Starting phenix.real_space_refine on Fri Jul 3 19:25:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bwx_44985/07_2026/9bwx_44985_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bwx_44985/07_2026/9bwx_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_44985/07_2026/9bwx_44985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bwx_44985/07_2026/9bwx_44985.map" model { file = "/net/cci-nas-00/data/ceres_data/9bwx_44985/07_2026/9bwx_44985_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bwx_44985/07_2026/9bwx_44985_neut.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 12 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10190 2.51 5 N 2598 2.21 5 O 3066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15954 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.38, per 1000 atoms: 0.21 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: 0.94 Conformation dependent library (CDL) restraints added in 544.0 milliseconds 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3688 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 10 sheets defined 64.3% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 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: 2.38 Time building geometry restraints manager: 1.29 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=" O3B TTP B 801 " pdb=" PG TTP B 801 " ideal model delta sigma weight residual 1.748 1.608 0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" O3B TTP A 801 " pdb=" PG TTP A 801 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.85e+01 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=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" O3A TTP A 801 " pdb=" PB TTP A 801 " ideal model delta sigma weight residual 1.675 1.608 0.067 2.00e-02 2.50e+03 1.12e+01 ... (remaining 16293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 21464 2.11 - 4.21: 467 4.21 - 6.32: 58 6.32 - 8.43: 8 8.43 - 10.53: 7 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=" O1A TTP A 801 " pdb=" PA TTP A 801 " pdb=" O2A TTP A 801 " ideal model delta sigma weight residual 121.23 110.70 10.53 3.00e+00 1.11e-01 1.23e+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 ... (remaining 21999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 8645 17.66 - 35.32: 853 35.32 - 52.98: 254 52.98 - 70.64: 64 70.64 - 88.29: 40 Dihedral angle restraints: 9856 sinusoidal: 4110 harmonic: 5746 Sorted by residual: 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 dihedral pdb=" N VAL C 125 " pdb=" C VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual 123.40 135.51 -12.11 0 2.50e+00 1.60e-01 2.35e+01 dihedral pdb=" C ASN C 98 " pdb=" N ASN C 98 " pdb=" CA ASN C 98 " pdb=" CB ASN C 98 " ideal model delta harmonic sigma weight residual -122.60 -134.31 11.71 0 2.50e+00 1.60e-01 2.19e+01 ... (remaining 9853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2122 0.093 - 0.187: 187 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 3.060 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 3.060 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 3.060 ... (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: 1.680 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.900 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 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 : 0.009 0.833 16299 Z= 0.732 Angle : 0.756 10.535 22004 Z= 0.462 Chirality : 0.059 0.467 2348 Planarity : 0.003 0.055 2812 Dihedral : 16.909 88.295 6168 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.000 ARG D 196 TYR 0.021 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.33 (16298) covalent geometry : angle 0.75591 / 0.46 (22004) hydrogen bonds : bond 0.16170 / 10.53 ( 896) hydrogen bonds : angle 6.35243 / 4.48 ( 2616) Misc. bond : bond 0.83345 / 43.87 ( 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 : 0.625 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: 0.8416 (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: 0.6437 time to fit residues: 301.1185 Evaluate side-chains 286 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 280 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0040 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN A 232 ASN A 668 ASN B 11 GLN B 14 ASN B 418 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN D 201 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.186936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.096752 restraints weight = 20846.888| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.42 r_work: 0.2831 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.42 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 = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16299 Z= 0.172 Angle : 0.576 10.912 22004 Z= 0.310 Chirality : 0.042 0.203 2348 Planarity : 0.004 0.053 2812 Dihedral : 6.950 63.617 2276 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.15 % Allowed : 16.74 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.19), residues: 1928 helix: 1.76 (0.15), residues: 1125 sheet: 0.61 (0.42), residues: 126 loop : 0.63 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 446 TYR 0.020 0.001 TYR D 105 PHE 0.021 0.001 PHE B 624 TRP 0.012 0.002 TRP B 9 HIS 0.004 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (16298) covalent geometry : angle 0.57619 / 0.31 (22004) hydrogen bonds : bond 0.04489 / 2.84 ( 896) hydrogen bonds : angle 4.94829 / 3.47 ( 2616) Misc. bond : bond 0.00219 / 0.12 ( 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 366 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 312 time to evaluate : 0.481 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: 0.8377 (mm-30) cc_final: 0.8032 (mm-30) REVERT: A 184 ARG cc_start: 0.9103 (tpp-160) cc_final: 0.8753 (tpp-160) REVERT: A 194 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8940 (tttm) REVERT: A 227 MET cc_start: 0.9553 (mtp) cc_final: 0.9352 (mtp) REVERT: A 232 ASN cc_start: 0.9061 (OUTLIER) cc_final: 0.8541 (m-40) REVERT: A 274 ARG cc_start: 0.8497 (ttt90) cc_final: 0.8162 (ttt90) REVERT: A 276 LYS cc_start: 0.9210 (mtpp) cc_final: 0.8763 (mmpt) REVERT: A 296 LYS cc_start: 0.8680 (mttt) cc_final: 0.8123 (mmmt) REVERT: A 570 MET cc_start: 0.9531 (mtp) cc_final: 0.9317 (ttm) REVERT: A 602 GLU cc_start: 0.9004 (tt0) cc_final: 0.8335 (tt0) REVERT: A 604 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8513 (mmt90) REVERT: B 15 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8505 (mm-30) REVERT: B 52 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.9117 (tptm) REVERT: B 56 ASP cc_start: 0.9183 (m-30) cc_final: 0.8886 (m-30) REVERT: B 112 LYS cc_start: 0.9367 (mtpp) cc_final: 0.9106 (mtmm) REVERT: B 120 ASP cc_start: 0.8958 (m-30) cc_final: 0.8685 (m-30) REVERT: B 274 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.7283 (ptp90) REVERT: B 341 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8969 (mmmm) REVERT: B 343 LEU cc_start: 0.9335 (mt) cc_final: 0.9107 (mt) REVERT: B 402 GLU cc_start: 0.8948 (tp30) cc_final: 0.8614 (mp0) REVERT: B 604 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8868 (mmp80) REVERT: B 610 LYS cc_start: 0.8990 (mtpp) cc_final: 0.8650 (mtpp) REVERT: B 659 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8232 (mtpp) REVERT: C 56 MET cc_start: -0.0557 (mmp) cc_final: -0.1015 (tpt) REVERT: C 287 LEU cc_start: 0.0134 (OUTLIER) cc_final: -0.0085 (pp) outliers start: 54 outliers final: 10 residues processed: 343 average time/residue: 0.6383 time to fit residues: 240.3636 Evaluate side-chains 281 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 262 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 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 10 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 156 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 668 ASN B 109 ASN B 232 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.184294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.095468 restraints weight = 21149.433| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.35 r_work: 0.2817 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 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 = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16299 Z= 0.184 Angle : 0.550 10.487 22004 Z= 0.294 Chirality : 0.041 0.187 2348 Planarity : 0.003 0.048 2812 Dihedral : 6.730 62.192 2267 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.86 % Allowed : 17.27 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.19), residues: 1928 helix: 1.72 (0.15), residues: 1137 sheet: 0.15 (0.41), residues: 132 loop : 0.70 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 446 TYR 0.019 0.001 TYR C 46 PHE 0.016 0.001 PHE B 261 TRP 0.010 0.001 TRP B 9 HIS 0.004 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (16298) covalent geometry : angle 0.55026 / 0.29 (22004) hydrogen bonds : bond 0.04048 / 2.56 ( 896) hydrogen bonds : angle 4.77209 / 3.35 ( 2616) Misc. bond : bond 0.00200 / 0.11 ( 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 318 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 269 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8025 (mm-30) REVERT: A 184 ARG cc_start: 0.9110 (tpp-160) cc_final: 0.8765 (tpp-160) REVERT: A 227 MET cc_start: 0.9600 (mtp) cc_final: 0.9391 (mtp) REVERT: A 232 ASN cc_start: 0.9024 (m-40) cc_final: 0.8745 (m110) REVERT: A 274 ARG cc_start: 0.8644 (ttt90) cc_final: 0.8260 (ttt90) REVERT: A 296 LYS cc_start: 0.8804 (mttt) cc_final: 0.8195 (mmmt) REVERT: A 444 ASP cc_start: 0.8664 (t70) cc_final: 0.8160 (p0) REVERT: A 602 GLU cc_start: 0.8923 (tt0) cc_final: 0.8647 (tt0) REVERT: B 15 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8504 (mm-30) REVERT: B 52 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9085 (tptm) REVERT: B 56 ASP cc_start: 0.9121 (m-30) cc_final: 0.8800 (m-30) REVERT: B 112 LYS cc_start: 0.9353 (mtpp) cc_final: 0.9012 (mtmm) REVERT: B 120 ASP cc_start: 0.9005 (m-30) cc_final: 0.8691 (m-30) REVERT: B 232 ASN cc_start: 0.8919 (OUTLIER) cc_final: 0.8650 (m110) REVERT: B 235 ARG cc_start: 0.8949 (mtm-85) cc_final: 0.8674 (mtm-85) REVERT: B 274 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7308 (ptp90) REVERT: B 341 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8966 (mmmm) REVERT: B 343 LEU cc_start: 0.9340 (mt) cc_final: 0.9083 (mt) REVERT: B 603 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7926 (mm-30) REVERT: B 604 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.8883 (mmp80) REVERT: B 610 LYS cc_start: 0.9053 (mtpp) cc_final: 0.8379 (tttp) REVERT: B 659 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8194 (mtpp) REVERT: C 287 LEU cc_start: 0.0312 (OUTLIER) cc_final: 0.0101 (pt) outliers start: 49 outliers final: 18 residues processed: 295 average time/residue: 0.6999 time to fit residues: 225.9693 Evaluate side-chains 267 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 242 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 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 684 TYR Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN 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 410 ASN Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 313 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 147 optimal weight: 50.0000 chunk 132 optimal weight: 0.5980 chunk 185 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 171 optimal weight: 30.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 668 ASN D 24 GLN D 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.181714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.092924 restraints weight = 21056.351| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.35 r_work: 0.2770 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 16299 Z= 0.275 Angle : 0.580 10.948 22004 Z= 0.309 Chirality : 0.043 0.173 2348 Planarity : 0.004 0.045 2812 Dihedral : 6.918 62.858 2267 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.50 % Allowed : 17.21 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.19), residues: 1928 helix: 1.63 (0.15), residues: 1135 sheet: -0.12 (0.41), residues: 132 loop : 0.61 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 446 TYR 0.032 0.001 TYR D 105 PHE 0.018 0.002 PHE A 492 TRP 0.010 0.001 TRP B 9 HIS 0.004 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.27 (16298) covalent geometry : angle 0.57997 / 0.31 (22004) hydrogen bonds : bond 0.04022 / 2.58 ( 896) hydrogen bonds : angle 4.76763 / 3.34 ( 2616) Misc. bond : bond 0.00491 / 0.26 ( 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 311 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 251 time to evaluate : 0.682 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 79 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8078 (mm-30) REVERT: A 181 ASP cc_start: 0.9129 (m-30) cc_final: 0.8920 (m-30) REVERT: A 184 ARG cc_start: 0.9163 (tpp-160) cc_final: 0.8878 (tpp-160) REVERT: A 227 MET cc_start: 0.9624 (mtp) cc_final: 0.9411 (mtp) REVERT: A 274 ARG cc_start: 0.8589 (ttt90) cc_final: 0.8215 (ttt90) REVERT: A 276 LYS cc_start: 0.9129 (mtpp) cc_final: 0.8744 (mmpt) REVERT: A 316 GLU cc_start: 0.8580 (tp30) cc_final: 0.8319 (tp30) REVERT: A 444 ASP cc_start: 0.8718 (t70) cc_final: 0.8180 (p0) REVERT: A 604 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8312 (mmt-90) REVERT: B 15 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8497 (mp0) REVERT: B 52 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.9059 (tptm) REVERT: B 56 ASP cc_start: 0.9148 (m-30) cc_final: 0.8792 (m-30) REVERT: B 79 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8148 (mm-30) REVERT: B 274 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8286 (ptm160) REVERT: B 341 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8988 (mmmm) REVERT: B 402 GLU cc_start: 0.8973 (tp30) cc_final: 0.8653 (mp0) REVERT: B 603 GLU cc_start: 0.8487 (tm-30) cc_final: 0.7928 (tm-30) REVERT: B 604 ARG cc_start: 0.9218 (OUTLIER) cc_final: 0.8968 (mmp80) REVERT: B 610 LYS cc_start: 0.9042 (mtpp) cc_final: 0.8529 (mtpp) REVERT: B 659 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8215 (mtpp) REVERT: C 56 MET cc_start: -0.0573 (mmp) cc_final: -0.1114 (tpt) REVERT: D 269 MET cc_start: 0.5842 (OUTLIER) cc_final: 0.5574 (mpm) outliers start: 60 outliers final: 24 residues processed: 288 average time/residue: 0.6933 time to fit residues: 218.8747 Evaluate side-chains 264 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain 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 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 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 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 Chi-restraints excluded: chain D residue 319 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 66 optimal weight: 2.9990 chunk 8 optimal weight: 0.0070 chunk 33 optimal weight: 0.9980 chunk 191 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 164 optimal weight: 9.9990 chunk 189 optimal weight: 50.0000 chunk 31 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 668 ASN B 232 ASN C 201 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.184009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.095723 restraints weight = 20967.483| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.34 r_work: 0.2820 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16299 Z= 0.184 Angle : 0.547 11.041 22004 Z= 0.290 Chirality : 0.041 0.167 2348 Planarity : 0.003 0.045 2812 Dihedral : 6.907 60.339 2265 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.63 % Allowed : 18.49 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.19), residues: 1928 helix: 1.66 (0.15), residues: 1134 sheet: -0.26 (0.41), residues: 132 loop : 0.58 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 446 TYR 0.014 0.001 TYR C 46 PHE 0.026 0.001 PHE B 624 TRP 0.008 0.001 TRP B 9 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (16298) covalent geometry : angle 0.54686 / 0.29 (22004) hydrogen bonds : bond 0.03717 / 2.37 ( 896) hydrogen bonds : angle 4.65276 / 3.26 ( 2616) Misc. bond : bond 0.00643 / 0.34 ( 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 308 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 263 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8091 (mm-30) REVERT: A 112 LYS cc_start: 0.9339 (mtpp) cc_final: 0.8976 (ptpp) REVERT: A 184 ARG cc_start: 0.9117 (tpp-160) cc_final: 0.8763 (tpp-160) REVERT: A 274 ARG cc_start: 0.8643 (ttt90) cc_final: 0.8366 (ttt90) REVERT: A 276 LYS cc_start: 0.9086 (mtpp) cc_final: 0.8880 (mmpt) REVERT: A 316 GLU cc_start: 0.8570 (tp30) cc_final: 0.8315 (tp30) REVERT: A 444 ASP cc_start: 0.8650 (t70) cc_final: 0.8091 (p0) REVERT: A 589 SER cc_start: 0.9622 (OUTLIER) cc_final: 0.9333 (t) REVERT: A 602 GLU cc_start: 0.8943 (tt0) cc_final: 0.8155 (tt0) REVERT: A 604 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8550 (mmt90) REVERT: B 52 LYS cc_start: 0.9402 (OUTLIER) cc_final: 0.9091 (tptm) REVERT: B 56 ASP cc_start: 0.9060 (m-30) cc_final: 0.8750 (m-30) REVERT: B 79 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8076 (mm-30) REVERT: B 120 ASP cc_start: 0.9000 (m-30) cc_final: 0.8738 (m-30) REVERT: B 184 ARG cc_start: 0.9195 (tpp-160) cc_final: 0.8888 (tpm170) REVERT: B 274 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7274 (ptp90) REVERT: B 335 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8237 (mt-10) REVERT: B 341 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8965 (mmmm) REVERT: B 343 LEU cc_start: 0.9317 (mt) cc_final: 0.9066 (mt) REVERT: B 603 GLU cc_start: 0.8446 (tm-30) cc_final: 0.7898 (tm-30) REVERT: B 610 LYS cc_start: 0.9087 (mtpp) cc_final: 0.8572 (mtpp) REVERT: B 659 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8222 (mtpp) REVERT: B 686 ARG cc_start: 0.8291 (mtp85) cc_final: 0.8021 (mtp85) REVERT: C 287 LEU cc_start: 0.0294 (OUTLIER) cc_final: 0.0092 (pp) REVERT: D 269 MET cc_start: 0.6133 (OUTLIER) cc_final: 0.5902 (mpm) outliers start: 45 outliers final: 22 residues processed: 288 average time/residue: 0.7326 time to fit residues: 230.3375 Evaluate side-chains 276 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 246 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR 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 246 SER Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 274 ARG 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 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 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 Chi-restraints excluded: chain D residue 319 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 92 optimal weight: 3.9990 chunk 14 optimal weight: 0.2980 chunk 23 optimal weight: 0.0770 chunk 4 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 668 ASN B 62 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.185261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.097907 restraints weight = 20748.531| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.33 r_work: 0.2882 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16299 Z= 0.125 Angle : 0.529 12.799 22004 Z= 0.280 Chirality : 0.039 0.165 2348 Planarity : 0.003 0.055 2812 Dihedral : 6.622 59.161 2265 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.28 % Allowed : 19.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.19), residues: 1928 helix: 1.74 (0.15), residues: 1132 sheet: -0.49 (0.39), residues: 144 loop : 0.60 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 446 TYR 0.039 0.001 TYR D 105 PHE 0.015 0.001 PHE A 492 TRP 0.008 0.001 TRP A 9 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (16298) covalent geometry : angle 0.52900 / 0.28 (22004) hydrogen bonds : bond 0.03480 / 2.21 ( 896) hydrogen bonds : angle 4.51619 / 3.16 ( 2616) Misc. bond : bond 0.00018 / 0.01 ( 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 308 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 269 time to evaluate : 0.509 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 79 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8198 (mm-30) REVERT: A 112 LYS cc_start: 0.9259 (mtpp) cc_final: 0.8944 (ptpp) REVERT: A 184 ARG cc_start: 0.9156 (tpp-160) cc_final: 0.8851 (tpp-160) REVERT: A 274 ARG cc_start: 0.8692 (ttt90) cc_final: 0.8249 (ttm170) REVERT: A 276 LYS cc_start: 0.9071 (mtpp) cc_final: 0.8703 (mmtt) REVERT: A 296 LYS cc_start: 0.8812 (mttt) cc_final: 0.8200 (mmmt) REVERT: A 316 GLU cc_start: 0.8580 (tp30) cc_final: 0.8350 (tp30) REVERT: A 402 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8447 (mt-10) REVERT: A 444 ASP cc_start: 0.8657 (t70) cc_final: 0.8080 (p0) REVERT: A 589 SER cc_start: 0.9641 (t) cc_final: 0.9350 (t) REVERT: A 599 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8888 (mt-10) REVERT: A 602 GLU cc_start: 0.8812 (tt0) cc_final: 0.7924 (tt0) REVERT: A 604 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8532 (mmt90) REVERT: B 15 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8516 (mm-30) REVERT: B 52 LYS cc_start: 0.9432 (OUTLIER) cc_final: 0.9114 (tptm) REVERT: B 56 ASP cc_start: 0.9004 (m-30) cc_final: 0.8715 (m-30) REVERT: B 79 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8050 (mm-30) REVERT: B 112 LYS cc_start: 0.9273 (mtpp) cc_final: 0.9004 (mtpm) REVERT: B 120 ASP cc_start: 0.8937 (m-30) cc_final: 0.8707 (m-30) REVERT: B 170 CYS cc_start: 0.8577 (p) cc_final: 0.8285 (m) REVERT: B 274 ARG cc_start: 0.8411 (ptm160) cc_final: 0.7305 (ptp90) REVERT: B 296 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8671 (ptpp) REVERT: B 335 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8371 (mt-10) REVERT: B 341 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8957 (mmmm) REVERT: B 343 LEU cc_start: 0.9348 (mt) cc_final: 0.9080 (mt) REVERT: B 362 ASP cc_start: 0.8611 (m-30) cc_final: 0.8235 (m-30) REVERT: B 396 ASP cc_start: 0.8876 (m-30) cc_final: 0.8585 (m-30) REVERT: B 402 GLU cc_start: 0.9008 (tp30) cc_final: 0.8785 (mp0) REVERT: B 603 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7955 (tm-30) REVERT: B 610 LYS cc_start: 0.9051 (mtpp) cc_final: 0.8594 (mtpp) REVERT: B 659 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8286 (mtpp) REVERT: C 56 MET cc_start: -0.0772 (mmp) cc_final: -0.1399 (tpt) REVERT: C 150 GLU cc_start: 0.6095 (pt0) cc_final: 0.5837 (pm20) REVERT: D 46 TYR cc_start: 0.8506 (m-10) cc_final: 0.8214 (p90) REVERT: D 269 MET cc_start: 0.6096 (OUTLIER) cc_final: 0.5861 (mpm) outliers start: 39 outliers final: 18 residues processed: 291 average time/residue: 0.6628 time to fit residues: 211.5438 Evaluate side-chains 275 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 250 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 584 ILE Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 667 LEU 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 658 LEU Chi-restraints excluded: chain B residue 659 LYS Chi-restraints excluded: chain B residue 667 LEU Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 147 LYS 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 2 optimal weight: 2.9990 chunk 165 optimal weight: 30.0000 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 23 optimal weight: 0.0870 chunk 100 optimal weight: 0.7980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 668 ASN B 131 ASN B 232 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.186234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.098563 restraints weight = 20762.481| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.33 r_work: 0.2869 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16299 Z= 0.149 Angle : 0.555 13.334 22004 Z= 0.292 Chirality : 0.040 0.164 2348 Planarity : 0.003 0.055 2812 Dihedral : 6.525 60.169 2264 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.10 % Allowed : 20.83 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.19), residues: 1928 helix: 1.75 (0.15), residues: 1134 sheet: -0.50 (0.40), residues: 148 loop : 0.58 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 446 TYR 0.026 0.001 TYR D 105 PHE 0.019 0.001 PHE A 492 TRP 0.008 0.001 TRP A 9 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (16298) covalent geometry : angle 0.55538 / 0.29 (22004) hydrogen bonds : bond 0.03480 / 2.22 ( 896) hydrogen bonds : angle 4.51400 / 3.16 ( 2616) Misc. bond : bond 0.00153 / 0.08 ( 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 294 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 258 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.9232 (ttmm) cc_final: 0.8830 (tptt) REVERT: A 66 GLU cc_start: 0.8599 (tp30) cc_final: 0.8394 (tp30) REVERT: A 79 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8186 (mm-30) REVERT: A 104 TYR cc_start: 0.9408 (m-80) cc_final: 0.9175 (m-80) REVERT: A 112 LYS cc_start: 0.9271 (mtpp) cc_final: 0.9045 (ptpp) REVERT: A 184 ARG cc_start: 0.9089 (tpp-160) cc_final: 0.8772 (tpp-160) REVERT: A 194 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8786 (tttm) REVERT: A 274 ARG cc_start: 0.8732 (ttt90) cc_final: 0.8423 (ttm-80) REVERT: A 276 LYS cc_start: 0.9090 (mtpp) cc_final: 0.8711 (mmpt) REVERT: A 316 GLU cc_start: 0.8572 (tp30) cc_final: 0.8357 (tp30) REVERT: A 402 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8405 (mt-10) REVERT: A 444 ASP cc_start: 0.8695 (t70) cc_final: 0.8259 (p0) REVERT: A 452 ARG cc_start: 0.8962 (ttp80) cc_final: 0.8561 (ttm-80) REVERT: A 589 SER cc_start: 0.9639 (t) cc_final: 0.9374 (t) REVERT: A 599 GLU cc_start: 0.9131 (OUTLIER) cc_final: 0.8924 (mt-10) REVERT: A 602 GLU cc_start: 0.8834 (tt0) cc_final: 0.7973 (tt0) REVERT: A 604 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8499 (mmt90) REVERT: B 52 LYS cc_start: 0.9436 (OUTLIER) cc_final: 0.9127 (tptm) REVERT: B 56 ASP cc_start: 0.9024 (m-30) cc_final: 0.8730 (m-30) REVERT: B 79 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8070 (mm-30) REVERT: B 112 LYS cc_start: 0.9281 (mtpp) cc_final: 0.8986 (mtpm) REVERT: B 120 ASP cc_start: 0.8960 (m-30) cc_final: 0.8730 (m-30) REVERT: B 170 CYS cc_start: 0.8567 (p) cc_final: 0.8262 (m) REVERT: B 274 ARG cc_start: 0.8375 (ptm160) cc_final: 0.7303 (ptp90) REVERT: B 296 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8633 (ptpp) REVERT: B 335 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8241 (mt-10) REVERT: B 341 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8949 (mmmm) REVERT: B 343 LEU cc_start: 0.9350 (mt) cc_final: 0.9073 (mt) REVERT: B 362 ASP cc_start: 0.8607 (m-30) cc_final: 0.8246 (m-30) REVERT: B 396 ASP cc_start: 0.8775 (m-30) cc_final: 0.8450 (m-30) REVERT: B 402 GLU cc_start: 0.9007 (tp30) cc_final: 0.8732 (mp0) REVERT: B 526 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8455 (mp0) REVERT: B 603 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7996 (tm-30) REVERT: B 610 LYS cc_start: 0.9068 (mtpp) cc_final: 0.8568 (mtpp) REVERT: B 659 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8309 (mtpp) REVERT: C 56 MET cc_start: -0.0330 (mmp) cc_final: -0.0891 (tpt) REVERT: D 46 TYR cc_start: 0.8532 (m-10) cc_final: 0.8232 (p90) REVERT: D 105 TYR cc_start: 0.2425 (OUTLIER) cc_final: 0.1532 (p90) REVERT: D 269 MET cc_start: 0.6152 (OUTLIER) cc_final: 0.5823 (mmp) outliers start: 36 outliers final: 18 residues processed: 277 average time/residue: 0.6397 time to fit residues: 194.8204 Evaluate side-chains 274 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 247 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 348 MET Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 667 LEU 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 460 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 658 LEU 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 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 138 optimal weight: 40.0000 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 184 optimal weight: 9.9990 chunk 167 optimal weight: 50.0000 chunk 154 optimal weight: 40.0000 chunk 174 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 chunk 122 optimal weight: 0.0470 overall best weight: 1.0880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4117 r_free = 0.4117 target = 0.185453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.098083 restraints weight = 20930.655| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.37 r_work: 0.2852 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16299 Z= 0.165 Angle : 0.568 15.881 22004 Z= 0.297 Chirality : 0.040 0.231 2348 Planarity : 0.003 0.057 2812 Dihedral : 6.533 61.067 2264 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.10 % Allowed : 21.00 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.19), residues: 1928 helix: 1.73 (0.15), residues: 1134 sheet: -0.57 (0.39), residues: 144 loop : 0.57 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 446 TYR 0.024 0.001 TYR D 105 PHE 0.019 0.001 PHE A 492 TRP 0.008 0.001 TRP A 9 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (16298) covalent geometry : angle 0.56834 / 0.30 (22004) hydrogen bonds : bond 0.03545 / 2.27 ( 896) hydrogen bonds : angle 4.52635 / 3.17 ( 2616) Misc. bond : bond 0.00544 / 0.29 ( 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 286 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 250 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.9247 (ttmm) cc_final: 0.8800 (tptt) REVERT: A 66 GLU cc_start: 0.8636 (tp30) cc_final: 0.8417 (tp30) REVERT: A 79 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8148 (mm-30) REVERT: A 112 LYS cc_start: 0.9266 (mtpp) cc_final: 0.8999 (ptpp) REVERT: A 194 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8768 (tttm) REVERT: A 274 ARG cc_start: 0.8798 (ttt90) cc_final: 0.8507 (ttm-80) REVERT: A 276 LYS cc_start: 0.9093 (mtpp) cc_final: 0.8721 (mmpt) REVERT: A 316 GLU cc_start: 0.8534 (tp30) cc_final: 0.8310 (tp30) REVERT: A 402 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8386 (mt-10) REVERT: A 444 ASP cc_start: 0.8722 (t70) cc_final: 0.8247 (p0) REVERT: A 452 ARG cc_start: 0.9016 (ttp80) cc_final: 0.8607 (ttm-80) REVERT: A 589 SER cc_start: 0.9635 (t) cc_final: 0.9359 (t) REVERT: A 602 GLU cc_start: 0.8834 (tt0) cc_final: 0.7990 (tt0) REVERT: A 604 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8494 (mmt90) REVERT: B 52 LYS cc_start: 0.9437 (OUTLIER) cc_final: 0.9126 (tptm) REVERT: B 56 ASP cc_start: 0.9042 (m-30) cc_final: 0.8736 (m-30) REVERT: B 79 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8084 (mm-30) REVERT: B 112 LYS cc_start: 0.9273 (mtpp) cc_final: 0.8959 (mtpm) REVERT: B 120 ASP cc_start: 0.9020 (m-30) cc_final: 0.8771 (m-30) REVERT: B 170 CYS cc_start: 0.8520 (p) cc_final: 0.8314 (m) REVERT: B 246 SER cc_start: 0.8359 (OUTLIER) cc_final: 0.7815 (p) REVERT: B 274 ARG cc_start: 0.8359 (ptm160) cc_final: 0.7332 (ptp90) REVERT: B 335 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8210 (mt-10) REVERT: B 341 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8951 (mmmm) REVERT: B 343 LEU cc_start: 0.9375 (mt) cc_final: 0.9099 (mt) REVERT: B 362 ASP cc_start: 0.8646 (m-30) cc_final: 0.8291 (m-30) REVERT: B 396 ASP cc_start: 0.8765 (m-30) cc_final: 0.8421 (m-30) REVERT: B 402 GLU cc_start: 0.9033 (tp30) cc_final: 0.8712 (mp0) REVERT: B 610 LYS cc_start: 0.9078 (mtpp) cc_final: 0.8661 (mtpp) REVERT: B 659 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8341 (mtpp) REVERT: C 56 MET cc_start: -0.0291 (mmp) cc_final: -0.0824 (tpt) REVERT: C 319 ASP cc_start: 0.9214 (m-30) cc_final: 0.8540 (m-30) REVERT: D 46 TYR cc_start: 0.8546 (m-10) cc_final: 0.8274 (p90) REVERT: D 105 TYR cc_start: 0.2237 (OUTLIER) cc_final: 0.1333 (p90) REVERT: D 269 MET cc_start: 0.6280 (OUTLIER) cc_final: 0.5989 (mmp) outliers start: 36 outliers final: 19 residues processed: 269 average time/residue: 0.7007 time to fit residues: 207.0987 Evaluate side-chains 270 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 243 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 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 604 ARG Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 246 SER 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 658 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 143 optimal weight: 50.0000 chunk 28 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 76 optimal weight: 0.1980 chunk 68 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4120 r_free = 0.4120 target = 0.185814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.099069 restraints weight = 20855.870| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.36 r_work: 0.2867 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- 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: 2 | |-----------------------------------------------------------------------------| |-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: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16299 Z= 0.151 Angle : 0.575 17.666 22004 Z= 0.298 Chirality : 0.040 0.222 2348 Planarity : 0.003 0.062 2812 Dihedral : 6.394 61.175 2264 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.04 % Allowed : 21.47 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.19), residues: 1928 helix: 1.76 (0.15), residues: 1132 sheet: -0.54 (0.39), residues: 144 loop : 0.56 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 446 TYR 0.023 0.001 TYR D 105 PHE 0.019 0.001 PHE A 492 TRP 0.008 0.001 TRP A 9 HIS 0.006 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (16298) covalent geometry : angle 0.57482 / 0.30 (22004) hydrogen bonds : bond 0.03476 / 2.23 ( 896) hydrogen bonds : angle 4.50190 / 3.15 ( 2616) Misc. bond : bond 0.00318 / 0.17 ( 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 293 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 258 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.9238 (ttmm) cc_final: 0.8726 (tptt) REVERT: A 79 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8139 (mm-30) REVERT: A 112 LYS cc_start: 0.9259 (mtpp) cc_final: 0.8979 (ptpp) REVERT: A 184 ARG cc_start: 0.9090 (tpp-160) cc_final: 0.8872 (tpp-160) REVERT: A 194 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8696 (tttm) REVERT: A 274 ARG cc_start: 0.8774 (ttt90) cc_final: 0.8491 (ttm-80) REVERT: A 276 LYS cc_start: 0.9071 (mtpp) cc_final: 0.8676 (mmpt) REVERT: A 296 LYS cc_start: 0.8688 (mttt) cc_final: 0.8037 (mmmt) REVERT: A 316 GLU cc_start: 0.8513 (tp30) cc_final: 0.8267 (tp30) REVERT: A 384 GLU cc_start: 0.9327 (OUTLIER) cc_final: 0.8543 (pp20) REVERT: A 402 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8345 (mt-10) REVERT: A 444 ASP cc_start: 0.8677 (t70) cc_final: 0.8235 (p0) REVERT: A 452 ARG cc_start: 0.8955 (ttp80) cc_final: 0.8549 (ttm-80) REVERT: A 589 SER cc_start: 0.9625 (t) cc_final: 0.9361 (t) REVERT: A 602 GLU cc_start: 0.8837 (tt0) cc_final: 0.7994 (tt0) REVERT: A 604 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8473 (mmt90) REVERT: B 15 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8500 (mm-30) REVERT: B 52 LYS cc_start: 0.9415 (OUTLIER) cc_final: 0.9088 (tptm) REVERT: B 56 ASP cc_start: 0.9045 (m-30) cc_final: 0.8733 (m-30) REVERT: B 79 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8053 (mm-30) REVERT: B 111 LYS cc_start: 0.9093 (mmtm) cc_final: 0.8783 (mmpt) REVERT: B 112 LYS cc_start: 0.9254 (mtpp) cc_final: 0.8932 (mtpm) REVERT: B 120 ASP cc_start: 0.9019 (m-30) cc_final: 0.8750 (m-30) REVERT: B 246 SER cc_start: 0.8346 (OUTLIER) cc_final: 0.7786 (p) REVERT: B 274 ARG cc_start: 0.8328 (ptm160) cc_final: 0.7311 (ptp90) REVERT: B 335 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8241 (mt-10) REVERT: B 341 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8917 (mmmm) REVERT: B 343 LEU cc_start: 0.9322 (mt) cc_final: 0.9071 (mt) REVERT: B 362 ASP cc_start: 0.8615 (m-30) cc_final: 0.8239 (m-30) REVERT: B 396 ASP cc_start: 0.8734 (m-30) cc_final: 0.8392 (m-30) REVERT: B 526 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8366 (mp0) REVERT: B 598 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8757 (mmm) REVERT: B 603 GLU cc_start: 0.8310 (tm-30) cc_final: 0.8013 (tm-30) REVERT: B 604 ARG cc_start: 0.9271 (mmp80) cc_final: 0.8860 (mmp80) REVERT: B 659 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8285 (mtpp) REVERT: C 56 MET cc_start: -0.0303 (mmp) cc_final: -0.0834 (tpt) REVERT: D 46 TYR cc_start: 0.8588 (m-10) cc_final: 0.8340 (p90) REVERT: D 105 TYR cc_start: 0.2155 (OUTLIER) cc_final: 0.1223 (p90) REVERT: D 269 MET cc_start: 0.6277 (OUTLIER) cc_final: 0.6008 (mmp) outliers start: 35 outliers final: 20 residues processed: 277 average time/residue: 0.6454 time to fit residues: 196.1476 Evaluate side-chains 277 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 247 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 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 384 GLU Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 277 THR 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 659 LYS 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 157 MET 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 51 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 191 optimal weight: 0.0050 chunk 49 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 174 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 121 optimal weight: 0.0980 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 GLN A 239 GLN B 232 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.188136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.101798 restraints weight = 20938.932| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.39 r_work: 0.2923 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4100 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= 0.119 Angle : 0.577 18.122 22004 Z= 0.301 Chirality : 0.040 0.250 2348 Planarity : 0.003 0.058 2812 Dihedral : 6.345 61.166 2264 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.40 % Favored : 98.55 % Rotamer: Outliers : 1.58 % Allowed : 22.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.19), residues: 1928 helix: 1.80 (0.16), residues: 1134 sheet: -0.11 (0.41), residues: 128 loop : 0.40 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 446 TYR 0.028 0.001 TYR C 179 PHE 0.017 0.001 PHE A 492 TRP 0.008 0.001 TRP A 9 HIS 0.004 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (16298) covalent geometry : angle 0.57673 / 0.30 (22004) hydrogen bonds : bond 0.03276 / 2.10 ( 896) hydrogen bonds : angle 4.46016 / 3.12 ( 2616) Misc. bond : bond 0.00213 / 0.11 ( 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 295 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 268 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.9221 (ttmm) cc_final: 0.8701 (tptt) REVERT: A 104 TYR cc_start: 0.9373 (m-80) cc_final: 0.9165 (m-80) REVERT: A 112 LYS cc_start: 0.9205 (mtpp) cc_final: 0.8925 (ptpp) REVERT: A 184 ARG cc_start: 0.9014 (tpp-160) cc_final: 0.8794 (tpp-160) REVERT: A 274 ARG cc_start: 0.8797 (ttt90) cc_final: 0.8350 (ttm170) REVERT: A 276 LYS cc_start: 0.9060 (mtpp) cc_final: 0.8662 (mmtt) REVERT: A 296 LYS cc_start: 0.8660 (mttt) cc_final: 0.8023 (mmmt) REVERT: A 316 GLU cc_start: 0.8453 (tp30) cc_final: 0.8208 (tp30) REVERT: A 384 GLU cc_start: 0.9288 (OUTLIER) cc_final: 0.8436 (pm20) REVERT: A 402 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8369 (mt-10) REVERT: A 411 LEU cc_start: 0.9068 (mt) cc_final: 0.8836 (mt) REVERT: A 444 ASP cc_start: 0.8778 (t70) cc_final: 0.8188 (p0) REVERT: A 452 ARG cc_start: 0.8957 (ttp80) cc_final: 0.8571 (ttm-80) REVERT: A 602 GLU cc_start: 0.8793 (tt0) cc_final: 0.8212 (tt0) REVERT: A 604 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8325 (mmt-90) REVERT: B 15 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8457 (mm-30) REVERT: B 52 LYS cc_start: 0.9399 (OUTLIER) cc_final: 0.9076 (tptm) REVERT: B 56 ASP cc_start: 0.9035 (m-30) cc_final: 0.8735 (m-30) REVERT: B 79 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8038 (mm-30) REVERT: B 112 LYS cc_start: 0.9212 (mtpp) cc_final: 0.8901 (mtpm) REVERT: B 120 ASP cc_start: 0.8954 (m-30) cc_final: 0.8667 (m-30) REVERT: B 274 ARG cc_start: 0.8303 (ptm160) cc_final: 0.7332 (ptp90) REVERT: B 296 LYS cc_start: 0.9022 (mtpp) cc_final: 0.8642 (ptpp) REVERT: B 335 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8331 (mt-10) REVERT: B 341 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8896 (mmmm) REVERT: B 343 LEU cc_start: 0.9329 (mt) cc_final: 0.9052 (mt) REVERT: B 362 ASP cc_start: 0.8577 (m-30) cc_final: 0.8210 (m-30) REVERT: B 396 ASP cc_start: 0.8590 (m-30) cc_final: 0.8208 (m-30) REVERT: B 402 GLU cc_start: 0.8936 (tp30) cc_final: 0.8687 (mp0) REVERT: B 526 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8349 (mp0) REVERT: B 598 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8783 (mmm) REVERT: B 602 GLU cc_start: 0.8794 (tt0) cc_final: 0.8373 (tt0) REVERT: B 612 TYR cc_start: 0.8989 (m-80) cc_final: 0.8447 (m-80) REVERT: B 686 ARG cc_start: 0.7887 (ptm160) cc_final: 0.7391 (ptm-80) REVERT: C 56 MET cc_start: -0.0321 (mmp) cc_final: -0.0814 (tpt) REVERT: C 185 MET cc_start: 0.1538 (mmp) cc_final: 0.1295 (mmt) REVERT: C 317 ASP cc_start: 0.9130 (m-30) cc_final: 0.8854 (m-30) REVERT: D 46 TYR cc_start: 0.8581 (m-10) cc_final: 0.8336 (p90) REVERT: D 105 TYR cc_start: 0.2193 (OUTLIER) cc_final: 0.1251 (p90) REVERT: D 269 MET cc_start: 0.6378 (OUTLIER) cc_final: 0.6139 (mmp) outliers start: 27 outliers final: 16 residues processed: 283 average time/residue: 0.6775 time to fit residues: 211.0635 Evaluate side-chains 274 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 251 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 267 ILE 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 410 ASN Chi-restraints excluded: chain A residue 604 ARG Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 277 THR 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 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 157 MET 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 97 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 151 optimal weight: 40.0000 chunk 162 optimal weight: 50.0000 chunk 146 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 102 ASN B 252 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 = 0.4111 r_free = 0.4111 target = 0.183529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.097339 restraints weight = 20890.684| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.35 r_work: 0.2844 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4052 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= 0.192 Angle : 0.608 18.081 22004 Z= 0.316 Chirality : 0.042 0.250 2348 Planarity : 0.003 0.057 2812 Dihedral : 6.446 63.056 2264 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.34 % Allowed : 22.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.19), residues: 1928 helix: 1.71 (0.16), residues: 1138 sheet: -0.68 (0.38), residues: 144 loop : 0.59 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 446 TYR 0.022 0.001 TYR D 105 PHE 0.019 0.001 PHE A 492 TRP 0.008 0.001 TRP A 9 HIS 0.005 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (16298) covalent geometry : angle 0.60805 / 0.32 (22004) hydrogen bonds : bond 0.03508 / 2.27 ( 896) hydrogen bonds : angle 4.52307 / 3.17 ( 2616) Misc. bond : bond 0.00355 / 0.19 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9469.91 seconds wall clock time: 161 minutes 40.65 seconds (9700.65 seconds total)