Starting phenix.real_space_refine on Sat Jun 14 05:41:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bx8_44999/06_2025/9bx8_44999_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bx8_44999/06_2025/9bx8_44999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bx8_44999/06_2025/9bx8_44999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bx8_44999/06_2025/9bx8_44999.map" model { file = "/net/cci-nas-00/data/ceres_data/9bx8_44999/06_2025/9bx8_44999_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bx8_44999/06_2025/9bx8_44999_neut.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 12 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10190 2.51 5 N 2598 2.21 5 O 3066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15954 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 9.30, per 1000 atoms: 0.58 Number of scatterers: 15954 At special positions: 0 Unit cell: (93.002, 127.75, 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: 4.10 Conformation dependent library (CDL) restraints added in 2.0 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: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 27 through 41 removed outlier: 3.555A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.075A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 4.058A 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: 3.872A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.793A pdb=" N GLN A 242 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.639A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 318 through 329 removed outlier: 6.056A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.520A 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: 3.548A pdb=" N GLU B 31 " --> pdb=" O ASP B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.949A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.960A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.721A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 222 through 237 removed outlier: 3.779A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.574A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 318 through 329 removed outlier: 5.841A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 367 removed outlier: 4.174A pdb=" N VAL B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 424 through 443 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 474 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.566A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 589 removed outlier: 4.403A 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: 6.888A pdb=" N GLY A 462 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASN A 410 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLY A 464 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.170A 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: 5.890A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 removed outlier: 6.456A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AA9, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB1, first strand: chain 'B' and resid 655 through 659 898 hydrogen bonds defined for protein. 2616 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.50 Time building geometry restraints manager: 4.86 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: 5014 1.34 - 1.46: 2987 1.46 - 1.58: 8122 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 -0.038 1.20e-02 6.94e+03 1.01e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.574 -0.031 1.08e-02 8.57e+03 8.31e+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 7.53e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.573 -0.033 1.25e-02 6.40e+03 6.76e+00 ... (remaining 16293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 21502 2.10 - 4.19: 465 4.19 - 6.29: 34 6.29 - 8.38: 1 8.38 - 10.48: 2 Bond angle restraints: 22004 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.63 -6.09 1.36e+00 5.41e-01 2.00e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.10 -4.39 1.15e+00 7.56e-01 1.46e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.82 -4.32 1.23e+00 6.61e-01 1.23e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.69 -3.98 1.15e+00 7.56e-01 1.20e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.55 3.64 1.06e+00 8.90e-01 1.18e+01 ... (remaining 21999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.32: 9428 34.32 - 68.64: 331 68.64 - 102.96: 47 102.96 - 137.29: 0 137.29 - 171.61: 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 301.68 130.08 171.61 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 301.68 135.68 166.00 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 -134.30 12.30 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: 2128 0.093 - 0.186: 182 0.186 - 0.279: 31 0.279 - 0.372: 5 0.372 - 0.465: 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 5.42e+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 4.64e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+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 5.50e-02 4.83e+00 pdb=" N PRO B 7 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 7 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 7 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO D 75 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.017 2.00e-02 2.50e+03 1.11e-02 2.15e+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 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.009 2.00e-02 2.50e+03 ... (remaining 2809 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 132 2.51 - 3.11: 11874 3.11 - 3.70: 26443 3.70 - 4.30: 41240 4.30 - 4.90: 65005 Nonbonded interactions: 144694 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 1.918 2.170 nonbonded pdb=" O2A TTP B 801 " pdb="MG MG B 802 " model vdw 1.929 2.170 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 2.320 ... (remaining 144689 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.550 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: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 38.030 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:3.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 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 : 0.708 10.476 22004 Z= 0.453 Chirality : 0.059 0.465 2348 Planarity : 0.003 0.055 2812 Dihedral : 17.174 171.608 6120 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.46 % Allowed : 14.00 % 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: 1.10 (0.18), residues: 1928 helix: 1.05 (0.15), residues: 1133 sheet: 0.46 (0.39), residues: 146 loop : 0.45 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 PHE 0.020 0.002 PHE C 227 TYR 0.020 0.002 TYR D 179 ARG 0.004 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.16169 ( 896) hydrogen bonds : angle 6.35333 ( 2616) covalent geometry : bond 0.00542 (16298) covalent geometry : angle 0.70775 (22004) Misc. bond : bond 0.83327 ( 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 899 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 874 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.7281 (p0) cc_final: 0.7071 (p0) REVERT: A 194 LYS cc_start: 0.8712 (tttt) cc_final: 0.8509 (tttp) REVERT: A 231 ASP cc_start: 0.8573 (t70) cc_final: 0.8361 (t70) REVERT: A 259 ASN cc_start: 0.7820 (m-40) cc_final: 0.7555 (m-40) REVERT: A 286 ASP cc_start: 0.7608 (m-30) cc_final: 0.6919 (m-30) REVERT: A 362 ASP cc_start: 0.6787 (m-30) cc_final: 0.6355 (m-30) REVERT: A 379 SER cc_start: 0.8842 (t) cc_final: 0.8400 (t) REVERT: A 591 THR cc_start: 0.8603 (p) cc_final: 0.8391 (m) REVERT: A 652 ILE cc_start: 0.9357 (mt) cc_final: 0.9057 (mt) REVERT: A 679 ILE cc_start: 0.9348 (mm) cc_final: 0.9120 (mm) REVERT: B 67 GLU cc_start: 0.7290 (mp0) cc_final: 0.7087 (mp0) REVERT: B 155 THR cc_start: 0.9148 (m) cc_final: 0.8846 (t) REVERT: B 177 ASP cc_start: 0.8411 (t0) cc_final: 0.8195 (t0) REVERT: B 194 LYS cc_start: 0.8972 (tttt) cc_final: 0.8725 (ttpt) REVERT: B 211 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6994 (mm-30) REVERT: B 250 TYR cc_start: 0.8678 (m-80) cc_final: 0.7887 (m-80) REVERT: B 286 ASP cc_start: 0.7187 (m-30) cc_final: 0.6392 (m-30) REVERT: B 357 TYR cc_start: 0.8718 (m-10) cc_final: 0.8351 (m-80) REVERT: B 362 ASP cc_start: 0.7219 (m-30) cc_final: 0.6432 (m-30) REVERT: B 379 SER cc_start: 0.9080 (t) cc_final: 0.8197 (t) REVERT: B 456 LYS cc_start: 0.8749 (ttpp) cc_final: 0.8482 (ttpp) REVERT: B 598 MET cc_start: 0.7652 (mtm) cc_final: 0.7062 (mtm) REVERT: B 628 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7662 (mt-10) REVERT: C 66 ASP cc_start: 0.5021 (m-30) cc_final: 0.4490 (m-30) REVERT: C 92 PHE cc_start: 0.7840 (t80) cc_final: 0.7524 (t80) REVERT: C 131 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6461 (mt) REVERT: D 178 PHE cc_start: 0.5738 (m-80) cc_final: 0.5168 (m-80) REVERT: D 213 TYR cc_start: 0.4890 (t80) cc_final: 0.4610 (t80) REVERT: D 260 ILE cc_start: 0.7299 (mt) cc_final: 0.6409 (mp) REVERT: D 321 TYR cc_start: 0.7759 (m-80) cc_final: 0.6590 (m-80) outliers start: 25 outliers final: 4 residues processed: 882 average time/residue: 0.3000 time to fit residues: 380.4934 Evaluate side-chains 636 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 631 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 131 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 112 optimal weight: 0.3980 chunk 174 optimal weight: 5.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 14 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 312 GLN A 370 ASN B 14 ASN ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 GLN B 418 ASN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN C 24 GLN C 28 GLN C 84 HIS C 107 ASN C 192 ASN ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 91 ASN D 127 GLN D 136 GLN D 233 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.141689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.098371 restraints weight = 28089.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.102062 restraints weight = 12243.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.104360 restraints weight = 7154.929| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3789 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= 0.193 Angle : 0.668 8.645 22004 Z= 0.355 Chirality : 0.045 0.198 2348 Planarity : 0.004 0.060 2812 Dihedral : 8.876 155.376 2222 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.62 % Allowed : 17.85 % Favored : 78.53 % 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: 1.52 (0.18), residues: 1928 helix: 1.43 (0.15), residues: 1124 sheet: 0.38 (0.41), residues: 136 loop : 0.64 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 124 HIS 0.023 0.001 HIS C 201 PHE 0.032 0.002 PHE B 261 TYR 0.027 0.002 TYR C 173 ARG 0.008 0.001 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.04711 ( 896) hydrogen bonds : angle 5.18323 ( 2616) covalent geometry : bond 0.00431 (16298) covalent geometry : angle 0.66769 (22004) Misc. bond : bond 0.00118 ( 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 715 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 653 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7627 (mt-10) REVERT: A 107 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8164 (mttp) REVERT: A 246 SER cc_start: 0.7486 (m) cc_final: 0.6966 (p) REVERT: A 286 ASP cc_start: 0.8696 (m-30) cc_final: 0.7520 (m-30) REVERT: A 344 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7758 (mt-10) REVERT: A 355 TYR cc_start: 0.8990 (m-80) cc_final: 0.8727 (m-80) REVERT: A 362 ASP cc_start: 0.7514 (m-30) cc_final: 0.6463 (m-30) REVERT: A 379 SER cc_start: 0.9079 (t) cc_final: 0.8863 (t) REVERT: A 535 ASP cc_start: 0.8328 (t0) cc_final: 0.7850 (t0) REVERT: A 668 ASN cc_start: 0.9304 (m-40) cc_final: 0.9087 (m110) REVERT: B 54 LYS cc_start: 0.9547 (tttp) cc_final: 0.9283 (tttt) REVERT: B 109 ASN cc_start: 0.9105 (OUTLIER) cc_final: 0.8692 (m-40) REVERT: B 211 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7869 (mm-30) REVERT: B 250 TYR cc_start: 0.9350 (m-80) cc_final: 0.7927 (m-80) REVERT: B 263 ASP cc_start: 0.8881 (m-30) cc_final: 0.8492 (m-30) REVERT: B 286 ASP cc_start: 0.8152 (m-30) cc_final: 0.7157 (m-30) REVERT: B 321 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7631 (tm-30) REVERT: B 322 MET cc_start: 0.9321 (mmm) cc_final: 0.9070 (mmt) REVERT: B 335 GLU cc_start: 0.7893 (tt0) cc_final: 0.7680 (mt-10) REVERT: B 355 TYR cc_start: 0.8839 (m-80) cc_final: 0.8460 (m-80) REVERT: B 357 TYR cc_start: 0.9122 (m-10) cc_final: 0.8660 (m-80) REVERT: B 362 ASP cc_start: 0.7925 (m-30) cc_final: 0.6752 (m-30) REVERT: B 366 LYS cc_start: 0.8668 (ptmt) cc_final: 0.8391 (ptmt) REVERT: B 379 SER cc_start: 0.9241 (t) cc_final: 0.8475 (t) REVERT: B 402 GLU cc_start: 0.8350 (tp30) cc_final: 0.8122 (tm-30) REVERT: B 426 GLU cc_start: 0.8386 (pm20) cc_final: 0.8084 (pm20) REVERT: B 466 MET cc_start: 0.8877 (ptm) cc_final: 0.8591 (ptm) REVERT: B 475 ASN cc_start: 0.9462 (m-40) cc_final: 0.9172 (m110) REVERT: B 493 MET cc_start: 0.9484 (tmm) cc_final: 0.9171 (tmm) REVERT: B 529 ASP cc_start: 0.8375 (m-30) cc_final: 0.8169 (m-30) REVERT: B 599 GLU cc_start: 0.8331 (pm20) cc_final: 0.7837 (pm20) REVERT: B 604 ARG cc_start: 0.8566 (tpp80) cc_final: 0.8031 (tpp80) REVERT: B 628 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7871 (mm-30) REVERT: C 21 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.8240 (t80) REVERT: C 25 ASN cc_start: 0.8599 (m-40) cc_final: 0.8385 (m-40) REVERT: C 42 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7583 (pp) REVERT: C 53 ASP cc_start: 0.8413 (t0) cc_final: 0.8212 (t0) REVERT: C 92 PHE cc_start: 0.8181 (t80) cc_final: 0.7866 (t80) REVERT: C 95 MET cc_start: 0.8450 (tmm) cc_final: 0.8072 (tmm) REVERT: C 122 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8224 (m-10) REVERT: C 183 LYS cc_start: 0.8116 (pttt) cc_final: 0.7885 (pttp) REVERT: C 212 ILE cc_start: 0.9035 (mt) cc_final: 0.8771 (mm) REVERT: C 242 TYR cc_start: 0.9012 (t80) cc_final: 0.8612 (t80) REVERT: C 260 ILE cc_start: 0.8173 (pt) cc_final: 0.7654 (pt) REVERT: C 283 ASN cc_start: 0.7681 (p0) cc_final: 0.6946 (p0) REVERT: D 17 PHE cc_start: 0.5819 (m-80) cc_final: 0.5379 (m-80) REVERT: D 42 LEU cc_start: 0.8792 (tp) cc_final: 0.8500 (mp) REVERT: D 117 THR cc_start: 0.8907 (m) cc_final: 0.7854 (m) REVERT: D 137 MET cc_start: 0.4555 (mtp) cc_final: 0.4066 (mmm) REVERT: D 154 PHE cc_start: 0.9340 (t80) cc_final: 0.8764 (t80) REVERT: D 169 TYR cc_start: 0.8207 (m-80) cc_final: 0.7762 (m-80) REVERT: D 181 GLN cc_start: 0.8497 (mt0) cc_final: 0.8105 (mp10) REVERT: D 212 ILE cc_start: 0.9636 (mt) cc_final: 0.9326 (mt) REVERT: D 213 TYR cc_start: 0.8047 (t80) cc_final: 0.7654 (t80) REVERT: D 233 ASN cc_start: 0.8083 (m-40) cc_final: 0.7881 (m110) REVERT: D 242 TYR cc_start: 0.7964 (t80) cc_final: 0.7668 (t80) REVERT: D 244 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7851 (pt0) REVERT: D 287 LEU cc_start: 0.5801 (mt) cc_final: 0.5494 (mp) REVERT: D 315 LEU cc_start: 0.9155 (mt) cc_final: 0.8817 (mt) outliers start: 62 outliers final: 26 residues processed: 681 average time/residue: 0.2782 time to fit residues: 279.9641 Evaluate side-chains 604 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 573 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 191 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 175 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 370 ASN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN B 304 HIS ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN C 186 GLN C 263 ASN C 265 ASN D 127 GLN D 210 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.136628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.093952 restraints weight = 28629.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.097486 restraints weight = 12142.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.099734 restraints weight = 7050.065| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16299 Z= 0.191 Angle : 0.633 9.427 22004 Z= 0.335 Chirality : 0.043 0.170 2348 Planarity : 0.004 0.056 2812 Dihedral : 8.716 155.384 2219 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.73 % Allowed : 19.89 % Favored : 76.37 % 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: 1.36 (0.19), residues: 1928 helix: 1.30 (0.15), residues: 1136 sheet: 0.15 (0.40), residues: 144 loop : 0.60 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 124 HIS 0.025 0.001 HIS C 201 PHE 0.037 0.002 PHE D 172 TYR 0.041 0.002 TYR D 242 ARG 0.006 0.001 ARG B 669 Details of bonding type rmsd hydrogen bonds : bond 0.04342 ( 896) hydrogen bonds : angle 5.05113 ( 2616) covalent geometry : bond 0.00433 (16298) covalent geometry : angle 0.63330 (22004) Misc. bond : bond 0.00082 ( 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 675 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 611 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 VAL cc_start: 0.9517 (t) cc_final: 0.9279 (t) REVERT: A 286 ASP cc_start: 0.8744 (m-30) cc_final: 0.7597 (m-30) REVERT: A 344 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7712 (mt-10) REVERT: A 362 ASP cc_start: 0.7472 (m-30) cc_final: 0.6660 (m-30) REVERT: A 379 SER cc_start: 0.9124 (t) cc_final: 0.8880 (t) REVERT: A 444 ASP cc_start: 0.8463 (t0) cc_final: 0.8190 (t0) REVERT: A 485 ARG cc_start: 0.8461 (mtm-85) cc_final: 0.7893 (mtm-85) REVERT: A 602 GLU cc_start: 0.8028 (tt0) cc_final: 0.6833 (tt0) REVERT: A 604 ARG cc_start: 0.8208 (ttm110) cc_final: 0.7389 (ttm110) REVERT: B 98 PHE cc_start: 0.9306 (t80) cc_final: 0.8748 (t80) REVERT: B 109 ASN cc_start: 0.9131 (OUTLIER) cc_final: 0.7992 (m-40) REVERT: B 174 GLU cc_start: 0.8369 (tp30) cc_final: 0.8086 (tp30) REVERT: B 202 ASN cc_start: 0.9111 (t0) cc_final: 0.8599 (t0) REVERT: B 211 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7894 (mt-10) REVERT: B 250 TYR cc_start: 0.9376 (m-80) cc_final: 0.7754 (m-80) REVERT: B 286 ASP cc_start: 0.8178 (m-30) cc_final: 0.7440 (m-30) REVERT: B 318 ASP cc_start: 0.8409 (t0) cc_final: 0.7437 (t0) REVERT: B 334 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8778 (ptpt) REVERT: B 355 TYR cc_start: 0.8816 (m-80) cc_final: 0.8497 (m-80) REVERT: B 362 ASP cc_start: 0.8006 (m-30) cc_final: 0.6895 (m-30) REVERT: B 379 SER cc_start: 0.9210 (t) cc_final: 0.8606 (t) REVERT: B 599 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7895 (pm20) REVERT: B 602 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7494 (tm-30) REVERT: B 603 GLU cc_start: 0.8192 (tp30) cc_final: 0.7626 (tp30) REVERT: B 612 TYR cc_start: 0.8608 (m-80) cc_final: 0.6875 (m-80) REVERT: B 628 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7930 (mm-30) REVERT: B 668 ASN cc_start: 0.8748 (m-40) cc_final: 0.8377 (m110) REVERT: C 20 MET cc_start: 0.8112 (tpt) cc_final: 0.7698 (ptt) REVERT: C 21 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.8227 (t80) REVERT: C 25 ASN cc_start: 0.8884 (m-40) cc_final: 0.8615 (m-40) REVERT: C 42 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7722 (pt) REVERT: C 92 PHE cc_start: 0.8323 (t80) cc_final: 0.8081 (t80) REVERT: C 95 MET cc_start: 0.8516 (tmm) cc_final: 0.8273 (tmm) REVERT: C 105 TYR cc_start: 0.7595 (m-80) cc_final: 0.7242 (m-80) REVERT: C 122 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.8147 (m-10) REVERT: C 145 ILE cc_start: 0.8476 (tp) cc_final: 0.8074 (tp) REVERT: C 178 PHE cc_start: 0.9276 (m-10) cc_final: 0.8818 (m-10) REVERT: C 183 LYS cc_start: 0.7872 (pttt) cc_final: 0.7493 (pttp) REVERT: C 213 TYR cc_start: 0.7913 (t80) cc_final: 0.7691 (t80) REVERT: C 227 PHE cc_start: 0.8615 (t80) cc_final: 0.8253 (t80) REVERT: C 242 TYR cc_start: 0.9074 (t80) cc_final: 0.8775 (t80) REVERT: C 260 ILE cc_start: 0.8348 (pt) cc_final: 0.8081 (pt) REVERT: C 268 LEU cc_start: 0.8664 (mt) cc_final: 0.7777 (pp) REVERT: C 287 LEU cc_start: 0.1338 (OUTLIER) cc_final: 0.0915 (mt) REVERT: D 30 TRP cc_start: 0.8628 (p-90) cc_final: 0.8177 (p-90) REVERT: D 42 LEU cc_start: 0.8738 (tp) cc_final: 0.8420 (tp) REVERT: D 46 TYR cc_start: 0.8931 (m-10) cc_final: 0.8401 (m-10) REVERT: D 56 MET cc_start: 0.7004 (mmm) cc_final: 0.6667 (ptp) REVERT: D 112 LEU cc_start: 0.7534 (mt) cc_final: 0.7248 (mt) REVERT: D 137 MET cc_start: 0.5216 (mtp) cc_final: 0.4725 (mmt) REVERT: D 154 PHE cc_start: 0.9360 (t80) cc_final: 0.8785 (t80) REVERT: D 178 PHE cc_start: 0.9291 (m-80) cc_final: 0.8579 (m-80) REVERT: D 212 ILE cc_start: 0.9696 (mt) cc_final: 0.9413 (mt) REVERT: D 213 TYR cc_start: 0.8438 (t80) cc_final: 0.7682 (t80) REVERT: D 215 LYS cc_start: 0.8929 (mtmm) cc_final: 0.8659 (mtmm) REVERT: D 244 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7931 (pt0) outliers start: 64 outliers final: 36 residues processed: 635 average time/residue: 0.2811 time to fit residues: 262.9304 Evaluate side-chains 602 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 559 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 250 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS A 646 GLN A 668 ASN B 131 ASN B 304 HIS ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 568 HIS ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 263 ASN D 210 GLN D 233 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.134628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.092613 restraints weight = 28836.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.096032 restraints weight = 12321.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.098218 restraints weight = 7167.077| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.5130 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 : 0.652 11.060 22004 Z= 0.342 Chirality : 0.044 0.163 2348 Planarity : 0.004 0.055 2812 Dihedral : 8.749 153.072 2217 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 4.55 % Allowed : 20.83 % Favored : 74.62 % 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: 1.17 (0.19), residues: 1928 helix: 1.23 (0.15), residues: 1147 sheet: -0.28 (0.40), residues: 156 loop : 0.45 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 124 HIS 0.025 0.001 HIS C 201 PHE 0.031 0.002 PHE D 172 TYR 0.024 0.002 TYR D 236 ARG 0.005 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 896) hydrogen bonds : angle 5.05929 ( 2616) covalent geometry : bond 0.00499 (16298) covalent geometry : angle 0.65237 (22004) Misc. bond : bond 0.00066 ( 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 678 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 600 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8924 (t0) cc_final: 0.8465 (t0) REVERT: A 228 LYS cc_start: 0.9004 (mmtt) cc_final: 0.8731 (mmtt) REVERT: A 266 LYS cc_start: 0.9051 (mttt) cc_final: 0.8801 (mttt) REVERT: A 286 ASP cc_start: 0.8663 (m-30) cc_final: 0.7763 (m-30) REVERT: A 344 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7700 (mt-10) REVERT: A 362 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.6713 (m-30) REVERT: A 379 SER cc_start: 0.9107 (t) cc_final: 0.8887 (t) REVERT: A 444 ASP cc_start: 0.8388 (t0) cc_final: 0.7918 (t70) REVERT: A 446 ARG cc_start: 0.8026 (tpp80) cc_final: 0.7671 (tpp80) REVERT: A 485 ARG cc_start: 0.8567 (mtm-85) cc_final: 0.8045 (mtm-85) REVERT: A 639 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8223 (m-30) REVERT: A 684 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.7798 (m-80) REVERT: B 98 PHE cc_start: 0.9368 (t80) cc_final: 0.8735 (t80) REVERT: B 109 ASN cc_start: 0.8956 (OUTLIER) cc_final: 0.8582 (m-40) REVERT: B 121 ARG cc_start: 0.9406 (OUTLIER) cc_final: 0.8804 (tpt170) REVERT: B 167 LEU cc_start: 0.9113 (mt) cc_final: 0.8610 (mp) REVERT: B 211 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8079 (mt-10) REVERT: B 250 TYR cc_start: 0.9414 (m-80) cc_final: 0.7628 (m-80) REVERT: B 286 ASP cc_start: 0.8123 (m-30) cc_final: 0.7491 (m-30) REVERT: B 318 ASP cc_start: 0.7999 (t0) cc_final: 0.7511 (t0) REVERT: B 342 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9310 (tt) REVERT: B 355 TYR cc_start: 0.8796 (m-80) cc_final: 0.8520 (m-80) REVERT: B 362 ASP cc_start: 0.8050 (m-30) cc_final: 0.6906 (m-30) REVERT: B 379 SER cc_start: 0.9179 (t) cc_final: 0.8609 (t) REVERT: B 493 MET cc_start: 0.9485 (tmm) cc_final: 0.9279 (tmm) REVERT: B 586 TYR cc_start: 0.9211 (m-80) cc_final: 0.8501 (m-80) REVERT: B 599 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8074 (pm20) REVERT: B 602 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7347 (tm-30) REVERT: B 603 GLU cc_start: 0.8303 (tp30) cc_final: 0.7485 (tp30) REVERT: B 612 TYR cc_start: 0.8741 (m-80) cc_final: 0.7544 (m-80) REVERT: B 628 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7980 (mm-30) REVERT: B 686 ARG cc_start: 0.7708 (tpp-160) cc_final: 0.7422 (ttm-80) REVERT: C 20 MET cc_start: 0.8177 (tpt) cc_final: 0.7579 (ptp) REVERT: C 21 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8324 (t80) REVERT: C 25 ASN cc_start: 0.9043 (m-40) cc_final: 0.8708 (m-40) REVERT: C 40 ASP cc_start: 0.8155 (p0) cc_final: 0.7933 (p0) REVERT: C 42 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7650 (pp) REVERT: C 44 TRP cc_start: 0.7867 (t-100) cc_final: 0.7650 (t-100) REVERT: C 92 PHE cc_start: 0.8345 (t80) cc_final: 0.7950 (t80) REVERT: C 95 MET cc_start: 0.8678 (tmm) cc_final: 0.8276 (tmm) REVERT: C 122 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.8101 (m-10) REVERT: C 149 ASP cc_start: 0.8554 (t0) cc_final: 0.8306 (t0) REVERT: C 227 PHE cc_start: 0.8701 (t80) cc_final: 0.8420 (t80) REVERT: C 242 TYR cc_start: 0.9247 (t80) cc_final: 0.8687 (t80) REVERT: D 46 TYR cc_start: 0.8974 (m-10) cc_final: 0.8700 (m-10) REVERT: D 56 MET cc_start: 0.7433 (mmm) cc_final: 0.6764 (ptp) REVERT: D 112 LEU cc_start: 0.7681 (mt) cc_final: 0.7318 (mt) REVERT: D 137 MET cc_start: 0.5563 (mtp) cc_final: 0.5161 (mmp) REVERT: D 154 PHE cc_start: 0.9374 (t80) cc_final: 0.8846 (t80) REVERT: D 178 PHE cc_start: 0.9290 (m-80) cc_final: 0.8719 (m-80) REVERT: D 186 GLN cc_start: 0.8204 (mp10) cc_final: 0.7811 (mp10) REVERT: D 207 LEU cc_start: 0.9460 (mm) cc_final: 0.9042 (mm) REVERT: D 210 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8555 (pp30) REVERT: D 213 TYR cc_start: 0.8468 (t80) cc_final: 0.7956 (t80) REVERT: D 225 ARG cc_start: 0.9205 (mtm-85) cc_final: 0.8689 (mtm180) REVERT: D 236 TYR cc_start: 0.7782 (t80) cc_final: 0.7355 (t80) REVERT: D 244 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7943 (pt0) REVERT: D 263 ASN cc_start: 0.8630 (p0) cc_final: 0.8240 (p0) outliers start: 78 outliers final: 45 residues processed: 636 average time/residue: 0.2808 time to fit residues: 263.7120 Evaluate side-chains 598 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 542 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 441 GLU 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 599 GLU Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 250 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 109 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 107 ASN C 214 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.135580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.093917 restraints weight = 29346.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.097328 restraints weight = 12334.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.099504 restraints weight = 7117.754| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16299 Z= 0.176 Angle : 0.647 15.157 22004 Z= 0.337 Chirality : 0.044 0.162 2348 Planarity : 0.004 0.055 2812 Dihedral : 8.693 150.933 2217 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 4.38 % Allowed : 22.11 % Favored : 73.51 % 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: 1.01 (0.19), residues: 1928 helix: 1.12 (0.15), residues: 1149 sheet: -0.53 (0.40), residues: 156 loop : 0.39 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 124 HIS 0.024 0.001 HIS C 201 PHE 0.028 0.002 PHE D 172 TYR 0.023 0.001 TYR C 142 ARG 0.007 0.001 ARG B 117 Details of bonding type rmsd hydrogen bonds : bond 0.03919 ( 896) hydrogen bonds : angle 5.08730 ( 2616) covalent geometry : bond 0.00400 (16298) covalent geometry : angle 0.64682 (22004) Misc. bond : bond 0.00053 ( 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 653 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 578 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.8105 (m-70) cc_final: 0.7868 (m-70) REVERT: A 218 ASN cc_start: 0.8934 (t0) cc_final: 0.8517 (t0) REVERT: A 286 ASP cc_start: 0.8678 (m-30) cc_final: 0.7769 (m-30) REVERT: A 344 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7620 (mt-10) REVERT: A 362 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.6707 (m-30) REVERT: A 379 SER cc_start: 0.9092 (t) cc_final: 0.8863 (t) REVERT: A 384 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.6469 (pm20) REVERT: A 444 ASP cc_start: 0.8503 (t0) cc_final: 0.8286 (t0) REVERT: A 485 ARG cc_start: 0.8547 (mtm-85) cc_final: 0.7689 (mtm110) REVERT: A 570 MET cc_start: 0.8876 (mtp) cc_final: 0.8577 (mtp) REVERT: A 586 TYR cc_start: 0.8919 (m-10) cc_final: 0.8633 (m-10) REVERT: A 639 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8195 (m-30) REVERT: A 684 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.7812 (m-80) REVERT: B 15 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8354 (mp0) REVERT: B 98 PHE cc_start: 0.9372 (t80) cc_final: 0.8756 (t80) REVERT: B 109 ASN cc_start: 0.8943 (OUTLIER) cc_final: 0.8579 (m-40) REVERT: B 121 ARG cc_start: 0.9353 (OUTLIER) cc_final: 0.8814 (tpt170) REVERT: B 167 LEU cc_start: 0.9119 (mt) cc_final: 0.8619 (mp) REVERT: B 250 TYR cc_start: 0.9406 (m-80) cc_final: 0.7614 (m-80) REVERT: B 263 ASP cc_start: 0.8791 (m-30) cc_final: 0.8394 (m-30) REVERT: B 286 ASP cc_start: 0.8109 (m-30) cc_final: 0.7312 (m-30) REVERT: B 342 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9313 (tt) REVERT: B 355 TYR cc_start: 0.8725 (m-80) cc_final: 0.8398 (m-80) REVERT: B 357 TYR cc_start: 0.9008 (m-10) cc_final: 0.8706 (m-80) REVERT: B 362 ASP cc_start: 0.8000 (m-30) cc_final: 0.6572 (m-30) REVERT: B 379 SER cc_start: 0.9213 (t) cc_final: 0.8507 (t) REVERT: B 493 MET cc_start: 0.9474 (tmm) cc_final: 0.9267 (tmm) REVERT: B 599 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8015 (pm20) REVERT: B 603 GLU cc_start: 0.8405 (tp30) cc_final: 0.8038 (tp30) REVERT: B 612 TYR cc_start: 0.8714 (m-80) cc_final: 0.7975 (m-80) REVERT: B 628 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8004 (mm-30) REVERT: B 659 LYS cc_start: 0.8431 (mmmt) cc_final: 0.7699 (mmmt) REVERT: B 668 ASN cc_start: 0.8718 (m-40) cc_final: 0.8403 (m110) REVERT: C 20 MET cc_start: 0.8079 (tpt) cc_final: 0.7802 (ptp) REVERT: C 21 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8337 (t80) REVERT: C 25 ASN cc_start: 0.9024 (m-40) cc_final: 0.8667 (m-40) REVERT: C 82 ASP cc_start: 0.8667 (m-30) cc_final: 0.7979 (p0) REVERT: C 92 PHE cc_start: 0.8145 (t80) cc_final: 0.7669 (t80) REVERT: C 95 MET cc_start: 0.8663 (tmm) cc_final: 0.8303 (tmm) REVERT: C 105 TYR cc_start: 0.7961 (m-80) cc_final: 0.7610 (m-80) REVERT: C 122 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.8076 (m-10) REVERT: C 192 ASN cc_start: 0.8995 (p0) cc_final: 0.8609 (p0) REVERT: C 212 ILE cc_start: 0.8561 (mm) cc_final: 0.8315 (mm) REVERT: C 227 PHE cc_start: 0.8736 (t80) cc_final: 0.8361 (t80) REVERT: C 231 LEU cc_start: 0.9373 (mm) cc_final: 0.8893 (pp) REVERT: C 242 TYR cc_start: 0.9205 (t80) cc_final: 0.8662 (t80) REVERT: C 255 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.8517 (t0) REVERT: C 270 ASN cc_start: 0.8707 (m-40) cc_final: 0.8476 (m-40) REVERT: D 23 ASN cc_start: 0.9264 (t0) cc_final: 0.8728 (t0) REVERT: D 27 LYS cc_start: 0.8931 (mttt) cc_final: 0.8682 (pttp) REVERT: D 30 TRP cc_start: 0.8577 (p-90) cc_final: 0.8210 (p-90) REVERT: D 46 TYR cc_start: 0.8989 (m-10) cc_final: 0.8656 (m-10) REVERT: D 137 MET cc_start: 0.6055 (mtp) cc_final: 0.5689 (mmt) REVERT: D 154 PHE cc_start: 0.9396 (t80) cc_final: 0.9073 (t80) REVERT: D 178 PHE cc_start: 0.9323 (m-80) cc_final: 0.8852 (m-80) REVERT: D 181 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8011 (mp10) REVERT: D 210 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8589 (pp30) REVERT: D 212 ILE cc_start: 0.9651 (mt) cc_final: 0.9425 (mp) REVERT: D 213 TYR cc_start: 0.8484 (t80) cc_final: 0.8189 (t80) REVERT: D 236 TYR cc_start: 0.7852 (t80) cc_final: 0.7458 (t80) REVERT: D 263 ASN cc_start: 0.8609 (p0) cc_final: 0.8191 (p0) outliers start: 75 outliers final: 42 residues processed: 608 average time/residue: 0.2804 time to fit residues: 250.6566 Evaluate side-chains 581 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 526 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 262 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 143 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN D 216 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.136070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.094177 restraints weight = 28872.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.097601 restraints weight = 12338.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.099746 restraints weight = 7154.342| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.5724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16299 Z= 0.151 Angle : 0.643 13.523 22004 Z= 0.334 Chirality : 0.043 0.189 2348 Planarity : 0.004 0.052 2812 Dihedral : 8.494 143.125 2216 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.15 % Allowed : 24.74 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.03 (0.19), residues: 1928 helix: 1.14 (0.15), residues: 1149 sheet: -0.56 (0.40), residues: 156 loop : 0.40 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 124 HIS 0.024 0.001 HIS C 201 PHE 0.028 0.002 PHE D 172 TYR 0.028 0.001 TYR B 613 ARG 0.006 0.001 ARG B 117 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 896) hydrogen bonds : angle 5.01095 ( 2616) covalent geometry : bond 0.00342 (16298) covalent geometry : angle 0.64284 (22004) Misc. bond : bond 0.00039 ( 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 616 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 562 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.8178 (m-70) cc_final: 0.7920 (m-70) REVERT: A 102 ASN cc_start: 0.8879 (m-40) cc_final: 0.8431 (t0) REVERT: A 228 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8663 (mmtt) REVERT: A 266 LYS cc_start: 0.9019 (mttt) cc_final: 0.8768 (mttp) REVERT: A 286 ASP cc_start: 0.8685 (m-30) cc_final: 0.7778 (m-30) REVERT: A 344 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7644 (mt-10) REVERT: A 355 TYR cc_start: 0.8897 (m-80) cc_final: 0.8472 (m-80) REVERT: A 362 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.6666 (m-30) REVERT: A 379 SER cc_start: 0.9110 (t) cc_final: 0.8879 (t) REVERT: A 384 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.6453 (pm20) REVERT: A 444 ASP cc_start: 0.8350 (t0) cc_final: 0.8021 (t0) REVERT: A 485 ARG cc_start: 0.8540 (mtm-85) cc_final: 0.7688 (mtm110) REVERT: A 570 MET cc_start: 0.8897 (mtp) cc_final: 0.8568 (mtp) REVERT: A 586 TYR cc_start: 0.8943 (m-10) cc_final: 0.8674 (m-10) REVERT: A 604 ARG cc_start: 0.8109 (ttm110) cc_final: 0.7872 (ttm110) REVERT: A 639 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8184 (m-30) REVERT: A 684 TYR cc_start: 0.8381 (OUTLIER) cc_final: 0.7906 (m-80) REVERT: B 15 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8414 (mp0) REVERT: B 98 PHE cc_start: 0.9342 (t80) cc_final: 0.8673 (t80) REVERT: B 109 ASN cc_start: 0.8891 (OUTLIER) cc_final: 0.8520 (m-40) REVERT: B 167 LEU cc_start: 0.9090 (mt) cc_final: 0.8587 (mp) REVERT: B 250 TYR cc_start: 0.9376 (m-80) cc_final: 0.7715 (m-80) REVERT: B 263 ASP cc_start: 0.8818 (m-30) cc_final: 0.8354 (m-30) REVERT: B 286 ASP cc_start: 0.8067 (m-30) cc_final: 0.7475 (m-30) REVERT: B 355 TYR cc_start: 0.8622 (m-80) cc_final: 0.8306 (m-80) REVERT: B 357 TYR cc_start: 0.8980 (m-10) cc_final: 0.8626 (m-80) REVERT: B 362 ASP cc_start: 0.7999 (m-30) cc_final: 0.6713 (m-30) REVERT: B 379 SER cc_start: 0.9202 (t) cc_final: 0.8557 (t) REVERT: B 586 TYR cc_start: 0.8908 (m-80) cc_final: 0.8531 (m-80) REVERT: B 599 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8048 (pm20) REVERT: B 602 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7667 (tm-30) REVERT: B 603 GLU cc_start: 0.8341 (tp30) cc_final: 0.8117 (tp30) REVERT: B 612 TYR cc_start: 0.8743 (m-80) cc_final: 0.7989 (m-80) REVERT: B 628 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8034 (mm-30) REVERT: B 655 THR cc_start: 0.9386 (m) cc_final: 0.8937 (p) REVERT: C 20 MET cc_start: 0.8106 (tpt) cc_final: 0.7882 (ptp) REVERT: C 21 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8325 (t80) REVERT: C 82 ASP cc_start: 0.8575 (m-30) cc_final: 0.7954 (p0) REVERT: C 92 PHE cc_start: 0.8175 (t80) cc_final: 0.7712 (t80) REVERT: C 95 MET cc_start: 0.8626 (tmm) cc_final: 0.8201 (tmm) REVERT: C 105 TYR cc_start: 0.8034 (m-80) cc_final: 0.7627 (m-80) REVERT: C 122 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.8031 (m-10) REVERT: C 134 LYS cc_start: 0.9331 (pttt) cc_final: 0.8956 (tppt) REVERT: C 178 PHE cc_start: 0.9181 (m-10) cc_final: 0.8967 (m-10) REVERT: C 192 ASN cc_start: 0.8951 (p0) cc_final: 0.8589 (p0) REVERT: C 227 PHE cc_start: 0.8728 (t80) cc_final: 0.8389 (t80) REVERT: C 231 LEU cc_start: 0.9416 (mm) cc_final: 0.8985 (pp) REVERT: C 233 ASN cc_start: 0.8847 (m110) cc_final: 0.8330 (p0) REVERT: C 242 TYR cc_start: 0.9209 (t80) cc_final: 0.8702 (t80) REVERT: C 255 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8542 (t0) REVERT: C 270 ASN cc_start: 0.8792 (m-40) cc_final: 0.8557 (m-40) REVERT: D 30 TRP cc_start: 0.8636 (p-90) cc_final: 0.8153 (p-90) REVERT: D 116 GLU cc_start: 0.8157 (pm20) cc_final: 0.7439 (pm20) REVERT: D 137 MET cc_start: 0.6192 (mtp) cc_final: 0.5777 (mmt) REVERT: D 154 PHE cc_start: 0.9391 (t80) cc_final: 0.9053 (t80) REVERT: D 169 TYR cc_start: 0.8644 (m-80) cc_final: 0.8189 (m-80) REVERT: D 178 PHE cc_start: 0.9374 (m-80) cc_final: 0.8858 (m-80) REVERT: D 211 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8744 (tm-30) REVERT: D 213 TYR cc_start: 0.8557 (t80) cc_final: 0.8234 (t80) REVERT: D 215 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.7946 (ptpp) REVERT: D 227 PHE cc_start: 0.9000 (m-80) cc_final: 0.8797 (m-80) REVERT: D 236 TYR cc_start: 0.7788 (t80) cc_final: 0.7558 (t80) REVERT: D 242 TYR cc_start: 0.8282 (t80) cc_final: 0.7911 (t80) REVERT: D 263 ASN cc_start: 0.8546 (p0) cc_final: 0.8112 (p0) outliers start: 54 outliers final: 33 residues processed: 582 average time/residue: 0.2738 time to fit residues: 235.5185 Evaluate side-chains 583 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 539 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 262 TYR Chi-restraints excluded: chain D residue 287 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 7 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 109 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN B 131 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 25 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.136048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.094251 restraints weight = 29263.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.097727 restraints weight = 12321.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.099878 restraints weight = 7125.994| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.5879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16299 Z= 0.165 Angle : 0.655 12.701 22004 Z= 0.341 Chirality : 0.044 0.275 2348 Planarity : 0.003 0.051 2812 Dihedral : 8.490 141.958 2216 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.68 % Allowed : 25.73 % Favored : 70.60 % 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: 1.06 (0.19), residues: 1928 helix: 1.19 (0.15), residues: 1137 sheet: -0.57 (0.40), residues: 156 loop : 0.39 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 124 HIS 0.027 0.001 HIS C 201 PHE 0.027 0.002 PHE C 172 TYR 0.020 0.001 TYR D 22 ARG 0.007 0.001 ARG B 117 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 896) hydrogen bonds : angle 5.07221 ( 2616) covalent geometry : bond 0.00374 (16298) covalent geometry : angle 0.65546 (22004) Misc. bond : bond 0.00039 ( 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 615 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 552 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.8168 (m-70) cc_final: 0.7881 (m-70) REVERT: A 102 ASN cc_start: 0.8888 (m-40) cc_final: 0.8420 (t0) REVERT: A 286 ASP cc_start: 0.8682 (m-30) cc_final: 0.7802 (m-30) REVERT: A 344 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7651 (mt-10) REVERT: A 355 TYR cc_start: 0.8909 (m-80) cc_final: 0.8445 (m-80) REVERT: A 362 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.6687 (m-30) REVERT: A 379 SER cc_start: 0.9086 (t) cc_final: 0.8856 (t) REVERT: A 384 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.6435 (pm20) REVERT: A 485 ARG cc_start: 0.8551 (mtm-85) cc_final: 0.7699 (mtm110) REVERT: A 570 MET cc_start: 0.8923 (mtp) cc_final: 0.8581 (mtp) REVERT: A 602 GLU cc_start: 0.7842 (tt0) cc_final: 0.7049 (tt0) REVERT: A 639 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8164 (m-30) REVERT: A 684 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.7901 (m-80) REVERT: B 44 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8346 (t0) REVERT: B 98 PHE cc_start: 0.9354 (t80) cc_final: 0.8630 (t80) REVERT: B 109 ASN cc_start: 0.8928 (OUTLIER) cc_final: 0.8532 (m-40) REVERT: B 167 LEU cc_start: 0.9132 (mt) cc_final: 0.8621 (mp) REVERT: B 250 TYR cc_start: 0.9398 (m-80) cc_final: 0.7760 (m-80) REVERT: B 263 ASP cc_start: 0.8844 (m-30) cc_final: 0.8373 (m-30) REVERT: B 286 ASP cc_start: 0.8100 (m-30) cc_final: 0.7343 (m-30) REVERT: B 342 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9340 (tt) REVERT: B 355 TYR cc_start: 0.8633 (m-80) cc_final: 0.8379 (m-80) REVERT: B 357 TYR cc_start: 0.9030 (m-10) cc_final: 0.8685 (m-80) REVERT: B 362 ASP cc_start: 0.8001 (m-30) cc_final: 0.6565 (m-30) REVERT: B 379 SER cc_start: 0.9198 (t) cc_final: 0.8564 (t) REVERT: B 586 TYR cc_start: 0.9088 (m-80) cc_final: 0.8629 (m-80) REVERT: B 599 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8080 (pm20) REVERT: B 602 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7660 (tm-30) REVERT: B 603 GLU cc_start: 0.8352 (tp30) cc_final: 0.8006 (tp30) REVERT: B 612 TYR cc_start: 0.8601 (m-80) cc_final: 0.7932 (m-80) REVERT: B 628 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7891 (mt-10) REVERT: B 659 LYS cc_start: 0.8319 (mmmt) cc_final: 0.7932 (mmmt) REVERT: C 21 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.8409 (t80) REVERT: C 30 TRP cc_start: 0.8029 (p-90) cc_final: 0.7281 (p-90) REVERT: C 66 ASP cc_start: 0.6036 (p0) cc_final: 0.5797 (p0) REVERT: C 92 PHE cc_start: 0.8226 (t80) cc_final: 0.7785 (t80) REVERT: C 95 MET cc_start: 0.8727 (tmm) cc_final: 0.8387 (tmm) REVERT: C 105 TYR cc_start: 0.8177 (m-80) cc_final: 0.7935 (m-80) REVERT: C 107 ASN cc_start: 0.8982 (p0) cc_final: 0.8768 (p0) REVERT: C 122 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.8031 (m-10) REVERT: C 149 ASP cc_start: 0.8536 (t0) cc_final: 0.8275 (t0) REVERT: C 192 ASN cc_start: 0.8968 (p0) cc_final: 0.8544 (p0) REVERT: C 204 TYR cc_start: 0.8117 (t80) cc_final: 0.7776 (t80) REVERT: C 227 PHE cc_start: 0.8802 (t80) cc_final: 0.8467 (t80) REVERT: C 231 LEU cc_start: 0.9426 (mm) cc_final: 0.8998 (pp) REVERT: C 233 ASN cc_start: 0.8879 (m110) cc_final: 0.8503 (p0) REVERT: C 245 ASP cc_start: 0.9345 (t0) cc_final: 0.8908 (m-30) REVERT: C 255 ASP cc_start: 0.8835 (OUTLIER) cc_final: 0.8600 (t0) REVERT: C 270 ASN cc_start: 0.8817 (m-40) cc_final: 0.8556 (m-40) REVERT: C 276 TYR cc_start: 0.8031 (t80) cc_final: 0.7796 (t80) REVERT: D 30 TRP cc_start: 0.8645 (p-90) cc_final: 0.7832 (p-90) REVERT: D 116 GLU cc_start: 0.8193 (pm20) cc_final: 0.7513 (pm20) REVERT: D 137 MET cc_start: 0.6251 (mtp) cc_final: 0.5864 (mmt) REVERT: D 154 PHE cc_start: 0.9395 (t80) cc_final: 0.8989 (t80) REVERT: D 157 MET cc_start: 0.9170 (ptp) cc_final: 0.8969 (ptp) REVERT: D 169 TYR cc_start: 0.8664 (m-80) cc_final: 0.8190 (m-80) REVERT: D 178 PHE cc_start: 0.9377 (m-80) cc_final: 0.8996 (m-80) REVERT: D 213 TYR cc_start: 0.8606 (t80) cc_final: 0.8262 (t80) REVERT: D 215 LYS cc_start: 0.8815 (ptpp) cc_final: 0.8494 (ptpp) REVERT: D 236 TYR cc_start: 0.7884 (t80) cc_final: 0.7601 (t80) REVERT: D 242 TYR cc_start: 0.8219 (t80) cc_final: 0.7900 (t80) REVERT: D 263 ASN cc_start: 0.8495 (p0) cc_final: 0.8043 (p0) outliers start: 63 outliers final: 38 residues processed: 577 average time/residue: 0.2776 time to fit residues: 236.4796 Evaluate side-chains 565 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 516 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 146 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 174 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 chunk 4 optimal weight: 0.1980 chunk 11 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN B 62 GLN B 131 ASN B 387 GLN C 24 GLN C 132 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.138379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.096692 restraints weight = 28775.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.100243 restraints weight = 12189.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.102449 restraints weight = 7068.291| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.6088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16299 Z= 0.137 Angle : 0.674 12.246 22004 Z= 0.349 Chirality : 0.044 0.291 2348 Planarity : 0.004 0.050 2812 Dihedral : 8.343 138.240 2216 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.92 % Allowed : 27.19 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.19), residues: 1928 helix: 1.15 (0.15), residues: 1144 sheet: -0.32 (0.42), residues: 144 loop : 0.39 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 44 HIS 0.029 0.001 HIS C 201 PHE 0.025 0.002 PHE D 172 TYR 0.020 0.001 TYR D 22 ARG 0.007 0.001 ARG B 669 Details of bonding type rmsd hydrogen bonds : bond 0.03711 ( 896) hydrogen bonds : angle 5.05671 ( 2616) covalent geometry : bond 0.00303 (16298) covalent geometry : angle 0.67447 (22004) Misc. bond : bond 0.00021 ( 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 599 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 549 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.8142 (m-70) cc_final: 0.7842 (m-70) REVERT: A 102 ASN cc_start: 0.8936 (m-40) cc_final: 0.8460 (t0) REVERT: A 228 LYS cc_start: 0.8940 (mmtt) cc_final: 0.8690 (mmtt) REVERT: A 286 ASP cc_start: 0.8675 (m-30) cc_final: 0.7925 (m-30) REVERT: A 344 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7637 (mt-10) REVERT: A 355 TYR cc_start: 0.8836 (m-80) cc_final: 0.8471 (m-80) REVERT: A 362 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.6709 (m-30) REVERT: A 406 ASP cc_start: 0.8204 (m-30) cc_final: 0.7908 (m-30) REVERT: A 485 ARG cc_start: 0.8480 (mtm-85) cc_final: 0.7873 (mtm-85) REVERT: A 570 MET cc_start: 0.8901 (mtp) cc_final: 0.8583 (mtp) REVERT: A 639 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8142 (m-30) REVERT: A 662 MET cc_start: 0.8625 (mtp) cc_final: 0.8392 (mtm) REVERT: A 684 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.7914 (m-80) REVERT: B 15 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8421 (mp0) REVERT: B 44 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8418 (t0) REVERT: B 98 PHE cc_start: 0.9314 (t80) cc_final: 0.8603 (t80) REVERT: B 121 ARG cc_start: 0.9331 (OUTLIER) cc_final: 0.8820 (tpt170) REVERT: B 167 LEU cc_start: 0.9091 (mt) cc_final: 0.8571 (mp) REVERT: B 250 TYR cc_start: 0.9342 (m-80) cc_final: 0.7747 (m-80) REVERT: B 263 ASP cc_start: 0.8816 (m-30) cc_final: 0.8338 (m-30) REVERT: B 286 ASP cc_start: 0.8096 (m-30) cc_final: 0.7350 (m-30) REVERT: B 355 TYR cc_start: 0.8558 (m-80) cc_final: 0.8331 (m-80) REVERT: B 357 TYR cc_start: 0.8944 (m-10) cc_final: 0.8639 (m-80) REVERT: B 362 ASP cc_start: 0.8000 (m-30) cc_final: 0.6752 (m-30) REVERT: B 379 SER cc_start: 0.9194 (t) cc_final: 0.8500 (t) REVERT: B 586 TYR cc_start: 0.9107 (m-80) cc_final: 0.8648 (m-80) REVERT: B 599 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7991 (pm20) REVERT: B 602 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7565 (tm-30) REVERT: B 610 LYS cc_start: 0.8702 (tppt) cc_final: 0.7472 (tppt) REVERT: B 612 TYR cc_start: 0.8505 (m-80) cc_final: 0.7967 (m-80) REVERT: B 628 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7880 (mt-10) REVERT: B 659 LYS cc_start: 0.8208 (mmmt) cc_final: 0.7978 (mmmt) REVERT: C 20 MET cc_start: 0.8731 (ptt) cc_final: 0.7911 (tpt) REVERT: C 21 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8324 (t80) REVERT: C 40 ASP cc_start: 0.8921 (p0) cc_final: 0.7796 (p0) REVERT: C 82 ASP cc_start: 0.8473 (m-30) cc_final: 0.7943 (p0) REVERT: C 92 PHE cc_start: 0.7937 (t80) cc_final: 0.7399 (t80) REVERT: C 95 MET cc_start: 0.8685 (tmm) cc_final: 0.8353 (tmm) REVERT: C 105 TYR cc_start: 0.8174 (m-80) cc_final: 0.7802 (m-80) REVERT: C 107 ASN cc_start: 0.8978 (p0) cc_final: 0.8753 (p0) REVERT: C 122 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.8046 (m-10) REVERT: C 192 ASN cc_start: 0.8954 (p0) cc_final: 0.8422 (p0) REVERT: C 227 PHE cc_start: 0.8769 (t80) cc_final: 0.8445 (t80) REVERT: C 231 LEU cc_start: 0.9423 (mm) cc_final: 0.8988 (pp) REVERT: C 233 ASN cc_start: 0.8843 (m110) cc_final: 0.8463 (p0) REVERT: C 270 ASN cc_start: 0.8831 (m-40) cc_final: 0.8595 (m-40) REVERT: C 276 TYR cc_start: 0.8036 (t80) cc_final: 0.7805 (t80) REVERT: D 30 TRP cc_start: 0.8566 (p-90) cc_final: 0.8031 (p-90) REVERT: D 116 GLU cc_start: 0.8160 (pm20) cc_final: 0.7514 (pm20) REVERT: D 137 MET cc_start: 0.6449 (mtp) cc_final: 0.6036 (mmt) REVERT: D 154 PHE cc_start: 0.9413 (t80) cc_final: 0.8806 (t80) REVERT: D 157 MET cc_start: 0.9107 (ptp) cc_final: 0.8488 (ptp) REVERT: D 169 TYR cc_start: 0.8755 (m-80) cc_final: 0.8317 (m-80) REVERT: D 213 TYR cc_start: 0.8594 (t80) cc_final: 0.8292 (t80) REVERT: D 236 TYR cc_start: 0.7918 (t80) cc_final: 0.7668 (t80) REVERT: D 242 TYR cc_start: 0.8276 (t80) cc_final: 0.7946 (t80) REVERT: D 263 ASN cc_start: 0.8418 (p0) cc_final: 0.8006 (p0) outliers start: 50 outliers final: 27 residues processed: 569 average time/residue: 0.2709 time to fit residues: 227.9812 Evaluate side-chains 556 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 521 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 181 GLN Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 200 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 140 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 83 optimal weight: 0.4980 chunk 162 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 68 optimal weight: 7.9990 chunk 1 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN B 131 ASN C 24 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.137997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.096575 restraints weight = 28948.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.100126 restraints weight = 12272.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.102246 restraints weight = 7066.673| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.6198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16299 Z= 0.148 Angle : 0.705 17.518 22004 Z= 0.364 Chirality : 0.045 0.265 2348 Planarity : 0.004 0.050 2812 Dihedral : 8.323 139.407 2216 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.57 % Allowed : 27.25 % Favored : 70.19 % 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: 1.00 (0.19), residues: 1928 helix: 1.08 (0.15), residues: 1147 sheet: -0.52 (0.42), residues: 148 loop : 0.46 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 30 HIS 0.030 0.001 HIS C 201 PHE 0.023 0.002 PHE D 172 TYR 0.022 0.001 TYR D 22 ARG 0.009 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.03751 ( 896) hydrogen bonds : angle 5.08286 ( 2616) covalent geometry : bond 0.00336 (16298) covalent geometry : angle 0.70544 (22004) Misc. bond : bond 0.00021 ( 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 573 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 529 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.8122 (m-70) cc_final: 0.7782 (m-70) REVERT: A 102 ASN cc_start: 0.8947 (m-40) cc_final: 0.8436 (t0) REVERT: A 228 LYS cc_start: 0.8938 (mmtt) cc_final: 0.8680 (mmtt) REVERT: A 286 ASP cc_start: 0.8687 (m-30) cc_final: 0.7909 (m-30) REVERT: A 344 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7550 (mt-10) REVERT: A 355 TYR cc_start: 0.8855 (m-80) cc_final: 0.8488 (m-80) REVERT: A 362 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.6719 (m-30) REVERT: A 406 ASP cc_start: 0.8195 (m-30) cc_final: 0.7904 (m-30) REVERT: A 485 ARG cc_start: 0.8466 (mtm-85) cc_final: 0.7599 (mtm110) REVERT: A 570 MET cc_start: 0.8908 (mtp) cc_final: 0.8573 (mtp) REVERT: A 586 TYR cc_start: 0.8911 (m-10) cc_final: 0.8704 (m-10) REVERT: A 602 GLU cc_start: 0.8000 (tt0) cc_final: 0.7608 (tt0) REVERT: A 639 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8163 (m-30) REVERT: A 684 TYR cc_start: 0.8366 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: B 15 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8434 (mp0) REVERT: B 44 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8388 (t0) REVERT: B 98 PHE cc_start: 0.9308 (t80) cc_final: 0.8576 (t80) REVERT: B 167 LEU cc_start: 0.9110 (mt) cc_final: 0.8591 (mp) REVERT: B 250 TYR cc_start: 0.9349 (m-80) cc_final: 0.7762 (m-80) REVERT: B 263 ASP cc_start: 0.8815 (m-30) cc_final: 0.8341 (m-30) REVERT: B 286 ASP cc_start: 0.8099 (m-30) cc_final: 0.7358 (m-30) REVERT: B 355 TYR cc_start: 0.8547 (m-80) cc_final: 0.8326 (m-80) REVERT: B 357 TYR cc_start: 0.8962 (m-10) cc_final: 0.8646 (m-80) REVERT: B 362 ASP cc_start: 0.7987 (m-30) cc_final: 0.6742 (m-30) REVERT: B 379 SER cc_start: 0.9193 (t) cc_final: 0.8509 (t) REVERT: B 586 TYR cc_start: 0.9154 (m-80) cc_final: 0.8586 (m-80) REVERT: B 599 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7908 (pm20) REVERT: B 602 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7637 (tm-30) REVERT: B 610 LYS cc_start: 0.8949 (tppt) cc_final: 0.8609 (tppt) REVERT: B 612 TYR cc_start: 0.8442 (m-80) cc_final: 0.8044 (m-80) REVERT: B 628 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7989 (mt-10) REVERT: B 688 LYS cc_start: 0.8659 (tmmt) cc_final: 0.7940 (tmmt) REVERT: C 20 MET cc_start: 0.8711 (ptt) cc_final: 0.7901 (mmt) REVERT: C 21 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8274 (t80) REVERT: C 40 ASP cc_start: 0.8869 (p0) cc_final: 0.7996 (p0) REVERT: C 82 ASP cc_start: 0.8500 (m-30) cc_final: 0.7978 (p0) REVERT: C 92 PHE cc_start: 0.7974 (t80) cc_final: 0.7519 (t80) REVERT: C 95 MET cc_start: 0.8831 (tmm) cc_final: 0.8374 (tmm) REVERT: C 105 TYR cc_start: 0.8302 (m-80) cc_final: 0.7992 (m-80) REVERT: C 122 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.8026 (m-10) REVERT: C 134 LYS cc_start: 0.9220 (ttpt) cc_final: 0.8812 (tppt) REVERT: C 178 PHE cc_start: 0.9165 (m-10) cc_final: 0.8871 (m-10) REVERT: C 192 ASN cc_start: 0.8931 (p0) cc_final: 0.8424 (p0) REVERT: C 227 PHE cc_start: 0.8786 (t80) cc_final: 0.8487 (t80) REVERT: C 231 LEU cc_start: 0.9441 (mm) cc_final: 0.9028 (pp) REVERT: C 233 ASN cc_start: 0.8822 (m110) cc_final: 0.8451 (p0) REVERT: C 270 ASN cc_start: 0.8873 (m-40) cc_final: 0.8639 (m-40) REVERT: D 30 TRP cc_start: 0.8552 (p-90) cc_final: 0.7922 (p-90) REVERT: D 46 TYR cc_start: 0.8933 (m-10) cc_final: 0.8568 (m-10) REVERT: D 137 MET cc_start: 0.6526 (mtp) cc_final: 0.6060 (mmt) REVERT: D 154 PHE cc_start: 0.9398 (t80) cc_final: 0.8884 (t80) REVERT: D 157 MET cc_start: 0.9095 (ptp) cc_final: 0.8799 (ptp) REVERT: D 169 TYR cc_start: 0.8826 (m-80) cc_final: 0.8357 (m-80) REVERT: D 178 PHE cc_start: 0.9021 (m-80) cc_final: 0.8368 (m-80) REVERT: D 205 VAL cc_start: 0.9589 (t) cc_final: 0.9384 (p) REVERT: D 213 TYR cc_start: 0.8631 (t80) cc_final: 0.8098 (t80) REVERT: D 236 TYR cc_start: 0.7814 (t80) cc_final: 0.7552 (t80) REVERT: D 242 TYR cc_start: 0.8379 (t80) cc_final: 0.8012 (t80) REVERT: D 263 ASN cc_start: 0.8383 (p0) cc_final: 0.7962 (p0) outliers start: 44 outliers final: 25 residues processed: 543 average time/residue: 0.2827 time to fit residues: 226.8181 Evaluate side-chains 548 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 516 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 200 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 165 optimal weight: 0.0070 chunk 180 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 164 optimal weight: 8.9990 chunk 190 optimal weight: 0.0370 chunk 129 optimal weight: 6.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN B 131 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.139993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.099011 restraints weight = 29009.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.102497 restraints weight = 12355.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.104710 restraints weight = 7129.569| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.6354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 16299 Z= 0.139 Angle : 0.716 16.998 22004 Z= 0.367 Chirality : 0.044 0.253 2348 Planarity : 0.004 0.050 2812 Dihedral : 8.248 138.149 2216 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.87 % Allowed : 28.18 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.19), residues: 1928 helix: 1.04 (0.15), residues: 1147 sheet: -0.02 (0.45), residues: 128 loop : 0.28 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 44 HIS 0.033 0.001 HIS C 201 PHE 0.023 0.002 PHE D 172 TYR 0.022 0.001 TYR D 22 ARG 0.009 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 896) hydrogen bonds : angle 5.10185 ( 2616) covalent geometry : bond 0.00314 (16298) covalent geometry : angle 0.71607 (22004) Misc. bond : bond 0.00013 ( 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 558 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 526 time to evaluate : 1.929 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 49 HIS cc_start: 0.8076 (m-70) cc_final: 0.7717 (m-70) REVERT: A 102 ASN cc_start: 0.8922 (m-40) cc_final: 0.8406 (t0) REVERT: A 228 LYS cc_start: 0.8941 (mmtt) cc_final: 0.8684 (mmtt) REVERT: A 286 ASP cc_start: 0.8721 (m-30) cc_final: 0.8108 (m-30) REVERT: A 322 MET cc_start: 0.8178 (tpp) cc_final: 0.7952 (tpp) REVERT: A 344 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7549 (mt-10) REVERT: A 355 TYR cc_start: 0.8820 (m-80) cc_final: 0.8489 (m-80) REVERT: A 362 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.6723 (m-30) REVERT: A 406 ASP cc_start: 0.8188 (m-30) cc_final: 0.7913 (m-30) REVERT: A 485 ARG cc_start: 0.8445 (mtm-85) cc_final: 0.7573 (mtm110) REVERT: A 493 MET cc_start: 0.9076 (tmm) cc_final: 0.8828 (tmm) REVERT: A 570 MET cc_start: 0.8850 (mtp) cc_final: 0.8540 (mtp) REVERT: A 586 TYR cc_start: 0.8859 (m-10) cc_final: 0.8449 (m-10) REVERT: A 602 GLU cc_start: 0.7903 (tt0) cc_final: 0.6482 (tt0) REVERT: A 639 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8085 (m-30) REVERT: A 684 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.8024 (m-80) REVERT: B 15 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8400 (mp0) REVERT: B 98 PHE cc_start: 0.9260 (t80) cc_final: 0.8534 (t80) REVERT: B 167 LEU cc_start: 0.9101 (mt) cc_final: 0.8573 (mp) REVERT: B 250 TYR cc_start: 0.9318 (m-80) cc_final: 0.7740 (m-80) REVERT: B 263 ASP cc_start: 0.8804 (m-30) cc_final: 0.8325 (m-30) REVERT: B 286 ASP cc_start: 0.8078 (m-30) cc_final: 0.7354 (m-30) REVERT: B 317 MET cc_start: 0.8663 (mmm) cc_final: 0.8173 (mtp) REVERT: B 362 ASP cc_start: 0.7944 (m-30) cc_final: 0.6757 (m-30) REVERT: B 379 SER cc_start: 0.9170 (t) cc_final: 0.8438 (t) REVERT: B 586 TYR cc_start: 0.9132 (m-80) cc_final: 0.8586 (m-80) REVERT: B 602 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7639 (tm-30) REVERT: B 610 LYS cc_start: 0.9020 (tppt) cc_final: 0.8718 (tppt) REVERT: B 612 TYR cc_start: 0.8358 (m-80) cc_final: 0.8030 (m-80) REVERT: B 628 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7995 (mt-10) REVERT: B 634 MET cc_start: 0.8597 (mmm) cc_final: 0.8369 (tpp) REVERT: C 20 MET cc_start: 0.8733 (ptt) cc_final: 0.7874 (mmt) REVERT: C 21 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8293 (t80) REVERT: C 40 ASP cc_start: 0.9009 (p0) cc_final: 0.7928 (p0) REVERT: C 82 ASP cc_start: 0.8554 (m-30) cc_final: 0.8035 (p0) REVERT: C 91 ASN cc_start: 0.9146 (m-40) cc_final: 0.8863 (m-40) REVERT: C 95 MET cc_start: 0.8789 (tmm) cc_final: 0.8492 (tmm) REVERT: C 105 TYR cc_start: 0.8339 (m-80) cc_final: 0.8022 (m-80) REVERT: C 122 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.8031 (m-10) REVERT: C 134 LYS cc_start: 0.9177 (ttpt) cc_final: 0.8800 (tppt) REVERT: C 137 MET cc_start: 0.8482 (ptp) cc_final: 0.8064 (ptt) REVERT: C 227 PHE cc_start: 0.8808 (t80) cc_final: 0.8526 (t80) REVERT: C 231 LEU cc_start: 0.9448 (mm) cc_final: 0.9055 (pp) REVERT: C 233 ASN cc_start: 0.8933 (m110) cc_final: 0.8448 (p0) REVERT: C 237 GLU cc_start: 0.9353 (pt0) cc_final: 0.9126 (pp20) REVERT: C 270 ASN cc_start: 0.8871 (m-40) cc_final: 0.8629 (m-40) REVERT: D 30 TRP cc_start: 0.8538 (p-90) cc_final: 0.7876 (p-90) REVERT: D 46 TYR cc_start: 0.8921 (m-10) cc_final: 0.8576 (m-10) REVERT: D 86 ARG cc_start: 0.7913 (mmt180) cc_final: 0.7560 (mpt-90) REVERT: D 116 GLU cc_start: 0.8378 (pm20) cc_final: 0.7807 (pm20) REVERT: D 137 MET cc_start: 0.6513 (mtp) cc_final: 0.6036 (mmt) REVERT: D 154 PHE cc_start: 0.9356 (t80) cc_final: 0.8895 (t80) REVERT: D 157 MET cc_start: 0.9052 (ptp) cc_final: 0.8708 (ptp) REVERT: D 169 TYR cc_start: 0.8880 (m-80) cc_final: 0.8374 (m-80) REVERT: D 205 VAL cc_start: 0.9591 (t) cc_final: 0.9206 (p) REVERT: D 208 LEU cc_start: 0.9487 (mt) cc_final: 0.9231 (pp) REVERT: D 213 TYR cc_start: 0.8499 (t80) cc_final: 0.7978 (t80) REVERT: D 236 TYR cc_start: 0.7805 (t80) cc_final: 0.7555 (t80) REVERT: D 242 TYR cc_start: 0.8335 (t80) cc_final: 0.7994 (t80) outliers start: 32 outliers final: 22 residues processed: 535 average time/residue: 0.2775 time to fit residues: 218.8443 Evaluate side-chains 542 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 515 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 639 ASP Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 200 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 186 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.139496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.098441 restraints weight = 29080.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.101961 restraints weight = 12337.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.104070 restraints weight = 7083.962| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.6413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 16299 Z= 0.153 Angle : 0.726 17.161 22004 Z= 0.372 Chirality : 0.045 0.224 2348 Planarity : 0.004 0.050 2812 Dihedral : 8.303 139.981 2216 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.87 % Allowed : 28.12 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.19), residues: 1928 helix: 0.97 (0.15), residues: 1159 sheet: -0.58 (0.43), residues: 148 loop : 0.35 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 44 HIS 0.036 0.001 HIS C 201 PHE 0.022 0.002 PHE D 172 TYR 0.023 0.001 TYR D 22 ARG 0.009 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 896) hydrogen bonds : angle 5.15375 ( 2616) covalent geometry : bond 0.00349 (16298) covalent geometry : angle 0.72640 (22004) Misc. bond : bond 0.00021 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6732.86 seconds wall clock time: 117 minutes 6.73 seconds (7026.73 seconds total)