Starting phenix.real_space_refine on Sat Jun 14 05:35:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bwx_44985/06_2025/9bwx_44985_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bwx_44985/06_2025/9bwx_44985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bwx_44985/06_2025/9bwx_44985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bwx_44985/06_2025/9bwx_44985.map" model { file = "/net/cci-nas-00/data/ceres_data/9bwx_44985/06_2025/9bwx_44985_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bwx_44985/06_2025/9bwx_44985_neut.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 12 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10190 2.51 5 N 2598 2.21 5 O 3066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-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: 10.01, per 1000 atoms: 0.63 Number of scatterers: 15954 At special positions: 0 Unit cell: (93.002, 134.904, 133.882, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 12 15.00 Mg 2 11.99 O 3066 8.00 N 2598 7.00 C 10190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.50 Conformation dependent library (CDL) restraints added in 2.2 seconds 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3688 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 10 sheets defined 64.3% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 27 through 41 removed outlier: 3.554A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.076A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 4.057A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.706A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.873A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.793A pdb=" N GLN A 242 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.638A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 318 through 329 removed outlier: 6.056A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.520A pdb=" N PHE A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 589 removed outlier: 4.274A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 677 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 27 through 41 removed outlier: 3.547A pdb=" N GLU B 31 " --> pdb=" O ASP B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.949A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.960A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.722A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 222 through 237 removed outlier: 3.779A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.573A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 318 through 329 removed outlier: 5.842A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 367 removed outlier: 4.173A pdb=" N VAL B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 424 through 443 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 474 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.565A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 589 removed outlier: 4.403A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 677 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.514A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.889A pdb=" N GLY A 462 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASN A 410 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLY A 464 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 3.736A pdb=" N CYS A 409 " --> pdb=" O CYS A 170 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N CYS A 170 " --> pdb=" O CYS A 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA5, first strand: chain 'A' and resid 655 through 658 Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 removed outlier: 5.889A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 removed outlier: 6.456A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AA9, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB1, first strand: chain 'B' and resid 655 through 659 898 hydrogen bonds defined for protein. 2616 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.92 Time building geometry restraints manager: 5.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4956 1.34 - 1.46: 2920 1.46 - 1.58: 8247 1.58 - 1.70: 19 1.70 - 1.82: 156 Bond restraints: 16298 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.061 1.25e-02 6.40e+03 2.37e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.039 1.20e-02 6.94e+03 1.05e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.574 -0.032 1.08e-02 8.57e+03 8.76e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.569 -0.032 1.17e-02 7.31e+03 7.60e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.574 -0.033 1.25e-02 6.40e+03 7.18e+00 ... (remaining 16293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21496 2.09 - 4.17: 471 4.17 - 6.26: 33 6.26 - 8.35: 2 8.35 - 10.43: 2 Bond angle restraints: 22004 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.62 -6.08 1.36e+00 5.41e-01 2.00e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.12 -4.41 1.15e+00 7.56e-01 1.47e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.25 -3.97 1.09e+00 8.42e-01 1.33e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.80 -4.30 1.23e+00 6.61e-01 1.22e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.68 -3.97 1.15e+00 7.56e-01 1.19e+01 ... (remaining 21999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.31: 9429 34.31 - 68.63: 329 68.63 - 102.94: 48 102.94 - 137.25: 0 137.25 - 171.56: 2 Dihedral angle restraints: 9808 sinusoidal: 4062 harmonic: 5746 Sorted by residual: dihedral pdb=" C2 TTP A 801 " pdb=" C1' TTP A 801 " pdb=" N1 TTP A 801 " pdb=" O4' TTP A 801 " ideal model delta sinusoidal sigma weight residual 301.68 130.12 171.56 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual 301.68 135.69 165.99 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C VAL C 125 " pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual -122.00 -134.29 12.29 0 2.50e+00 1.60e-01 2.42e+01 ... (remaining 9805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2126 0.093 - 0.187: 183 0.187 - 0.280: 34 0.280 - 0.374: 3 0.374 - 0.467: 2 Chirality restraints: 2348 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.45e+00 chirality pdb=" CA TYR C 169 " pdb=" N TYR C 169 " pdb=" C TYR C 169 " pdb=" CB TYR C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 2345 not shown) Planarity restraints: 2812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 6 " 0.036 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO B 7 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 7 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 7 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.017 2.00e-02 2.50e+03 1.11e-02 2.17e+00 pdb=" CG PHE D 92 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.009 2.00e-02 2.50e+03 ... (remaining 2809 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 131 2.51 - 3.11: 11880 3.11 - 3.70: 26437 3.70 - 4.30: 41184 4.30 - 4.90: 64920 Nonbonded interactions: 144552 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" O1B TTP A 801 " pdb="MG MG A 802 " model vdw 1.919 2.170 nonbonded pdb=" O2A TTP B 801 " pdb="MG MG B 802 " model vdw 1.928 2.170 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 ... (remaining 144547 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 40.210 Find NCS groups from input model: 0.550 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:15.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.833 16299 Z= 0.724 Angle : 0.707 10.433 22004 Z= 0.453 Chirality : 0.059 0.467 2348 Planarity : 0.003 0.055 2812 Dihedral : 17.179 171.563 6120 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.34 % Allowed : 14.12 % Favored : 84.54 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.18), residues: 1928 helix: 1.04 (0.15), residues: 1133 sheet: 0.46 (0.39), residues: 146 loop : 0.45 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 PHE 0.021 0.002 PHE C 227 TYR 0.021 0.002 TYR D 179 ARG 0.004 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.16170 ( 896) hydrogen bonds : angle 6.35243 ( 2616) covalent geometry : bond 0.00542 (16298) covalent geometry : angle 0.70717 (22004) Misc. bond : bond 0.83345 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 411 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 ARG cc_start: 0.8631 (tpp-160) cc_final: 0.8417 (tpp-160) REVERT: B 274 ARG cc_start: 0.8031 (ptm160) cc_final: 0.7762 (ptp-110) outliers start: 23 outliers final: 6 residues processed: 427 average time/residue: 1.4198 time to fit residues: 663.9053 Evaluate side-chains 285 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 279 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 127 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 150 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 112 optimal weight: 0.2980 chunk 174 optimal weight: 8.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 232 ASN A 668 ASN B 11 GLN B 14 ASN B 49 HIS B 418 ASN D 80 HIS D 186 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.187100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.097463 restraints weight = 20548.539| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.43 r_work: 0.2824 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2663 r_free = 0.2663 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16299 Z= 0.189 Angle : 0.582 12.132 22004 Z= 0.312 Chirality : 0.042 0.186 2348 Planarity : 0.004 0.053 2812 Dihedral : 9.076 166.125 2228 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.03 % Allowed : 16.57 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.19), residues: 1928 helix: 1.74 (0.15), residues: 1125 sheet: 0.47 (0.41), residues: 132 loop : 0.65 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 9 HIS 0.004 0.001 HIS A 255 PHE 0.021 0.002 PHE B 624 TYR 0.022 0.001 TYR D 105 ARG 0.007 0.001 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.04452 ( 896) hydrogen bonds : angle 4.93361 ( 2616) covalent geometry : bond 0.00421 (16298) covalent geometry : angle 0.58234 (22004) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 310 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8114 (mm-30) REVERT: A 184 ARG cc_start: 0.9121 (tpp-160) cc_final: 0.8788 (tpp-160) REVERT: A 194 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8926 (tttm) REVERT: A 227 MET cc_start: 0.9558 (mtp) cc_final: 0.9348 (mtp) REVERT: A 232 ASN cc_start: 0.9060 (OUTLIER) cc_final: 0.8531 (m-40) REVERT: A 274 ARG cc_start: 0.8534 (ttt90) cc_final: 0.8261 (ttt90) REVERT: A 276 LYS cc_start: 0.9186 (mtpp) cc_final: 0.8914 (mmpt) REVERT: A 296 LYS cc_start: 0.8715 (mttt) cc_final: 0.8136 (mmmt) REVERT: A 570 MET cc_start: 0.9543 (mtp) cc_final: 0.9332 (ttm) REVERT: A 602 GLU cc_start: 0.8991 (tt0) cc_final: 0.8335 (tt0) REVERT: A 604 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8496 (mmt90) REVERT: B 11 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8259 (mt0) REVERT: B 15 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8499 (mm-30) REVERT: B 52 LYS cc_start: 0.9383 (OUTLIER) cc_final: 0.9107 (tptm) REVERT: B 56 ASP cc_start: 0.9167 (m-30) cc_final: 0.8844 (m-30) REVERT: B 112 LYS cc_start: 0.9353 (mtpp) cc_final: 0.9099 (mtmm) REVERT: B 120 ASP cc_start: 0.8972 (m-30) cc_final: 0.8703 (m-30) REVERT: B 235 ARG cc_start: 0.9014 (mtm-85) cc_final: 0.8767 (mtm-85) REVERT: B 274 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7313 (ptp90) REVERT: B 341 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8962 (mmmm) REVERT: B 343 LEU cc_start: 0.9334 (mt) cc_final: 0.9097 (mt) REVERT: B 402 GLU cc_start: 0.8927 (tp30) cc_final: 0.8618 (mp0) REVERT: B 604 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8890 (mmp80) REVERT: B 610 LYS cc_start: 0.8992 (mtpp) cc_final: 0.8696 (mtpp) REVERT: B 659 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8258 (mtpp) REVERT: C 56 MET cc_start: -0.0609 (mmp) cc_final: -0.1089 (tpt) outliers start: 52 outliers final: 11 residues processed: 340 average time/residue: 1.4679 time to fit residues: 546.5035 Evaluate side-chains 280 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 260 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 313 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 191 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 175 optimal weight: 30.0000 chunk 56 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 136 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 232 ASN A 668 ASN B 109 ASN D 71 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.183252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.094044 restraints weight = 20833.078| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.34 r_work: 0.2788 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16299 Z= 0.240 Angle : 0.572 10.853 22004 Z= 0.303 Chirality : 0.042 0.187 2348 Planarity : 0.004 0.053 2812 Dihedral : 8.956 165.502 2219 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.56 % Allowed : 16.63 % Favored : 79.81 % 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: 1.70 (0.19), residues: 1928 helix: 1.63 (0.15), residues: 1135 sheet: 0.12 (0.41), residues: 132 loop : 0.64 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 9 HIS 0.004 0.001 HIS B 438 PHE 0.017 0.002 PHE B 261 TYR 0.019 0.001 TYR C 46 ARG 0.009 0.001 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 896) hydrogen bonds : angle 4.83595 ( 2616) covalent geometry : bond 0.00544 (16298) covalent geometry : angle 0.57168 (22004) Misc. bond : bond 0.00143 ( 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 321 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 260 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8145 (mm-30) REVERT: A 184 ARG cc_start: 0.9153 (tpp-160) cc_final: 0.8825 (tpp-160) REVERT: A 274 ARG cc_start: 0.8666 (ttt90) cc_final: 0.8177 (ttt90) REVERT: A 276 LYS cc_start: 0.9167 (mtpp) cc_final: 0.8733 (mmpt) REVERT: A 296 LYS cc_start: 0.8817 (mttt) cc_final: 0.8197 (mmmt) REVERT: A 316 GLU cc_start: 0.8565 (tp30) cc_final: 0.8327 (tp30) REVERT: A 444 ASP cc_start: 0.8684 (t70) cc_final: 0.8214 (p0) REVERT: A 570 MET cc_start: 0.9552 (mtp) cc_final: 0.9327 (ttm) REVERT: A 602 GLU cc_start: 0.8955 (tt0) cc_final: 0.8619 (tt0) REVERT: B 15 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8523 (mm-30) REVERT: B 31 GLU cc_start: 0.9361 (mt-10) cc_final: 0.9081 (mt-10) REVERT: B 52 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.9053 (tptm) REVERT: B 56 ASP cc_start: 0.9098 (m-30) cc_final: 0.8786 (m-30) REVERT: B 120 ASP cc_start: 0.9027 (m-30) cc_final: 0.8745 (m-30) REVERT: B 228 LYS cc_start: 0.9015 (mtmt) cc_final: 0.8766 (mttt) REVERT: B 232 ASN cc_start: 0.9005 (OUTLIER) cc_final: 0.8716 (m-40) REVERT: B 235 ARG cc_start: 0.8925 (mtm-85) cc_final: 0.8696 (mtm-85) REVERT: B 274 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7010 (ptp90) REVERT: B 276 LYS cc_start: 0.9031 (ptpp) cc_final: 0.8742 (mmtm) REVERT: B 341 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8980 (mmmm) REVERT: B 343 LEU cc_start: 0.9379 (mt) cc_final: 0.9113 (mt) REVERT: B 603 GLU cc_start: 0.8448 (tm-30) cc_final: 0.7968 (mm-30) REVERT: B 610 LYS cc_start: 0.9035 (mtpp) cc_final: 0.8460 (tttp) REVERT: B 659 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8186 (mtpp) REVERT: B 686 ARG cc_start: 0.8432 (mtp85) cc_final: 0.8126 (mtp85) REVERT: D 103 LYS cc_start: 0.5274 (tptm) cc_final: 0.4916 (pptt) outliers start: 61 outliers final: 26 residues processed: 294 average time/residue: 1.5057 time to fit residues: 488.5008 Evaluate side-chains 278 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 247 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 646 GLN Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 8 LYS Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 313 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 153 optimal weight: 40.0000 chunk 136 optimal weight: 8.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN B 11 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.184912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.095436 restraints weight = 20884.387| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.46 r_work: 0.2817 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16299 Z= 0.177 Angle : 0.539 11.418 22004 Z= 0.285 Chirality : 0.040 0.158 2348 Planarity : 0.003 0.046 2812 Dihedral : 8.745 165.814 2219 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.15 % Allowed : 17.74 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.19), residues: 1928 helix: 1.65 (0.15), residues: 1137 sheet: -0.03 (0.42), residues: 132 loop : 0.61 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 9 HIS 0.004 0.001 HIS B 438 PHE 0.016 0.001 PHE A 100 TYR 0.026 0.001 TYR D 105 ARG 0.009 0.001 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 896) hydrogen bonds : angle 4.68233 ( 2616) covalent geometry : bond 0.00397 (16298) covalent geometry : angle 0.53877 (22004) Misc. bond : bond 0.00287 ( 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 319 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 265 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8139 (mm-30) REVERT: A 184 ARG cc_start: 0.9205 (tpp-160) cc_final: 0.8857 (tpp-160) REVERT: A 194 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.9100 (ptmt) REVERT: A 274 ARG cc_start: 0.8645 (ttt90) cc_final: 0.8163 (ttt90) REVERT: A 276 LYS cc_start: 0.9160 (mtpp) cc_final: 0.8736 (mmpt) REVERT: A 296 LYS cc_start: 0.8816 (mttt) cc_final: 0.8198 (mmmt) REVERT: A 316 GLU cc_start: 0.8611 (tp30) cc_final: 0.8357 (tp30) REVERT: A 444 ASP cc_start: 0.8596 (t70) cc_final: 0.8084 (p0) REVERT: B 11 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8021 (mt0) REVERT: B 15 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8523 (mp0) REVERT: B 52 LYS cc_start: 0.9425 (OUTLIER) cc_final: 0.9072 (tptm) REVERT: B 56 ASP cc_start: 0.9053 (m-30) cc_final: 0.8736 (m-30) REVERT: B 79 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8051 (mm-30) REVERT: B 120 ASP cc_start: 0.9049 (m-30) cc_final: 0.8758 (m-30) REVERT: B 232 ASN cc_start: 0.8958 (OUTLIER) cc_final: 0.8716 (m-40) REVERT: B 235 ARG cc_start: 0.8957 (ttm-80) cc_final: 0.8742 (mtm-85) REVERT: B 341 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.9011 (mmmm) REVERT: B 343 LEU cc_start: 0.9405 (mt) cc_final: 0.9157 (mt) REVERT: B 402 GLU cc_start: 0.9000 (tp30) cc_final: 0.8742 (mp0) REVERT: B 603 GLU cc_start: 0.8418 (tm-30) cc_final: 0.7831 (tm-30) REVERT: B 604 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8655 (mmp80) REVERT: B 610 LYS cc_start: 0.9047 (mtpp) cc_final: 0.8749 (ttmm) REVERT: B 659 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8249 (mtpp) REVERT: B 686 ARG cc_start: 0.8341 (mtp85) cc_final: 0.8116 (mtp85) REVERT: C 56 MET cc_start: -0.0538 (mmp) cc_final: -0.1082 (tpt) REVERT: C 287 LEU cc_start: 0.0199 (OUTLIER) cc_final: -0.0005 (pp) REVERT: D 103 LYS cc_start: 0.5284 (tptm) cc_final: 0.4919 (pptt) REVERT: D 269 MET cc_start: 0.5855 (OUTLIER) cc_final: 0.5616 (mpm) outliers start: 54 outliers final: 28 residues processed: 297 average time/residue: 1.4722 time to fit residues: 477.8473 Evaluate side-chains 283 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 246 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 109 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 188 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 165 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 24 GLN D 28 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.183130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.094624 restraints weight = 21209.903| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.40 r_work: 0.2793 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16299 Z= 0.234 Angle : 0.565 11.384 22004 Z= 0.295 Chirality : 0.041 0.148 2348 Planarity : 0.003 0.047 2812 Dihedral : 8.792 166.219 2219 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.44 % Allowed : 18.09 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.19), residues: 1928 helix: 1.61 (0.15), residues: 1138 sheet: -0.25 (0.42), residues: 132 loop : 0.62 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 623 HIS 0.004 0.001 HIS B 438 PHE 0.017 0.001 PHE A 492 TYR 0.013 0.001 TYR C 46 ARG 0.010 0.001 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 896) hydrogen bonds : angle 4.68090 ( 2616) covalent geometry : bond 0.00531 (16298) covalent geometry : angle 0.56482 (22004) Misc. bond : bond 0.00876 ( 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 317 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 258 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8095 (mm-30) REVERT: A 184 ARG cc_start: 0.9136 (tpp-160) cc_final: 0.8815 (tpp-160) REVERT: A 194 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8999 (ptmt) REVERT: A 274 ARG cc_start: 0.8625 (ttt90) cc_final: 0.8165 (ttt90) REVERT: A 276 LYS cc_start: 0.9154 (mtpp) cc_final: 0.8751 (mmpt) REVERT: A 316 GLU cc_start: 0.8585 (tp30) cc_final: 0.8325 (tp30) REVERT: A 402 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8348 (mt-10) REVERT: A 444 ASP cc_start: 0.8598 (t70) cc_final: 0.8149 (p0) REVERT: A 589 SER cc_start: 0.9598 (OUTLIER) cc_final: 0.9296 (t) REVERT: A 604 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8400 (mmt-90) REVERT: B 11 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8234 (mt0) REVERT: B 15 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8563 (mp0) REVERT: B 52 LYS cc_start: 0.9409 (OUTLIER) cc_final: 0.9056 (tptm) REVERT: B 56 ASP cc_start: 0.9090 (m-30) cc_final: 0.8768 (m-30) REVERT: B 112 LYS cc_start: 0.9373 (mtpp) cc_final: 0.9067 (mtmm) REVERT: B 120 ASP cc_start: 0.9073 (m-30) cc_final: 0.8769 (m-30) REVERT: B 232 ASN cc_start: 0.8952 (OUTLIER) cc_final: 0.8709 (m-40) REVERT: B 274 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7356 (ptp90) REVERT: B 335 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8187 (mt-10) REVERT: B 341 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8985 (mmmm) REVERT: B 402 GLU cc_start: 0.9005 (tp30) cc_final: 0.8661 (mp0) REVERT: B 659 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8202 (mtpp) REVERT: C 56 MET cc_start: -0.0654 (mmp) cc_final: -0.1139 (tpt) REVERT: D 269 MET cc_start: 0.5956 (OUTLIER) cc_final: 0.5721 (mpm) outliers start: 59 outliers final: 28 residues processed: 290 average time/residue: 1.5115 time to fit residues: 478.4374 Evaluate side-chains 278 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 240 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 143 optimal weight: 6.9990 chunk 51 optimal weight: 0.3980 chunk 88 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 182 optimal weight: 20.0000 chunk 56 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.186355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.098660 restraints weight = 20823.844| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.36 r_work: 0.2866 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3519 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= 0.127 Angle : 0.529 12.818 22004 Z= 0.277 Chirality : 0.039 0.161 2348 Planarity : 0.003 0.049 2812 Dihedral : 8.306 162.788 2219 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.68 % Allowed : 19.25 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.70 (0.19), residues: 1928 helix: 1.73 (0.15), residues: 1130 sheet: -0.47 (0.39), residues: 144 loop : 0.62 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 9 HIS 0.004 0.001 HIS B 438 PHE 0.015 0.001 PHE A 492 TYR 0.039 0.001 TYR D 105 ARG 0.011 0.001 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.03440 ( 896) hydrogen bonds : angle 4.52214 ( 2616) covalent geometry : bond 0.00283 (16298) covalent geometry : angle 0.52868 (22004) Misc. bond : bond 0.00438 ( 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 320 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 274 time to evaluate : 1.821 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 112 LYS cc_start: 0.9270 (mtpp) cc_final: 0.8946 (ptpp) REVERT: A 184 ARG cc_start: 0.9110 (tpp-160) cc_final: 0.8796 (tpp-160) REVERT: A 274 ARG cc_start: 0.8796 (ttt90) cc_final: 0.8436 (ttt90) REVERT: A 276 LYS cc_start: 0.9150 (mtpp) cc_final: 0.8759 (mmpt) REVERT: A 296 LYS cc_start: 0.8793 (mttt) cc_final: 0.8175 (mmmt) REVERT: A 316 GLU cc_start: 0.8597 (tp30) cc_final: 0.8379 (tp30) REVERT: A 402 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8357 (mt-10) REVERT: A 589 SER cc_start: 0.9639 (OUTLIER) cc_final: 0.9353 (t) REVERT: A 599 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8920 (mt-10) REVERT: A 602 GLU cc_start: 0.8877 (tt0) cc_final: 0.8059 (tt0) REVERT: A 604 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8547 (mmt90) REVERT: B 15 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8475 (mp0) REVERT: B 52 LYS cc_start: 0.9429 (OUTLIER) cc_final: 0.9124 (tptm) REVERT: B 56 ASP cc_start: 0.9035 (m-30) cc_final: 0.8729 (m-30) REVERT: B 79 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7966 (mm-30) REVERT: B 112 LYS cc_start: 0.9319 (mtpp) cc_final: 0.8963 (mtmm) REVERT: B 120 ASP cc_start: 0.9069 (m-30) cc_final: 0.8726 (m-30) REVERT: B 170 CYS cc_start: 0.8556 (p) cc_final: 0.8306 (m) REVERT: B 274 ARG cc_start: 0.8575 (ptm160) cc_final: 0.7387 (ptp90) REVERT: B 335 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8349 (mt-10) REVERT: B 341 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8957 (mmmm) REVERT: B 343 LEU cc_start: 0.9344 (mt) cc_final: 0.9101 (mt) REVERT: B 362 ASP cc_start: 0.8667 (m-30) cc_final: 0.8240 (m-30) REVERT: B 402 GLU cc_start: 0.9035 (tp30) cc_final: 0.8730 (mp0) REVERT: B 526 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8421 (mp0) REVERT: B 602 GLU cc_start: 0.8804 (tt0) cc_final: 0.7863 (tt0) REVERT: B 604 ARG cc_start: 0.9206 (mmp80) cc_final: 0.7730 (mmp80) REVERT: B 610 LYS cc_start: 0.9078 (mtpp) cc_final: 0.8118 (ttmm) REVERT: B 659 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8252 (mtpp) REVERT: D 269 MET cc_start: 0.6099 (OUTLIER) cc_final: 0.5765 (mmp) outliers start: 46 outliers final: 15 residues processed: 297 average time/residue: 1.4229 time to fit residues: 463.4547 Evaluate side-chains 269 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 247 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 7 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 65 optimal weight: 0.3980 chunk 109 optimal weight: 0.9980 chunk 26 optimal weight: 0.0030 chunk 84 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN B 102 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 ASN C 216 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.187360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.099485 restraints weight = 21001.991| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.42 r_work: 0.2887 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3703 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= 0.125 Angle : 0.544 13.656 22004 Z= 0.281 Chirality : 0.039 0.159 2348 Planarity : 0.003 0.056 2812 Dihedral : 8.136 161.305 2218 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.16 % Allowed : 21.00 % Favored : 76.84 % 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: 1.75 (0.19), residues: 1928 helix: 1.77 (0.15), residues: 1132 sheet: -0.39 (0.40), residues: 148 loop : 0.62 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 9 HIS 0.004 0.001 HIS B 438 PHE 0.019 0.001 PHE A 492 TYR 0.025 0.001 TYR D 105 ARG 0.012 0.001 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 896) hydrogen bonds : angle 4.49354 ( 2616) covalent geometry : bond 0.00280 (16298) covalent geometry : angle 0.54355 (22004) Misc. bond : bond 0.00573 ( 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 305 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 268 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.9218 (ttmm) cc_final: 0.8729 (tptt) REVERT: A 66 GLU cc_start: 0.8598 (tp30) cc_final: 0.8377 (tp30) REVERT: A 79 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8350 (mm-30) REVERT: A 112 LYS cc_start: 0.9275 (mtpp) cc_final: 0.8977 (ptpp) REVERT: A 184 ARG cc_start: 0.9055 (tpp-160) cc_final: 0.8743 (tpp-160) REVERT: A 274 ARG cc_start: 0.8804 (ttt90) cc_final: 0.8396 (ttt90) REVERT: A 276 LYS cc_start: 0.9143 (mtpp) cc_final: 0.8712 (mmpt) REVERT: A 316 GLU cc_start: 0.8589 (tp30) cc_final: 0.8382 (tp30) REVERT: A 384 GLU cc_start: 0.9329 (OUTLIER) cc_final: 0.8546 (pp20) REVERT: A 402 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8324 (mt-10) REVERT: A 446 ARG cc_start: 0.8110 (mmp-170) cc_final: 0.7876 (mmp-170) REVERT: A 589 SER cc_start: 0.9630 (t) cc_final: 0.9356 (t) REVERT: A 599 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8918 (mt-10) REVERT: A 602 GLU cc_start: 0.8876 (tt0) cc_final: 0.8096 (tt0) REVERT: A 604 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8469 (mmt90) REVERT: B 15 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8535 (mm-30) REVERT: B 52 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.9105 (tptm) REVERT: B 56 ASP cc_start: 0.9050 (m-30) cc_final: 0.8732 (m-30) REVERT: B 79 GLU cc_start: 0.8489 (mm-30) cc_final: 0.7991 (mm-30) REVERT: B 112 LYS cc_start: 0.9337 (mtpp) cc_final: 0.8952 (mtmm) REVERT: B 120 ASP cc_start: 0.9075 (m-30) cc_final: 0.8734 (m-30) REVERT: B 170 CYS cc_start: 0.8565 (p) cc_final: 0.8286 (m) REVERT: B 274 ARG cc_start: 0.8374 (ptm160) cc_final: 0.7123 (ptp90) REVERT: B 296 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8559 (ptpp) REVERT: B 335 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8287 (mt-10) REVERT: B 341 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8924 (mmmm) REVERT: B 343 LEU cc_start: 0.9300 (mt) cc_final: 0.9037 (mt) REVERT: B 362 ASP cc_start: 0.8644 (m-30) cc_final: 0.8239 (m-30) REVERT: B 526 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8443 (mp0) REVERT: C 56 MET cc_start: -0.0341 (mmp) cc_final: -0.1115 (tpt) REVERT: D 105 TYR cc_start: 0.2429 (OUTLIER) cc_final: 0.1589 (p90) REVERT: D 269 MET cc_start: 0.6185 (OUTLIER) cc_final: 0.5865 (mmp) outliers start: 37 outliers final: 15 residues processed: 285 average time/residue: 1.4580 time to fit residues: 456.7452 Evaluate side-chains 271 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 248 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 146 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 174 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 chunk 4 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 181 optimal weight: 40.0000 chunk 9 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.186500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.099179 restraints weight = 20848.899| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.34 r_work: 0.2867 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16299 Z= 0.153 Angle : 0.557 15.433 22004 Z= 0.290 Chirality : 0.040 0.177 2348 Planarity : 0.003 0.058 2812 Dihedral : 8.080 161.509 2218 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.93 % Allowed : 21.88 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.19), residues: 1928 helix: 1.74 (0.15), residues: 1134 sheet: -0.50 (0.39), residues: 148 loop : 0.63 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 9 HIS 0.004 0.001 HIS B 438 PHE 0.019 0.001 PHE A 492 TYR 0.028 0.001 TYR C 46 ARG 0.013 0.001 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.03391 ( 896) hydrogen bonds : angle 4.51449 ( 2616) covalent geometry : bond 0.00348 (16298) covalent geometry : angle 0.55725 (22004) Misc. bond : bond 0.00297 ( 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 287 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 254 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.9242 (ttmm) cc_final: 0.8795 (tptt) REVERT: A 66 GLU cc_start: 0.8575 (tp30) cc_final: 0.8355 (tp30) REVERT: A 79 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8351 (mm-30) REVERT: A 112 LYS cc_start: 0.9267 (mtpp) cc_final: 0.9038 (ptpp) REVERT: A 184 ARG cc_start: 0.9103 (tpp-160) cc_final: 0.8820 (tpp-160) REVERT: A 274 ARG cc_start: 0.8774 (ttt90) cc_final: 0.8348 (ttt90) REVERT: A 276 LYS cc_start: 0.9157 (mtpp) cc_final: 0.8724 (mmpt) REVERT: A 296 LYS cc_start: 0.8772 (mttt) cc_final: 0.8154 (mmmt) REVERT: A 316 GLU cc_start: 0.8604 (tp30) cc_final: 0.8391 (tp30) REVERT: A 589 SER cc_start: 0.9636 (t) cc_final: 0.9378 (t) REVERT: A 602 GLU cc_start: 0.8865 (tt0) cc_final: 0.8084 (tt0) REVERT: A 604 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8474 (mmt90) REVERT: B 15 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8544 (mm-30) REVERT: B 52 LYS cc_start: 0.9428 (OUTLIER) cc_final: 0.9118 (tptm) REVERT: B 56 ASP cc_start: 0.9017 (m-30) cc_final: 0.8709 (m-30) REVERT: B 79 GLU cc_start: 0.8484 (mm-30) cc_final: 0.7991 (mm-30) REVERT: B 112 LYS cc_start: 0.9300 (mtpp) cc_final: 0.9044 (mtpm) REVERT: B 120 ASP cc_start: 0.9079 (m-30) cc_final: 0.8767 (m-30) REVERT: B 170 CYS cc_start: 0.8605 (p) cc_final: 0.8285 (m) REVERT: B 274 ARG cc_start: 0.8363 (ptm160) cc_final: 0.7279 (ptp90) REVERT: B 335 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8290 (mt-10) REVERT: B 341 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8939 (mmmm) REVERT: B 343 LEU cc_start: 0.9334 (mt) cc_final: 0.9058 (mt) REVERT: B 362 ASP cc_start: 0.8657 (m-30) cc_final: 0.8272 (m-30) REVERT: B 402 GLU cc_start: 0.8977 (tp30) cc_final: 0.8750 (mp0) REVERT: B 602 GLU cc_start: 0.8847 (tt0) cc_final: 0.8116 (tt0) REVERT: B 604 ARG cc_start: 0.9030 (mmp80) cc_final: 0.7844 (mmp80) REVERT: C 56 MET cc_start: -0.0247 (mmp) cc_final: -0.0957 (tpt) REVERT: C 319 ASP cc_start: 0.9225 (m-30) cc_final: 0.9022 (m-30) REVERT: D 105 TYR cc_start: 0.2287 (OUTLIER) cc_final: 0.1481 (p90) REVERT: D 269 MET cc_start: 0.6139 (OUTLIER) cc_final: 0.5835 (mmp) outliers start: 33 outliers final: 22 residues processed: 272 average time/residue: 1.4811 time to fit residues: 442.5886 Evaluate side-chains 276 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 249 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 140 optimal weight: 50.0000 chunk 110 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 162 optimal weight: 50.0000 chunk 168 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 122 optimal weight: 0.0770 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.185201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.097197 restraints weight = 20911.112| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.43 r_work: 0.2839 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16299 Z= 0.191 Angle : 0.594 16.933 22004 Z= 0.306 Chirality : 0.041 0.158 2348 Planarity : 0.003 0.042 2812 Dihedral : 8.024 162.870 2216 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.81 % Allowed : 22.11 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.19), residues: 1928 helix: 1.72 (0.15), residues: 1136 sheet: -0.52 (0.40), residues: 136 loop : 0.58 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 9 HIS 0.003 0.001 HIS B 438 PHE 0.019 0.001 PHE A 492 TYR 0.030 0.001 TYR C 46 ARG 0.010 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03490 ( 896) hydrogen bonds : angle 4.56178 ( 2616) covalent geometry : bond 0.00438 (16298) covalent geometry : angle 0.59405 (22004) Misc. bond : bond 0.00268 ( 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 283 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 252 time to evaluate : 1.963 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 30 LYS cc_start: 0.9248 (ttmm) cc_final: 0.8778 (tptt) REVERT: A 79 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8395 (mm-30) REVERT: A 112 LYS cc_start: 0.9266 (mtpp) cc_final: 0.9004 (ptpp) REVERT: A 184 ARG cc_start: 0.9166 (tpp-160) cc_final: 0.8865 (tpp-160) REVERT: A 274 ARG cc_start: 0.8804 (ttt90) cc_final: 0.8364 (ttt90) REVERT: A 276 LYS cc_start: 0.9162 (mtpp) cc_final: 0.8736 (mmtt) REVERT: A 296 LYS cc_start: 0.8763 (mttt) cc_final: 0.8137 (mmmt) REVERT: A 384 GLU cc_start: 0.9353 (OUTLIER) cc_final: 0.8639 (pm20) REVERT: A 589 SER cc_start: 0.9626 (t) cc_final: 0.9374 (t) REVERT: A 602 GLU cc_start: 0.8869 (tt0) cc_final: 0.8081 (tt0) REVERT: A 604 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8521 (mmt90) REVERT: B 52 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9072 (tptm) REVERT: B 56 ASP cc_start: 0.9041 (m-30) cc_final: 0.8717 (m-30) REVERT: B 79 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8006 (mm-30) REVERT: B 112 LYS cc_start: 0.9319 (mtpp) cc_final: 0.9066 (mtpm) REVERT: B 120 ASP cc_start: 0.9110 (m-30) cc_final: 0.8798 (m-30) REVERT: B 170 CYS cc_start: 0.8656 (p) cc_final: 0.8282 (m) REVERT: B 246 SER cc_start: 0.8355 (OUTLIER) cc_final: 0.7792 (p) REVERT: B 274 ARG cc_start: 0.8379 (ptm160) cc_final: 0.7221 (ptp90) REVERT: B 335 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8220 (mt-10) REVERT: B 341 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8951 (mmmm) REVERT: B 343 LEU cc_start: 0.9367 (mt) cc_final: 0.9105 (mt) REVERT: B 402 GLU cc_start: 0.9001 (tp30) cc_final: 0.8759 (mp0) REVERT: B 604 ARG cc_start: 0.9011 (mmp80) cc_final: 0.8739 (mmp80) REVERT: B 686 ARG cc_start: 0.8007 (ptm160) cc_final: 0.7439 (ptm-80) REVERT: C 56 MET cc_start: -0.0252 (mmp) cc_final: -0.0995 (tpt) REVERT: C 317 ASP cc_start: 0.9127 (m-30) cc_final: 0.8417 (t0) REVERT: D 105 TYR cc_start: 0.2046 (OUTLIER) cc_final: 0.1046 (p90) REVERT: D 269 MET cc_start: 0.6099 (OUTLIER) cc_final: 0.5774 (mmp) outliers start: 31 outliers final: 19 residues processed: 269 average time/residue: 1.4535 time to fit residues: 429.2287 Evaluate side-chains 269 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 243 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 165 optimal weight: 40.0000 chunk 180 optimal weight: 7.9990 chunk 2 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 164 optimal weight: 9.9990 chunk 190 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN B 109 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.185719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.097421 restraints weight = 21025.716| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.40 r_work: 0.2830 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16299 Z= 0.197 Angle : 0.602 17.685 22004 Z= 0.312 Chirality : 0.041 0.182 2348 Planarity : 0.004 0.042 2812 Dihedral : 8.048 163.544 2216 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.69 % Allowed : 22.35 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.19), residues: 1928 helix: 1.69 (0.15), residues: 1133 sheet: -0.56 (0.40), residues: 136 loop : 0.63 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 44 HIS 0.004 0.001 HIS B 438 PHE 0.019 0.001 PHE A 492 TYR 0.024 0.001 TYR C 46 ARG 0.009 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 896) hydrogen bonds : angle 4.59734 ( 2616) covalent geometry : bond 0.00450 (16298) covalent geometry : angle 0.60187 (22004) Misc. bond : bond 0.00248 ( 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 272 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 243 time to evaluate : 1.848 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 30 LYS cc_start: 0.9227 (ttmm) cc_final: 0.8743 (tptt) REVERT: A 79 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8364 (mm-30) REVERT: A 112 LYS cc_start: 0.9287 (mtpp) cc_final: 0.8996 (ptpp) REVERT: A 184 ARG cc_start: 0.9109 (tpp-160) cc_final: 0.8811 (tpp-160) REVERT: A 274 ARG cc_start: 0.8778 (ttt90) cc_final: 0.8305 (ttt90) REVERT: A 276 LYS cc_start: 0.9159 (mtpp) cc_final: 0.8760 (mmtt) REVERT: A 296 LYS cc_start: 0.8718 (mttt) cc_final: 0.8094 (mmmt) REVERT: A 384 GLU cc_start: 0.9345 (OUTLIER) cc_final: 0.8487 (pm20) REVERT: A 589 SER cc_start: 0.9617 (t) cc_final: 0.9365 (t) REVERT: A 602 GLU cc_start: 0.8871 (tt0) cc_final: 0.8066 (tt0) REVERT: A 604 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8495 (mmt90) REVERT: B 52 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.9047 (tptm) REVERT: B 56 ASP cc_start: 0.9060 (m-30) cc_final: 0.8727 (m-30) REVERT: B 79 GLU cc_start: 0.8517 (mm-30) cc_final: 0.7997 (mm-30) REVERT: B 112 LYS cc_start: 0.9337 (mtpp) cc_final: 0.9054 (mtpm) REVERT: B 120 ASP cc_start: 0.9107 (m-30) cc_final: 0.8790 (m-30) REVERT: B 170 CYS cc_start: 0.8641 (p) cc_final: 0.8255 (m) REVERT: B 274 ARG cc_start: 0.8347 (ptm160) cc_final: 0.6964 (ptp90) REVERT: B 276 LYS cc_start: 0.8877 (ptpp) cc_final: 0.8455 (mmtm) REVERT: B 335 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8161 (mt-10) REVERT: B 341 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8921 (mmmm) REVERT: B 343 LEU cc_start: 0.9319 (mt) cc_final: 0.9077 (mt) REVERT: B 402 GLU cc_start: 0.8983 (tp30) cc_final: 0.8664 (mp0) REVERT: B 604 ARG cc_start: 0.9020 (mmp80) cc_final: 0.8745 (mmp80) REVERT: B 686 ARG cc_start: 0.8052 (ptm160) cc_final: 0.7504 (ptm-80) REVERT: C 56 MET cc_start: -0.0276 (mmp) cc_final: -0.1009 (tpt) REVERT: C 317 ASP cc_start: 0.9086 (m-30) cc_final: 0.8340 (t0) REVERT: D 105 TYR cc_start: 0.2164 (OUTLIER) cc_final: 0.1143 (p90) REVERT: D 269 MET cc_start: 0.6262 (OUTLIER) cc_final: 0.5966 (mmp) outliers start: 29 outliers final: 20 residues processed: 260 average time/residue: 1.8985 time to fit residues: 548.2773 Evaluate side-chains 266 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 240 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 186 optimal weight: 50.0000 chunk 119 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 140 optimal weight: 50.0000 chunk 168 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.187443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.099819 restraints weight = 20970.377| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.39 r_work: 0.2867 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16299 Z= 0.143 Angle : 0.590 17.354 22004 Z= 0.306 Chirality : 0.040 0.168 2348 Planarity : 0.003 0.042 2812 Dihedral : 7.889 161.393 2216 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.75 % Allowed : 22.35 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.19), residues: 1928 helix: 1.69 (0.15), residues: 1135 sheet: -0.59 (0.39), residues: 144 loop : 0.67 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 9 HIS 0.003 0.001 HIS B 438 PHE 0.019 0.001 PHE A 492 TYR 0.027 0.001 TYR C 46 ARG 0.008 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 896) hydrogen bonds : angle 4.52420 ( 2616) covalent geometry : bond 0.00326 (16298) covalent geometry : angle 0.58972 (22004) Misc. bond : bond 0.00233 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20021.70 seconds wall clock time: 344 minutes 2.24 seconds (20642.24 seconds total)