Starting phenix.real_space_refine on Sat Jun 14 05:27:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bx9_45000/06_2025/9bx9_45000_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bx9_45000/06_2025/9bx9_45000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bx9_45000/06_2025/9bx9_45000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bx9_45000/06_2025/9bx9_45000.map" model { file = "/net/cci-nas-00/data/ceres_data/9bx9_45000/06_2025/9bx9_45000_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bx9_45000/06_2025/9bx9_45000_neut.cif" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 12 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10190 2.51 5 N 2598 2.21 5 O 3066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15954 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 9.06, per 1000 atoms: 0.57 Number of scatterers: 15954 At special positions: 0 Unit cell: (93.002, 127.75, 132.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 12 15.00 Mg 2 11.99 O 3066 8.00 N 2598 7.00 C 10190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.39 Conformation dependent library (CDL) restraints added in 2.1 seconds 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3688 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 10 sheets defined 64.3% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 27 through 41 removed outlier: 3.554A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 70 removed outlier: 4.076A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 4.057A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.706A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.873A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.793A pdb=" N GLN A 242 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.638A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 318 through 329 removed outlier: 6.055A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.521A pdb=" N PHE A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 589 removed outlier: 4.274A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 677 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 27 through 41 removed outlier: 3.548A pdb=" N GLU B 31 " --> pdb=" O ASP B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.950A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.960A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.722A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 222 through 237 removed outlier: 3.779A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.573A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 318 through 329 removed outlier: 5.841A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 367 removed outlier: 4.174A pdb=" N VAL B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 424 through 443 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 474 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.566A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 589 removed outlier: 4.402A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 677 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.567A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.874A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.889A pdb=" N GLY A 462 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASN A 410 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLY A 464 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 3.736A pdb=" N CYS A 409 " --> pdb=" O CYS A 170 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N CYS A 170 " --> pdb=" O CYS A 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA5, first strand: chain 'A' and resid 655 through 658 Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 removed outlier: 5.890A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 removed outlier: 6.457A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AA9, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB1, first strand: chain 'B' and resid 655 through 659 898 hydrogen bonds defined for protein. 2616 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.92 Time building geometry restraints manager: 5.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4959 1.34 - 1.46: 2935 1.46 - 1.58: 8229 1.58 - 1.70: 19 1.70 - 1.82: 156 Bond restraints: 16298 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.061 1.25e-02 6.40e+03 2.36e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.038 1.20e-02 6.94e+03 1.02e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.574 -0.032 1.08e-02 8.57e+03 8.54e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.569 -0.032 1.17e-02 7.31e+03 7.32e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.573 -0.033 1.25e-02 6.40e+03 6.88e+00 ... (remaining 16293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21498 2.09 - 4.18: 469 4.18 - 6.27: 33 6.27 - 8.36: 2 8.36 - 10.45: 2 Bond angle restraints: 22004 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.58 -6.04 1.36e+00 5.41e-01 1.97e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.14 -4.43 1.15e+00 7.56e-01 1.48e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.83 -4.33 1.23e+00 6.61e-01 1.24e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.69 -3.98 1.15e+00 7.56e-01 1.20e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.52 3.67 1.06e+00 8.90e-01 1.20e+01 ... (remaining 21999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.31: 9427 34.31 - 68.62: 332 68.62 - 102.93: 47 102.93 - 137.23: 0 137.23 - 171.54: 2 Dihedral angle restraints: 9808 sinusoidal: 4062 harmonic: 5746 Sorted by residual: dihedral pdb=" C2 TTP A 801 " pdb=" C1' TTP A 801 " pdb=" N1 TTP A 801 " pdb=" O4' TTP A 801 " ideal model delta sinusoidal sigma weight residual 301.68 130.14 171.54 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual 301.68 135.73 165.95 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C VAL C 125 " pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual -122.00 -134.35 12.35 0 2.50e+00 1.60e-01 2.44e+01 ... (remaining 9805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2130 0.094 - 0.188: 179 0.188 - 0.282: 34 0.282 - 0.376: 3 0.376 - 0.470: 2 Chirality restraints: 2348 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.52e+00 chirality pdb=" CA TYR C 169 " pdb=" N TYR C 169 " pdb=" C TYR C 169 " pdb=" CB TYR C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 2345 not shown) Planarity restraints: 2812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 6 " 0.036 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO B 7 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 7 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 7 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO D 75 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.018 2.00e-02 2.50e+03 1.13e-02 2.22e+00 pdb=" CG PHE D 92 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.010 2.00e-02 2.50e+03 ... (remaining 2809 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 131 2.51 - 3.11: 11864 3.11 - 3.70: 26403 3.70 - 4.30: 41201 4.30 - 4.90: 64928 Nonbonded interactions: 144527 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.911 2.320 nonbonded pdb=" O1B TTP A 801 " pdb="MG MG A 802 " model vdw 1.918 2.170 nonbonded pdb=" O2A TTP B 801 " pdb="MG MG B 802 " model vdw 1.928 2.170 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 ... (remaining 144522 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 37.070 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.833 16299 Z= 0.724 Angle : 0.707 10.446 22004 Z= 0.453 Chirality : 0.059 0.470 2348 Planarity : 0.003 0.055 2812 Dihedral : 17.179 171.542 6120 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.40 % Allowed : 14.06 % Favored : 84.54 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.18), residues: 1928 helix: 1.05 (0.15), residues: 1133 sheet: 0.46 (0.39), residues: 146 loop : 0.45 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 PHE 0.021 0.002 PHE C 168 TYR 0.021 0.002 TYR D 179 ARG 0.004 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.16168 ( 896) hydrogen bonds : angle 6.35121 ( 2616) covalent geometry : bond 0.00542 (16298) covalent geometry : angle 0.70709 (22004) Misc. bond : bond 0.83310 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 694 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.7273 (p0) cc_final: 0.6878 (p0) REVERT: A 30 LYS cc_start: 0.8021 (tptt) cc_final: 0.7772 (tppt) REVERT: A 119 GLU cc_start: 0.7911 (mp0) cc_final: 0.7525 (mp0) REVERT: A 157 LEU cc_start: 0.9234 (tp) cc_final: 0.8952 (tt) REVERT: A 177 ASP cc_start: 0.8784 (t0) cc_final: 0.8271 (t0) REVERT: A 179 LEU cc_start: 0.9223 (tp) cc_final: 0.8935 (tp) REVERT: A 188 ILE cc_start: 0.9187 (mt) cc_final: 0.8973 (mt) REVERT: A 232 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8381 (m-40) REVERT: A 240 MET cc_start: 0.5912 (tpt) cc_final: 0.5632 (tpt) REVERT: A 262 LEU cc_start: 0.8711 (mt) cc_final: 0.8291 (mt) REVERT: A 362 ASP cc_start: 0.6953 (m-30) cc_final: 0.6566 (m-30) REVERT: A 379 SER cc_start: 0.9068 (t) cc_final: 0.8362 (t) REVERT: A 447 ASN cc_start: 0.8098 (m-40) cc_final: 0.7888 (m-40) REVERT: A 458 MET cc_start: 0.8982 (mmm) cc_final: 0.8567 (mmt) REVERT: A 494 MET cc_start: 0.7915 (mtp) cc_final: 0.7677 (mtp) REVERT: A 584 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8551 (tp) REVERT: A 591 THR cc_start: 0.9175 (p) cc_final: 0.8844 (m) REVERT: A 597 ILE cc_start: 0.9307 (pt) cc_final: 0.9059 (pt) REVERT: A 598 MET cc_start: 0.7733 (mtm) cc_final: 0.7476 (mtm) REVERT: A 654 PHE cc_start: 0.8807 (t80) cc_final: 0.8466 (t80) REVERT: B 104 TYR cc_start: 0.7947 (m-80) cc_final: 0.7481 (m-80) REVERT: B 172 LEU cc_start: 0.9169 (mp) cc_final: 0.8677 (mp) REVERT: B 177 ASP cc_start: 0.8208 (t0) cc_final: 0.7740 (t0) REVERT: B 194 LYS cc_start: 0.8863 (tttt) cc_final: 0.8662 (ttpt) REVERT: B 286 ASP cc_start: 0.6882 (m-30) cc_final: 0.6681 (m-30) REVERT: B 362 ASP cc_start: 0.7489 (m-30) cc_final: 0.6733 (m-30) REVERT: B 425 ILE cc_start: 0.8789 (mt) cc_final: 0.8578 (mt) REVERT: B 494 MET cc_start: 0.7901 (mtp) cc_final: 0.7694 (mtm) REVERT: B 496 ASN cc_start: 0.9058 (t0) cc_final: 0.8827 (t0) REVERT: B 550 MET cc_start: 0.8658 (ttm) cc_final: 0.8130 (mtm) REVERT: B 612 TYR cc_start: 0.7092 (m-80) cc_final: 0.6820 (m-80) REVERT: C 137 MET cc_start: -0.1844 (mtp) cc_final: -0.3145 (mmm) REVERT: C 287 LEU cc_start: -0.0458 (OUTLIER) cc_final: -0.1103 (tp) REVERT: D 137 MET cc_start: -0.1438 (mtp) cc_final: -0.3363 (mmt) REVERT: D 282 ILE cc_start: -0.0509 (OUTLIER) cc_final: -0.1124 (mt) outliers start: 24 outliers final: 5 residues processed: 712 average time/residue: 0.2866 time to fit residues: 293.4136 Evaluate side-chains 456 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 447 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 112 optimal weight: 0.0370 chunk 174 optimal weight: 3.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 14 ASN A 320 ASN A 370 ASN A 645 GLN A 668 ASN B 14 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 418 ASN B 645 GLN B 646 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 28 GLN C 91 ASN C 216 GLN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 146 GLN D 233 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.175196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.108443 restraints weight = 28638.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.112271 restraints weight = 13283.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114678 restraints weight = 8085.666| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16299 Z= 0.146 Angle : 0.613 10.439 22004 Z= 0.330 Chirality : 0.042 0.191 2348 Planarity : 0.004 0.053 2812 Dihedral : 9.113 162.477 2232 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.28 % Allowed : 15.81 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.18), residues: 1928 helix: 1.66 (0.15), residues: 1127 sheet: 0.98 (0.40), residues: 114 loop : 0.57 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 124 HIS 0.004 0.001 HIS A 568 PHE 0.031 0.002 PHE A 261 TYR 0.020 0.001 TYR C 22 ARG 0.008 0.001 ARG B 293 Details of bonding type rmsd hydrogen bonds : bond 0.04613 ( 896) hydrogen bonds : angle 5.07494 ( 2616) covalent geometry : bond 0.00318 (16298) covalent geometry : angle 0.61333 (22004) Misc. bond : bond 0.00028 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 503 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8195 (p0) cc_final: 0.7945 (p0) REVERT: A 119 GLU cc_start: 0.8765 (mp0) cc_final: 0.8431 (mp0) REVERT: A 147 GLN cc_start: 0.9268 (mt0) cc_final: 0.9061 (mt0) REVERT: A 177 ASP cc_start: 0.8871 (t0) cc_final: 0.8509 (t0) REVERT: A 179 LEU cc_start: 0.9516 (tp) cc_final: 0.9307 (tp) REVERT: A 232 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8151 (m-40) REVERT: A 250 TYR cc_start: 0.8751 (m-80) cc_final: 0.8295 (m-80) REVERT: A 334 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8572 (ptpt) REVERT: A 362 ASP cc_start: 0.7773 (m-30) cc_final: 0.7493 (m-30) REVERT: A 379 SER cc_start: 0.9172 (t) cc_final: 0.8586 (t) REVERT: A 640 MET cc_start: 0.9199 (tpp) cc_final: 0.8931 (tpp) REVERT: A 654 PHE cc_start: 0.9116 (t80) cc_final: 0.8741 (t80) REVERT: A 657 PHE cc_start: 0.9051 (m-80) cc_final: 0.8678 (m-80) REVERT: A 686 ARG cc_start: 0.7957 (mmt-90) cc_final: 0.7742 (mtt90) REVERT: B 109 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.8357 (m110) REVERT: B 119 GLU cc_start: 0.8678 (mp0) cc_final: 0.8420 (mp0) REVERT: B 135 GLU cc_start: 0.8420 (mp0) cc_final: 0.8115 (mp0) REVERT: B 158 ASN cc_start: 0.9006 (m-40) cc_final: 0.8775 (m110) REVERT: B 177 ASP cc_start: 0.8257 (t0) cc_final: 0.7820 (t0) REVERT: B 181 ASP cc_start: 0.8666 (m-30) cc_final: 0.8450 (m-30) REVERT: B 286 ASP cc_start: 0.8069 (m-30) cc_final: 0.7414 (m-30) REVERT: B 290 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7639 (tm-30) REVERT: B 334 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8768 (pttm) REVERT: B 362 ASP cc_start: 0.8113 (m-30) cc_final: 0.7256 (m-30) REVERT: B 483 GLU cc_start: 0.8813 (mp0) cc_final: 0.8381 (pm20) REVERT: B 586 TYR cc_start: 0.8554 (m-80) cc_final: 0.8314 (m-80) REVERT: B 604 ARG cc_start: 0.8672 (mmp80) cc_final: 0.8411 (mmp80) REVERT: B 612 TYR cc_start: 0.8048 (m-80) cc_final: 0.7297 (m-80) REVERT: B 640 MET cc_start: 0.9105 (tpp) cc_final: 0.8767 (tpp) REVERT: B 668 ASN cc_start: 0.9221 (m-40) cc_final: 0.8931 (m-40) REVERT: C 258 LYS cc_start: 0.7403 (pttm) cc_final: 0.6153 (tptt) REVERT: C 283 ASN cc_start: 0.4491 (t0) cc_final: 0.4102 (t0) REVERT: C 287 LEU cc_start: 0.0249 (OUTLIER) cc_final: -0.0364 (tp) REVERT: D 74 MET cc_start: 0.3579 (tpp) cc_final: 0.3240 (tpp) REVERT: D 76 ILE cc_start: 0.6283 (OUTLIER) cc_final: 0.5816 (tt) REVERT: D 110 MET cc_start: 0.5119 (mtt) cc_final: 0.4684 (tmm) REVERT: D 185 MET cc_start: 0.6258 (mmm) cc_final: 0.5955 (mmm) outliers start: 39 outliers final: 20 residues processed: 521 average time/residue: 0.2831 time to fit residues: 219.4221 Evaluate side-chains 458 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 432 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 76 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 191 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 136 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 121 optimal weight: 0.5980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 370 ASN B 62 GLN B 150 GLN B 646 GLN C 19 GLN C 84 HIS ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN D 119 ASN D 233 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.167100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.101715 restraints weight = 29366.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.105225 restraints weight = 13867.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.107321 restraints weight = 8467.880| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16299 Z= 0.200 Angle : 0.597 9.251 22004 Z= 0.318 Chirality : 0.042 0.258 2348 Planarity : 0.004 0.048 2812 Dihedral : 8.986 164.357 2222 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.62 % Allowed : 16.69 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.19), residues: 1928 helix: 1.70 (0.15), residues: 1130 sheet: -0.00 (0.39), residues: 144 loop : 0.64 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 124 HIS 0.005 0.001 HIS A 255 PHE 0.020 0.002 PHE A 74 TYR 0.031 0.001 TYR D 142 ARG 0.005 0.001 ARG B 164 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 896) hydrogen bonds : angle 4.91901 ( 2616) covalent geometry : bond 0.00446 (16298) covalent geometry : angle 0.59736 (22004) Misc. bond : bond 0.00032 ( 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 514 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 452 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8291 (p0) cc_final: 0.8086 (p0) REVERT: A 30 LYS cc_start: 0.9358 (tppt) cc_final: 0.9021 (tppt) REVERT: A 119 GLU cc_start: 0.8782 (mp0) cc_final: 0.8555 (mp0) REVERT: A 157 LEU cc_start: 0.9368 (tp) cc_final: 0.9158 (tp) REVERT: A 164 ARG cc_start: 0.8296 (ptt90) cc_final: 0.8083 (ptt90) REVERT: A 177 ASP cc_start: 0.8976 (t0) cc_final: 0.8626 (t0) REVERT: A 250 TYR cc_start: 0.8968 (m-80) cc_final: 0.8171 (m-80) REVERT: A 334 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8684 (ptpt) REVERT: A 362 ASP cc_start: 0.7993 (m-30) cc_final: 0.7579 (m-30) REVERT: A 379 SER cc_start: 0.9044 (t) cc_final: 0.8358 (t) REVERT: A 493 MET cc_start: 0.9283 (tmm) cc_final: 0.9033 (tmm) REVERT: A 604 ARG cc_start: 0.8549 (mmp80) cc_final: 0.8341 (mmp80) REVERT: A 686 ARG cc_start: 0.8093 (mmt-90) cc_final: 0.7800 (mtt90) REVERT: B 135 GLU cc_start: 0.8389 (mp0) cc_final: 0.8070 (mp0) REVERT: B 147 GLN cc_start: 0.9174 (mt0) cc_final: 0.8731 (mm-40) REVERT: B 276 LYS cc_start: 0.8844 (mtmm) cc_final: 0.8577 (mmtm) REVERT: B 286 ASP cc_start: 0.8117 (m-30) cc_final: 0.7482 (m-30) REVERT: B 334 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8977 (pttm) REVERT: B 361 GLN cc_start: 0.8851 (tt0) cc_final: 0.8516 (tt0) REVERT: B 362 ASP cc_start: 0.8119 (m-30) cc_final: 0.7295 (m-30) REVERT: B 526 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7509 (tp30) REVERT: B 586 TYR cc_start: 0.8693 (m-80) cc_final: 0.8314 (m-80) REVERT: B 590 SER cc_start: 0.9526 (p) cc_final: 0.9297 (t) REVERT: B 612 TYR cc_start: 0.8437 (m-80) cc_final: 0.8029 (m-80) REVERT: B 640 MET cc_start: 0.9032 (tpp) cc_final: 0.8613 (tpp) REVERT: C 74 MET cc_start: 0.8188 (mmm) cc_final: 0.7862 (mtm) REVERT: C 134 LYS cc_start: 0.2948 (ttpt) cc_final: 0.2563 (ttpt) REVERT: C 137 MET cc_start: -0.4350 (mtp) cc_final: -0.5627 (mmm) REVERT: C 287 LEU cc_start: 0.0289 (OUTLIER) cc_final: -0.0282 (tp) REVERT: D 34 GLU cc_start: 0.7821 (pt0) cc_final: 0.7588 (pp20) REVERT: D 110 MET cc_start: 0.5403 (mtt) cc_final: 0.5057 (tmm) REVERT: D 137 MET cc_start: -0.6283 (ptp) cc_final: -0.6572 (mmt) REVERT: D 185 MET cc_start: 0.6417 (mmm) cc_final: 0.6082 (mmm) outliers start: 62 outliers final: 40 residues processed: 483 average time/residue: 0.2831 time to fit residues: 203.3166 Evaluate side-chains 439 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 396 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 136 optimal weight: 0.0670 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 218 ASN C 24 GLN D 28 GLN D 107 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.169835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.104010 restraints weight = 29463.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.107557 restraints weight = 13718.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.109767 restraints weight = 8345.594| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16299 Z= 0.134 Angle : 0.562 7.010 22004 Z= 0.298 Chirality : 0.041 0.155 2348 Planarity : 0.003 0.055 2812 Dihedral : 8.534 150.392 2219 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.57 % Allowed : 18.61 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.18), residues: 1928 helix: 1.64 (0.15), residues: 1131 sheet: 0.53 (0.41), residues: 118 loop : 0.43 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 124 HIS 0.004 0.001 HIS A 675 PHE 0.014 0.001 PHE A 74 TYR 0.019 0.001 TYR D 142 ARG 0.005 0.000 ARG B 164 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 896) hydrogen bonds : angle 4.80570 ( 2616) covalent geometry : bond 0.00294 (16298) covalent geometry : angle 0.56199 (22004) Misc. bond : bond 0.00011 ( 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 490 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 446 time to evaluate : 1.794 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: 0.9360 (tppt) cc_final: 0.8992 (tppt) REVERT: A 119 GLU cc_start: 0.8830 (mp0) cc_final: 0.8490 (mp0) REVERT: A 177 ASP cc_start: 0.8864 (t0) cc_final: 0.8659 (t0) REVERT: A 178 SER cc_start: 0.9070 (OUTLIER) cc_final: 0.8703 (p) REVERT: A 250 TYR cc_start: 0.8934 (m-80) cc_final: 0.8304 (m-80) REVERT: A 379 SER cc_start: 0.9127 (t) cc_final: 0.8507 (t) REVERT: A 433 THR cc_start: 0.9701 (m) cc_final: 0.9377 (p) REVERT: A 493 MET cc_start: 0.9267 (tmm) cc_final: 0.9006 (tmm) REVERT: B 119 GLU cc_start: 0.8679 (mp0) cc_final: 0.8439 (mp0) REVERT: B 147 GLN cc_start: 0.9170 (mt0) cc_final: 0.8735 (mm-40) REVERT: B 232 ASN cc_start: 0.9031 (t0) cc_final: 0.8679 (m-40) REVERT: B 274 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.7199 (ttm-80) REVERT: B 286 ASP cc_start: 0.8080 (m-30) cc_final: 0.7481 (m-30) REVERT: B 334 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8813 (pttm) REVERT: B 348 MET cc_start: 0.8209 (tmm) cc_final: 0.7967 (tmm) REVERT: B 362 ASP cc_start: 0.8096 (m-30) cc_final: 0.7289 (m-30) REVERT: B 612 TYR cc_start: 0.8351 (m-80) cc_final: 0.8012 (m-80) REVERT: B 640 MET cc_start: 0.9056 (tpp) cc_final: 0.8624 (tpp) REVERT: B 668 ASN cc_start: 0.9109 (m-40) cc_final: 0.8838 (m-40) REVERT: C 74 MET cc_start: 0.8209 (mmm) cc_final: 0.7907 (mtm) REVERT: C 129 LYS cc_start: 0.7704 (tptp) cc_final: 0.6651 (ptmt) REVERT: C 134 LYS cc_start: 0.2982 (ttpt) cc_final: 0.2589 (ttpt) REVERT: C 137 MET cc_start: -0.4433 (mtp) cc_final: -0.5749 (mmm) REVERT: D 110 MET cc_start: 0.5615 (mtt) cc_final: 0.5207 (tmm) REVERT: D 185 MET cc_start: 0.6362 (mmm) cc_final: 0.6023 (mmm) outliers start: 44 outliers final: 32 residues processed: 464 average time/residue: 0.2880 time to fit residues: 198.4945 Evaluate side-chains 438 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 403 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 109 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 188 optimal weight: 20.0000 chunk 102 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 165 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 119 optimal weight: 0.5980 chunk 90 optimal weight: 5.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN A 232 ASN A 239 GLN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.161791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.097030 restraints weight = 30584.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.100275 restraints weight = 14462.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.102323 restraints weight = 8909.155| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 16299 Z= 0.308 Angle : 0.663 10.163 22004 Z= 0.355 Chirality : 0.044 0.155 2348 Planarity : 0.004 0.053 2812 Dihedral : 8.949 156.111 2217 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.50 % Allowed : 19.37 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.19), residues: 1928 helix: 1.45 (0.15), residues: 1129 sheet: -0.73 (0.39), residues: 146 loop : 0.56 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP D 124 HIS 0.011 0.002 HIS D 201 PHE 0.020 0.002 PHE A 261 TYR 0.024 0.002 TYR A 479 ARG 0.006 0.001 ARG B 274 Details of bonding type rmsd hydrogen bonds : bond 0.04191 ( 896) hydrogen bonds : angle 5.00369 ( 2616) covalent geometry : bond 0.00681 (16298) covalent geometry : angle 0.66263 (22004) Misc. bond : bond 0.00005 ( 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 469 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 409 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8939 (mp0) cc_final: 0.8573 (mp0) REVERT: A 157 LEU cc_start: 0.9623 (tp) cc_final: 0.9396 (tt) REVERT: A 232 ASN cc_start: 0.9098 (OUTLIER) cc_final: 0.8793 (m-40) REVERT: A 250 TYR cc_start: 0.9007 (m-80) cc_final: 0.8283 (m-80) REVERT: A 334 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8856 (ptpt) REVERT: A 379 SER cc_start: 0.8936 (t) cc_final: 0.8330 (t) REVERT: A 384 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.7002 (pm20) REVERT: A 493 MET cc_start: 0.9251 (tmm) cc_final: 0.8640 (tmm) REVERT: B 78 LYS cc_start: 0.9325 (ptpt) cc_final: 0.9059 (ptpt) REVERT: B 104 TYR cc_start: 0.9036 (m-80) cc_final: 0.8288 (m-80) REVERT: B 172 LEU cc_start: 0.9392 (mp) cc_final: 0.8374 (mp) REVERT: B 286 ASP cc_start: 0.8091 (m-30) cc_final: 0.7562 (m-30) REVERT: B 317 MET cc_start: 0.8644 (mtt) cc_final: 0.8442 (mtt) REVERT: B 334 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8894 (pttm) REVERT: B 362 ASP cc_start: 0.8245 (m-30) cc_final: 0.7316 (m-30) REVERT: B 406 ASP cc_start: 0.8101 (m-30) cc_final: 0.7748 (t0) REVERT: B 463 LEU cc_start: 0.9672 (tp) cc_final: 0.9449 (tp) REVERT: B 526 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7473 (tp30) REVERT: B 588 GLN cc_start: 0.9367 (mm-40) cc_final: 0.9153 (mm-40) REVERT: B 612 TYR cc_start: 0.8607 (m-80) cc_final: 0.8116 (m-80) REVERT: B 662 MET cc_start: 0.7446 (ppp) cc_final: 0.6597 (ppp) REVERT: C 134 LYS cc_start: 0.3014 (ttpt) cc_final: 0.2679 (ttpt) REVERT: C 137 MET cc_start: -0.4495 (mtp) cc_final: -0.5798 (mmm) REVERT: C 287 LEU cc_start: 0.0594 (OUTLIER) cc_final: -0.0005 (tp) REVERT: D 110 MET cc_start: 0.5606 (mtt) cc_final: 0.5159 (tmm) REVERT: D 205 VAL cc_start: 0.6469 (p) cc_final: 0.6237 (m) outliers start: 60 outliers final: 38 residues processed: 439 average time/residue: 0.2737 time to fit residues: 178.1466 Evaluate side-chains 417 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 374 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 143 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 110 optimal weight: 0.6980 chunk 182 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN A 232 ASN A 239 GLN A 668 ASN B 25 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN D 128 ASN D 233 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.167867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.103046 restraints weight = 29689.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.106475 restraints weight = 13807.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108668 restraints weight = 8434.338| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16299 Z= 0.139 Angle : 0.603 10.614 22004 Z= 0.314 Chirality : 0.042 0.206 2348 Planarity : 0.004 0.054 2812 Dihedral : 8.516 146.182 2217 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.57 % Allowed : 21.12 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.18), residues: 1928 helix: 1.43 (0.15), residues: 1136 sheet: -0.35 (0.40), residues: 128 loop : 0.38 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 124 HIS 0.011 0.001 HIS D 201 PHE 0.020 0.001 PHE A 657 TYR 0.022 0.001 TYR A 479 ARG 0.007 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 896) hydrogen bonds : angle 4.85731 ( 2616) covalent geometry : bond 0.00310 (16298) covalent geometry : angle 0.60302 (22004) Misc. bond : bond 0.00875 ( 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 472 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 428 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8812 (mp0) cc_final: 0.8448 (mp0) REVERT: A 173 LEU cc_start: 0.9642 (mt) cc_final: 0.9276 (mt) REVERT: A 178 SER cc_start: 0.9137 (OUTLIER) cc_final: 0.8909 (p) REVERT: A 250 TYR cc_start: 0.8872 (m-80) cc_final: 0.8206 (m-80) REVERT: A 334 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8765 (ptpt) REVERT: A 379 SER cc_start: 0.9109 (t) cc_final: 0.8296 (t) REVERT: A 406 ASP cc_start: 0.8084 (m-30) cc_final: 0.7832 (t0) REVERT: A 433 THR cc_start: 0.9675 (m) cc_final: 0.9355 (p) REVERT: A 493 MET cc_start: 0.9249 (tmm) cc_final: 0.8650 (tmm) REVERT: A 586 TYR cc_start: 0.8822 (m-10) cc_final: 0.8541 (m-10) REVERT: A 640 MET cc_start: 0.9206 (tpp) cc_final: 0.8949 (tpp) REVERT: B 78 LYS cc_start: 0.9313 (ptpt) cc_final: 0.9074 (ptpp) REVERT: B 147 GLN cc_start: 0.9276 (mt0) cc_final: 0.9003 (mm-40) REVERT: B 274 ARG cc_start: 0.7614 (tpp80) cc_final: 0.7354 (ttm-80) REVERT: B 286 ASP cc_start: 0.8022 (m-30) cc_final: 0.7488 (m-30) REVERT: B 317 MET cc_start: 0.8576 (mtt) cc_final: 0.8373 (mtt) REVERT: B 350 ARG cc_start: 0.9063 (mtp85) cc_final: 0.7956 (mtp85) REVERT: B 362 ASP cc_start: 0.8122 (m-30) cc_final: 0.7409 (m-30) REVERT: B 526 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7860 (mm-30) REVERT: B 588 GLN cc_start: 0.9138 (mm-40) cc_final: 0.8913 (mm-40) REVERT: B 640 MET cc_start: 0.8959 (tpp) cc_final: 0.8657 (tpp) REVERT: B 662 MET cc_start: 0.7451 (ppp) cc_final: 0.6529 (ppp) REVERT: B 668 ASN cc_start: 0.9051 (m-40) cc_final: 0.8805 (m-40) REVERT: C 74 MET cc_start: 0.7550 (mpp) cc_final: 0.7251 (mpp) REVERT: C 129 LYS cc_start: 0.7700 (tptp) cc_final: 0.6666 (ptmt) REVERT: C 197 ASP cc_start: 0.6610 (p0) cc_final: 0.6357 (p0) REVERT: D 110 MET cc_start: 0.5683 (mtt) cc_final: 0.5125 (tmm) outliers start: 44 outliers final: 31 residues processed: 452 average time/residue: 0.2789 time to fit residues: 187.7641 Evaluate side-chains 434 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 401 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLN Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 7 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 185 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN A 232 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.168312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.103542 restraints weight = 30152.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.107005 restraints weight = 14155.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.109144 restraints weight = 8557.159| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16299 Z= 0.167 Angle : 0.633 17.841 22004 Z= 0.325 Chirality : 0.043 0.241 2348 Planarity : 0.004 0.054 2812 Dihedral : 8.438 144.196 2217 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.51 % Allowed : 21.82 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.19), residues: 1928 helix: 1.42 (0.15), residues: 1139 sheet: -0.78 (0.39), residues: 144 loop : 0.42 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 124 HIS 0.004 0.001 HIS A 255 PHE 0.018 0.001 PHE A 261 TYR 0.018 0.001 TYR A 479 ARG 0.008 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 896) hydrogen bonds : angle 4.87937 ( 2616) covalent geometry : bond 0.00379 (16298) covalent geometry : angle 0.63294 (22004) Misc. bond : bond 0.00657 ( 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 428 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 385 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8820 (mp0) cc_final: 0.8425 (mp0) REVERT: A 178 SER cc_start: 0.9118 (OUTLIER) cc_final: 0.8917 (p) REVERT: A 232 ASN cc_start: 0.9117 (OUTLIER) cc_final: 0.8621 (m-40) REVERT: A 250 TYR cc_start: 0.8854 (m-80) cc_final: 0.8257 (m-80) REVERT: A 334 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8792 (ptpt) REVERT: A 379 SER cc_start: 0.9103 (t) cc_final: 0.8359 (t) REVERT: A 433 THR cc_start: 0.9681 (m) cc_final: 0.9377 (p) REVERT: A 493 MET cc_start: 0.9243 (tmm) cc_final: 0.8617 (tmm) REVERT: A 586 TYR cc_start: 0.8828 (m-10) cc_final: 0.8546 (m-10) REVERT: B 104 TYR cc_start: 0.8989 (m-80) cc_final: 0.8163 (m-80) REVERT: B 274 ARG cc_start: 0.7704 (tpp80) cc_final: 0.7456 (ttm-80) REVERT: B 286 ASP cc_start: 0.8025 (m-30) cc_final: 0.7500 (m-30) REVERT: B 362 ASP cc_start: 0.8115 (m-30) cc_final: 0.7377 (m-30) REVERT: B 526 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7858 (mm-30) REVERT: B 640 MET cc_start: 0.8888 (tpp) cc_final: 0.8535 (tpp) REVERT: B 662 MET cc_start: 0.7493 (ppp) cc_final: 0.6501 (ppp) REVERT: B 668 ASN cc_start: 0.9027 (m-40) cc_final: 0.8788 (m-40) REVERT: C 74 MET cc_start: 0.7356 (mpp) cc_final: 0.6971 (mpp) REVERT: C 129 LYS cc_start: 0.7771 (tptp) cc_final: 0.6771 (ptmt) REVERT: D 110 MET cc_start: 0.5443 (mtt) cc_final: 0.5091 (tmm) outliers start: 43 outliers final: 31 residues processed: 410 average time/residue: 0.2793 time to fit residues: 170.8779 Evaluate side-chains 401 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 367 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 146 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 174 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.169558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.106162 restraints weight = 29803.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.109545 restraints weight = 13826.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.111702 restraints weight = 8352.347| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16299 Z= 0.141 Angle : 0.619 13.532 22004 Z= 0.319 Chirality : 0.043 0.226 2348 Planarity : 0.004 0.058 2812 Dihedral : 8.267 141.274 2217 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.22 % Allowed : 22.81 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.19), residues: 1928 helix: 1.42 (0.15), residues: 1139 sheet: -0.68 (0.40), residues: 144 loop : 0.40 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 124 HIS 0.012 0.001 HIS C 101 PHE 0.019 0.001 PHE A 492 TYR 0.018 0.001 TYR A 479 ARG 0.008 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 896) hydrogen bonds : angle 4.85180 ( 2616) covalent geometry : bond 0.00319 (16298) covalent geometry : angle 0.61887 (22004) Misc. bond : bond 0.00266 ( 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 417 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 379 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.9338 (tppt) cc_final: 0.9015 (tppt) REVERT: A 119 GLU cc_start: 0.8771 (mp0) cc_final: 0.8376 (mp0) REVERT: A 157 LEU cc_start: 0.9426 (tp) cc_final: 0.9188 (tt) REVERT: A 178 SER cc_start: 0.9143 (OUTLIER) cc_final: 0.8936 (p) REVERT: A 250 TYR cc_start: 0.8725 (m-80) cc_final: 0.8192 (m-80) REVERT: A 274 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7784 (tpp-160) REVERT: A 334 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8749 (ptpt) REVERT: A 379 SER cc_start: 0.9138 (t) cc_final: 0.8396 (t) REVERT: A 393 SER cc_start: 0.9059 (t) cc_final: 0.8541 (p) REVERT: A 433 THR cc_start: 0.9676 (m) cc_final: 0.9383 (p) REVERT: A 493 MET cc_start: 0.9219 (tmm) cc_final: 0.8612 (tmm) REVERT: A 586 TYR cc_start: 0.8799 (m-10) cc_final: 0.8555 (m-10) REVERT: A 686 ARG cc_start: 0.7746 (mtp85) cc_final: 0.7538 (mtp85) REVERT: B 104 TYR cc_start: 0.8945 (m-80) cc_final: 0.8120 (m-80) REVERT: B 232 ASN cc_start: 0.9081 (OUTLIER) cc_final: 0.8621 (m-40) REVERT: B 274 ARG cc_start: 0.7769 (tpp80) cc_final: 0.7518 (ttm-80) REVERT: B 286 ASP cc_start: 0.7991 (m-30) cc_final: 0.7454 (m-30) REVERT: B 362 ASP cc_start: 0.8088 (m-30) cc_final: 0.7380 (m-30) REVERT: B 526 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7786 (mm-30) REVERT: B 590 SER cc_start: 0.9549 (t) cc_final: 0.8923 (p) REVERT: B 640 MET cc_start: 0.8908 (tpp) cc_final: 0.8578 (tpp) REVERT: B 662 MET cc_start: 0.7351 (ppp) cc_final: 0.6417 (ppp) REVERT: B 668 ASN cc_start: 0.9004 (m-40) cc_final: 0.8760 (m-40) REVERT: C 74 MET cc_start: 0.7415 (mpp) cc_final: 0.7103 (mpp) REVERT: C 287 LEU cc_start: 0.0453 (OUTLIER) cc_final: 0.0042 (tp) REVERT: D 110 MET cc_start: 0.5369 (mtt) cc_final: 0.5006 (tmm) outliers start: 38 outliers final: 25 residues processed: 402 average time/residue: 0.2685 time to fit residues: 162.0070 Evaluate side-chains 397 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 367 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 140 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 162 optimal weight: 20.0000 chunk 168 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN B 150 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN C 80 HIS ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.165918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.103173 restraints weight = 29926.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.106508 restraints weight = 13917.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.108631 restraints weight = 8406.933| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 16299 Z= 0.213 Angle : 0.680 13.533 22004 Z= 0.348 Chirality : 0.045 0.310 2348 Planarity : 0.004 0.058 2812 Dihedral : 8.452 146.379 2217 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.22 % Allowed : 22.87 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.19), residues: 1928 helix: 1.38 (0.15), residues: 1131 sheet: -0.46 (0.44), residues: 132 loop : 0.28 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 44 HIS 0.010 0.001 HIS C 101 PHE 0.020 0.002 PHE A 492 TYR 0.025 0.001 TYR C 204 ARG 0.007 0.001 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 896) hydrogen bonds : angle 4.97114 ( 2616) covalent geometry : bond 0.00482 (16298) covalent geometry : angle 0.68021 (22004) Misc. bond : bond 0.00698 ( 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 405 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 367 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8844 (mp0) cc_final: 0.8457 (mp0) REVERT: A 232 ASN cc_start: 0.8963 (OUTLIER) cc_final: 0.8535 (m-40) REVERT: A 250 TYR cc_start: 0.8791 (m-80) cc_final: 0.8194 (m-80) REVERT: A 274 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7862 (ttm170) REVERT: A 379 SER cc_start: 0.9037 (t) cc_final: 0.8324 (t) REVERT: A 433 THR cc_start: 0.9682 (m) cc_final: 0.9414 (p) REVERT: A 493 MET cc_start: 0.9222 (tmm) cc_final: 0.8587 (tmm) REVERT: A 586 TYR cc_start: 0.8818 (m-10) cc_final: 0.8553 (m-10) REVERT: A 640 MET cc_start: 0.9119 (tpp) cc_final: 0.8916 (tpp) REVERT: B 104 TYR cc_start: 0.9050 (m-80) cc_final: 0.8311 (m-80) REVERT: B 173 LEU cc_start: 0.9548 (mt) cc_final: 0.9343 (mt) REVERT: B 232 ASN cc_start: 0.9118 (OUTLIER) cc_final: 0.8507 (m-40) REVERT: B 286 ASP cc_start: 0.7997 (m-30) cc_final: 0.7498 (m-30) REVERT: B 362 ASP cc_start: 0.8072 (m-30) cc_final: 0.7290 (m-30) REVERT: B 406 ASP cc_start: 0.8095 (m-30) cc_final: 0.7678 (t0) REVERT: B 526 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7926 (mm-30) REVERT: B 588 GLN cc_start: 0.8954 (mt0) cc_final: 0.8719 (mt0) REVERT: B 590 SER cc_start: 0.9571 (t) cc_final: 0.8999 (p) REVERT: B 640 MET cc_start: 0.8849 (tpp) cc_final: 0.8485 (tpp) REVERT: B 662 MET cc_start: 0.7448 (ppp) cc_final: 0.6506 (ppp) REVERT: C 74 MET cc_start: 0.7386 (mpp) cc_final: 0.7066 (mpp) REVERT: C 287 LEU cc_start: 0.0487 (OUTLIER) cc_final: 0.0057 (tp) REVERT: D 110 MET cc_start: 0.5299 (mtt) cc_final: 0.4954 (tmm) outliers start: 38 outliers final: 27 residues processed: 387 average time/residue: 0.2739 time to fit residues: 159.0937 Evaluate side-chains 383 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 352 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 165 optimal weight: 0.0030 chunk 180 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.165034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.100878 restraints weight = 30270.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.104240 restraints weight = 14165.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.106299 restraints weight = 8570.088| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 16299 Z= 0.244 Angle : 0.698 12.715 22004 Z= 0.361 Chirality : 0.045 0.335 2348 Planarity : 0.004 0.056 2812 Dihedral : 8.738 151.923 2217 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.04 % Allowed : 22.93 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.19), residues: 1928 helix: 1.25 (0.15), residues: 1129 sheet: -0.58 (0.44), residues: 132 loop : 0.20 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP C 44 HIS 0.008 0.001 HIS C 101 PHE 0.022 0.002 PHE A 492 TYR 0.041 0.002 TYR C 204 ARG 0.008 0.001 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 896) hydrogen bonds : angle 5.10030 ( 2616) covalent geometry : bond 0.00550 (16298) covalent geometry : angle 0.69785 (22004) Misc. bond : bond 0.00559 ( 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 410 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 375 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8858 (mp0) cc_final: 0.8461 (mp0) REVERT: A 232 ASN cc_start: 0.9024 (OUTLIER) cc_final: 0.8317 (m-40) REVERT: A 250 TYR cc_start: 0.8790 (m-80) cc_final: 0.8187 (m-80) REVERT: A 379 SER cc_start: 0.8989 (t) cc_final: 0.8318 (t) REVERT: A 433 THR cc_start: 0.9683 (m) cc_final: 0.9422 (p) REVERT: A 493 MET cc_start: 0.9239 (tmm) cc_final: 0.8597 (tmm) REVERT: A 586 TYR cc_start: 0.8812 (m-10) cc_final: 0.8554 (m-10) REVERT: B 104 TYR cc_start: 0.9066 (m-80) cc_final: 0.8319 (m-80) REVERT: B 118 TYR cc_start: 0.9417 (t80) cc_final: 0.9190 (t80) REVERT: B 150 GLN cc_start: 0.9295 (tp40) cc_final: 0.8959 (tp-100) REVERT: B 173 LEU cc_start: 0.9573 (mt) cc_final: 0.9367 (mt) REVERT: B 232 ASN cc_start: 0.9155 (OUTLIER) cc_final: 0.8503 (m-40) REVERT: B 274 ARG cc_start: 0.7887 (tpp80) cc_final: 0.7612 (tpp80) REVERT: B 286 ASP cc_start: 0.8038 (m-30) cc_final: 0.7528 (m-30) REVERT: B 362 ASP cc_start: 0.8103 (m-30) cc_final: 0.7330 (m-30) REVERT: B 406 ASP cc_start: 0.8073 (m-30) cc_final: 0.7716 (t0) REVERT: B 463 LEU cc_start: 0.9609 (tp) cc_final: 0.9347 (tp) REVERT: B 526 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7693 (mm-30) REVERT: B 529 ASP cc_start: 0.8198 (m-30) cc_final: 0.7657 (m-30) REVERT: B 588 GLN cc_start: 0.9005 (mt0) cc_final: 0.8767 (mt0) REVERT: B 590 SER cc_start: 0.9570 (t) cc_final: 0.9004 (p) REVERT: B 640 MET cc_start: 0.8859 (tpp) cc_final: 0.8487 (tpp) REVERT: B 662 MET cc_start: 0.7554 (ppp) cc_final: 0.6637 (ppp) REVERT: C 74 MET cc_start: 0.7425 (mpp) cc_final: 0.7103 (mpp) REVERT: C 287 LEU cc_start: 0.0320 (OUTLIER) cc_final: -0.0041 (tp) REVERT: D 110 MET cc_start: 0.5433 (mtt) cc_final: 0.5048 (tmm) outliers start: 35 outliers final: 31 residues processed: 394 average time/residue: 0.2776 time to fit residues: 163.6512 Evaluate side-chains 387 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 353 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 186 optimal weight: 30.0000 chunk 119 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.168309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.104820 restraints weight = 29850.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.108149 restraints weight = 13818.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.110288 restraints weight = 8349.203| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 16299 Z= 0.138 Angle : 0.656 11.854 22004 Z= 0.338 Chirality : 0.043 0.334 2348 Planarity : 0.004 0.055 2812 Dihedral : 8.469 144.987 2217 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.81 % Allowed : 23.28 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.19), residues: 1928 helix: 1.28 (0.15), residues: 1121 sheet: -0.43 (0.44), residues: 128 loop : 0.07 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 44 HIS 0.008 0.001 HIS D 201 PHE 0.020 0.001 PHE A 492 TYR 0.021 0.001 TYR C 204 ARG 0.011 0.001 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.03818 ( 896) hydrogen bonds : angle 4.98750 ( 2616) covalent geometry : bond 0.00310 (16298) covalent geometry : angle 0.65552 (22004) Misc. bond : bond 0.00262 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6501.09 seconds wall clock time: 113 minutes 10.53 seconds (6790.53 seconds total)