000 chunk 168 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 ASN B 232 ASN ** D 265 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 = 0.4106 r_free = 0.4106 target = 0.183369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.095574 restraints weight = 20872.207| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.35 r_work: 0.2827 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16299 Z= 0.198 Angle : 0.585 16.863 22004 Z= 0.303 Chirality : 0.041 0.160 2348 Planarity : 0.003 0.054 2812 Dihedral : 8.224 163.542 2216 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.16 % Allowed : 21.53 % Favored : 76.31 % 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: 1.65 (0.19), residues: 1928 helix: 1.65 (0.15), residues: 1136 sheet: -0.44 (0.41), residues: 136 loop : 0.64 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 9 HIS 0.004 0.001 HIS B 438 PHE 0.019 0.001 PHE A 492 TYR 0.031 0.001 TYR C 46 ARG 0.008 0.001 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 896) hydrogen bonds : angle 4.54870 ( 2616) covalent geometry : bond 0.00452 (16298) covalent geometry : angle 0.58476 (22004) Misc. bond : bond 0.00186 ( 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 287 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 250 time to evaluate : 1.635 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: 0.9247 (ttmm) cc_final: 0.8803 (tptt) REVERT: A 79 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8411 (mm-30) REVERT: A 112 LYS cc_start: 0.9272 (mtpp) cc_final: 0.8995 (ptpp) REVERT: A 274 ARG cc_start: 0.8796 (ttt90) cc_final: 0.8496 (ttm110) REVERT: A 296 LYS cc_start: 0.8797 (mttt) cc_final: 0.8182 (mmmt) REVERT: A 384 GLU cc_start: 0.9351 (OUTLIER) cc_final: 0.8566 (pm20) REVERT: A 402 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8409 (mt-10) REVERT: A 589 SER cc_start: 0.9627 (t) cc_final: 0.9369 (t) REVERT: A 599 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8903 (mt-10) REVERT: A 602 GLU cc_start: 0.8897 (tt0) cc_final: 0.8120 (tt0) REVERT: A 604 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8517 (mmt90) REVERT: B 15 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8579 (mm-30) REVERT: B 52 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9082 (tptm) REVERT: B 56 ASP cc_start: 0.9056 (m-30) cc_final: 0.8741 (m-30) REVERT: B 79 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8019 (mm-30) REVERT: B 112 LYS cc_start: 0.9323 (mtpp) cc_final: 0.9060 (mtpm) REVERT: B 170 CYS cc_start: 0.8623 (p) cc_final: 0.8246 (m) REVERT: B 274 ARG cc_start: 0.8404 (ptm160) cc_final: 0.7356 (ptp90) REVERT: B 335 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8215 (mt-10) REVERT: B 341 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8954 (mmmm) REVERT: B 343 LEU cc_start: 0.9371 (mt) cc_final: 0.9107 (mt) REVERT: B 402 GLU cc_start: 0.8986 (tp30) cc_final: 0.8744 (mp0) REVERT: B 598 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8780 (mmm) REVERT: B 603 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7910 (tm-30) REVERT: B 610 LYS cc_start: 0.9083 (mtpp) cc_final: 0.8607 (mtpp) REVERT: B 686 ARG cc_start: 0.8083 (ptm160) cc_final: 0.7580 (ptm-80) REVERT: C 56 MET cc_start: -0.0680 (mmp) cc_final: -0.1243 (tpt) REVERT: C 317 ASP cc_start: 0.9138 (m-30) cc_final: 0.8433 (t0) REVERT: D 46 TYR cc_start: 0.8444 (m-10) cc_final: 0.8061 (p90) REVERT: D 105 TYR cc_start: 0.2009 (OUTLIER) cc_final: 0.1123 (p90) REVERT: D 269 MET cc_start: 0.6120 (OUTLIER) cc_final: 0.5794 (mmp) outliers start: 37 outliers final: 25 residues processed: 272 average time/residue: 1.3312 time to fit residues: 398.3570 Evaluate side-chains 271 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 239 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 165 optimal weight: 40.0000 chunk 180 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 chunk 190 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN B 232 ASN D 181 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.184722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.097462 restraints weight = 20953.316| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.38 r_work: 0.2854 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16299 Z= 0.151 Angle : 0.570 17.733 22004 Z= 0.296 Chirality : 0.040 0.176 2348 Planarity : 0.004 0.053 2812 Dihedral : 8.062 162.036 2216 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.75 % Allowed : 22.29 % Favored : 75.96 % 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: 1.69 (0.19), residues: 1928 helix: 1.70 (0.15), residues: 1132 sheet: -0.46 (0.41), residues: 136 loop : 0.64 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 9 HIS 0.004 0.001 HIS B 438 PHE 0.019 0.001 PHE A 492 TYR 0.030 0.001 TYR C 46 ARG 0.009 0.001 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 896) hydrogen bonds : angle 4.51575 ( 2616) covalent geometry : bond 0.00345 (16298) covalent geometry : angle 0.56995 (22004) Misc. bond : bond 0.00137 ( 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 282 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 252 time to evaluate : 1.660 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: 0.9235 (ttmm) cc_final: 0.8800 (tptt) REVERT: A 79 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8387 (mm-30) REVERT: A 112 LYS cc_start: 0.9246 (mtpp) cc_final: 0.9007 (ptpp) REVERT: A 274 ARG cc_start: 0.8704 (ttt90) cc_final: 0.8116 (ttm170) REVERT: A 296 LYS cc_start: 0.8735 (mttt) cc_final: 0.8098 (mmmt) REVERT: A 384 GLU cc_start: 0.9338 (OUTLIER) cc_final: 0.8544 (pm20) REVERT: A 402 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8272 (mp0) REVERT: A 446 ARG cc_start: 0.8204 (mmp-170) cc_final: 0.7951 (mmp-170) REVERT: A 589 SER cc_start: 0.9623 (t) cc_final: 0.9370 (t) REVERT: A 602 GLU cc_start: 0.8896 (tt0) cc_final: 0.8145 (tt0) REVERT: A 604 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8500 (mmt90) REVERT: B 15 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8602 (mm-30) REVERT: B 52 LYS cc_start: 0.9420 (OUTLIER) cc_final: 0.9073 (tptm) REVERT: B 56 ASP cc_start: 0.9040 (m-30) cc_final: 0.8719 (m-30) REVERT: B 79 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8017 (mm-30) REVERT: B 112 LYS cc_start: 0.9302 (mtpp) cc_final: 0.9037 (mtpm) REVERT: B 170 CYS cc_start: 0.8543 (p) cc_final: 0.8258 (m) REVERT: B 232 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8409 (m110) REVERT: B 246 SER cc_start: 0.8354 (OUTLIER) cc_final: 0.7799 (p) REVERT: B 274 ARG cc_start: 0.8422 (ptm160) cc_final: 0.7377 (ptp90) REVERT: B 335 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8269 (mt-10) REVERT: B 341 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8942 (mmmm) REVERT: B 343 LEU cc_start: 0.9360 (mt) cc_final: 0.9097 (mt) REVERT: B 362 ASP cc_start: 0.8674 (m-30) cc_final: 0.8293 (m-30) REVERT: B 402 GLU cc_start: 0.8996 (tp30) cc_final: 0.8713 (mp0) REVERT: B 526 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8399 (mp0) REVERT: B 598 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8737 (mmm) REVERT: B 603 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7891 (tm-30) REVERT: B 610 LYS cc_start: 0.9097 (mtpp) cc_final: 0.8632 (mtpp) REVERT: B 686 ARG cc_start: 0.7994 (ptm160) cc_final: 0.7486 (ptm-80) REVERT: C 56 MET cc_start: -0.0692 (mmp) cc_final: -0.1252 (tpt) REVERT: C 317 ASP cc_start: 0.9114 (m-30) cc_final: 0.8386 (t0) REVERT: D 46 TYR cc_start: 0.8432 (m-10) cc_final: 0.8057 (p90) REVERT: D 105 TYR cc_start: 0.2065 (OUTLIER) cc_final: 0.1128 (p90) REVERT: D 269 MET cc_start: 0.6163 (OUTLIER) cc_final: 0.5862 (mmp) outliers start: 30 outliers final: 20 residues processed: 268 average time/residue: 1.3530 time to fit residues: 400.6138 Evaluate side-chains 272 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 243 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 186 optimal weight: 50.0000 chunk 119 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 140 optimal weight: 50.0000 chunk 168 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 ASN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.186408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.099198 restraints weight = 20929.942| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.38 r_work: 0.2875 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16299 Z= 0.131 Angle : 0.577 17.409 22004 Z= 0.299 Chirality : 0.040 0.169 2348 Planarity : 0.003 0.052 2812 Dihedral : 7.879 160.774 2216 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.75 % Allowed : 22.70 % Favored : 75.55 % 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: 1.69 (0.19), residues: 1928 helix: 1.69 (0.15), residues: 1134 sheet: -0.44 (0.40), residues: 148 loop : 0.66 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 9 HIS 0.004 0.001 HIS B 438 PHE 0.019 0.001 PHE A 492 TYR 0.030 0.001 TYR C 46 ARG 0.009 0.001 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.03328 ( 896) hydrogen bonds : angle 4.48619 ( 2616) covalent geometry : bond 0.00295 (16298) covalent geometry : angle 0.57693 (22004) Misc. bond : bond 0.00118 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19088.49 seconds wall clock time: 327 minutes 14.39 seconds (19634.39 seconds total)