Starting phenix.real_space_refine on Sat May 17 15:05:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bx3_44992/05_2025/9bx3_44992_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bx3_44992/05_2025/9bx3_44992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bx3_44992/05_2025/9bx3_44992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bx3_44992/05_2025/9bx3_44992.map" model { file = "/net/cci-nas-00/data/ceres_data/9bx3_44992/05_2025/9bx3_44992_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bx3_44992/05_2025/9bx3_44992_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 12 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10190 2.51 5 N 2598 2.21 5 O 3066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15954 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 8.80, per 1000 atoms: 0.55 Number of scatterers: 15954 At special positions: 0 Unit cell: (91.98, 126.728, 133.882, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 12 15.00 Mg 2 11.99 O 3066 8.00 N 2598 7.00 C 10190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.79 Conformation dependent library (CDL) restraints added in 2.0 seconds 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3688 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 10 sheets defined 64.3% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 27 through 41 removed outlier: 3.553A 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: 3.705A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.872A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.792A pdb=" N GLN A 242 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.639A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 318 through 329 removed outlier: 6.056A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.521A 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: 4.273A 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: 3.961A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.721A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 222 through 237 removed outlier: 3.778A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.574A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 318 through 329 removed outlier: 5.841A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 4.621A 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: 4.175A 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: 3.881A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.514A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.876A 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: 6.314A 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: 3.737A 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: 7.058A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 removed outlier: 6.456A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AA9, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB1, first strand: chain 'B' and resid 655 through 659 898 hydrogen bonds defined for protein. 2616 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.88 Time building geometry restraints manager: 4.41 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: 4974 1.34 - 1.46: 2945 1.46 - 1.58: 8204 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 1.600 -0.060 1.25e-02 6.40e+03 2.30e+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 1.03e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.032 1.08e-02 8.57e+03 8.94e+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 7.26e+00 bond pdb=" CA ILE C 35 " pdb=" CB ILE C 35 " ideal model delta sigma weight residual 1.537 1.568 -0.031 1.21e-02 6.83e+03 6.68e+00 ... (remaining 16293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 21508 2.10 - 4.19: 459 4.19 - 6.29: 34 6.29 - 8.39: 1 8.39 - 10.49: 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 110.54 116.64 -6.10 1.36e+00 5.41e-01 2.01e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.12 -4.41 1.15e+00 7.56e-01 1.47e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.82 -4.32 1.23e+00 6.61e-01 1.23e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.68 -3.97 1.15e+00 7.56e-01 1.19e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.58 3.61 1.06e+00 8.90e-01 1.16e+01 ... (remaining 21999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.31: 9427 34.31 - 68.62: 331 68.62 - 102.93: 48 102.93 - 137.24: 0 137.24 - 171.55: 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 301.68 130.13 171.55 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 301.68 135.75 165.94 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 -134.32 12.32 0 2.50e+00 1.60e-01 2.43e+01 ... (remaining 9805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2126 0.093 - 0.187: 183 0.187 - 0.280: 33 0.280 - 0.374: 4 0.374 - 0.467: 2 Chirality restraints: 2348 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.46e+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 4.63e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 2345 not shown) Planarity restraints: 2812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 6 " 0.036 5.00e-02 4.00e+02 5.53e-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 4.10e-02 2.69e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.018 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 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.009 2.00e-02 2.50e+03 ... (remaining 2809 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 131 2.51 - 3.11: 11873 3.11 - 3.70: 26426 3.70 - 4.30: 41198 4.30 - 4.90: 64928 Nonbonded interactions: 144556 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" O1B TTP A 801 " pdb="MG MG A 802 " model vdw 1.919 2.170 nonbonded pdb=" O2A TTP B 801 " pdb="MG MG B 802 " model vdw 1.928 2.170 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 ... (remaining 144551 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 33.960 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 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 0.834 16299 Z= 0.724 Angle : 0.707 10.485 22004 Z= 0.453 Chirality : 0.059 0.467 2348 Planarity : 0.003 0.055 2812 Dihedral : 17.179 171.550 6120 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.34 % Allowed : 14.12 % Favored : 84.54 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.18), residues: 1928 helix: 1.04 (0.15), residues: 1133 sheet: 0.46 (0.39), residues: 146 loop : 0.45 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 PHE 0.021 0.002 PHE C 227 TYR 0.020 0.002 TYR D 179 ARG 0.003 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.16171 ( 896) hydrogen bonds : angle 6.35194 ( 2616) covalent geometry : bond 0.00542 (16298) covalent geometry : angle 0.70728 (22004) Misc. bond : bond 0.83355 ( 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 883 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 860 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.7477 (p0) cc_final: 0.7150 (p0) REVERT: A 35 SER cc_start: 0.8828 (OUTLIER) cc_final: 0.8210 (t) REVERT: A 200 SER cc_start: 0.8921 (t) cc_final: 0.8678 (t) REVERT: A 204 SER cc_start: 0.8532 (m) cc_final: 0.8303 (p) REVERT: A 319 MET cc_start: 0.8338 (tpp) cc_final: 0.7869 (tpp) REVERT: A 349 LEU cc_start: 0.8108 (tp) cc_final: 0.7852 (tp) REVERT: A 359 MET cc_start: 0.7680 (ttt) cc_final: 0.7416 (ttt) REVERT: A 411 LEU cc_start: 0.8571 (mt) cc_final: 0.8286 (mt) REVERT: A 658 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7461 (mt) REVERT: B 27 ASP cc_start: 0.7317 (p0) cc_final: 0.7087 (p0) REVERT: B 72 TYR cc_start: 0.7028 (m-80) cc_final: 0.6380 (m-10) REVERT: B 100 PHE cc_start: 0.8143 (t80) cc_final: 0.7859 (t80) REVERT: B 187 ASP cc_start: 0.7691 (t70) cc_final: 0.7424 (t0) REVERT: B 200 SER cc_start: 0.8916 (t) cc_final: 0.8321 (t) REVERT: B 211 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6852 (mm-30) REVERT: B 235 ARG cc_start: 0.7986 (mtm110) cc_final: 0.7589 (ttm-80) REVERT: B 246 SER cc_start: 0.8358 (m) cc_final: 0.7982 (p) REVERT: B 250 TYR cc_start: 0.8608 (m-80) cc_final: 0.8171 (m-80) REVERT: B 288 PHE cc_start: 0.8346 (t80) cc_final: 0.7904 (t80) REVERT: B 373 ILE cc_start: 0.8752 (mt) cc_final: 0.8166 (mt) REVERT: B 379 SER cc_start: 0.8708 (t) cc_final: 0.8097 (t) REVERT: B 396 ASP cc_start: 0.6997 (m-30) cc_final: 0.6634 (m-30) REVERT: B 415 ASN cc_start: 0.7985 (t0) cc_final: 0.7736 (t0) REVERT: B 420 MET cc_start: 0.8428 (mmm) cc_final: 0.8141 (mmm) REVERT: B 425 ILE cc_start: 0.9006 (mt) cc_final: 0.8713 (mt) REVERT: B 490 THR cc_start: 0.8636 (m) cc_final: 0.8416 (m) REVERT: B 494 MET cc_start: 0.7414 (mtp) cc_final: 0.7106 (mtp) REVERT: B 550 MET cc_start: 0.7872 (ttm) cc_final: 0.7308 (ttm) REVERT: B 558 TRP cc_start: 0.8481 (m100) cc_final: 0.8027 (m100) REVERT: B 626 TYR cc_start: 0.8053 (m-80) cc_final: 0.7759 (m-80) REVERT: C 157 MET cc_start: 0.7101 (mtt) cc_final: 0.6729 (mtp) REVERT: C 224 LEU cc_start: 0.4867 (mt) cc_final: 0.4581 (mt) REVERT: C 260 ILE cc_start: 0.6261 (pt) cc_final: 0.5565 (pt) REVERT: D 47 LEU cc_start: 0.4053 (mt) cc_final: 0.3754 (mp) REVERT: D 56 MET cc_start: 0.5125 (mmp) cc_final: 0.4726 (mtt) REVERT: D 67 THR cc_start: 0.7180 (m) cc_final: 0.6876 (m) REVERT: D 321 TYR cc_start: 0.6611 (m-80) cc_final: 0.6371 (m-10) outliers start: 23 outliers final: 4 residues processed: 875 average time/residue: 0.2970 time to fit residues: 373.0818 Evaluate side-chains 610 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 604 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain D residue 59 LEU 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: 5.9990 chunk 145 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 180 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN B 14 ASN B 158 ASN ** B 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN C 23 ASN C 25 ASN C 28 GLN C 52 GLN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN D 80 HIS D 186 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.137083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.094679 restraints weight = 33190.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.098185 restraints weight = 16588.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.100318 restraints weight = 10138.268| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16299 Z= 0.214 Angle : 0.695 13.308 22004 Z= 0.368 Chirality : 0.044 0.155 2348 Planarity : 0.004 0.055 2812 Dihedral : 9.152 159.138 2225 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.09 % Allowed : 20.13 % Favored : 76.78 % 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: 1.39 (0.18), residues: 1928 helix: 1.31 (0.15), residues: 1125 sheet: 0.32 (0.40), residues: 128 loop : 0.60 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 44 HIS 0.007 0.001 HIS C 201 PHE 0.035 0.002 PHE A 261 TYR 0.028 0.002 TYR C 142 ARG 0.006 0.001 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.04883 ( 896) hydrogen bonds : angle 5.29868 ( 2616) covalent geometry : bond 0.00473 (16298) covalent geometry : angle 0.69465 (22004) Misc. bond : bond 0.00179 ( 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 708 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 655 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LEU cc_start: 0.9258 (mp) cc_final: 0.8509 (mp) REVERT: A 179 LEU cc_start: 0.9428 (tp) cc_final: 0.9217 (tp) REVERT: A 204 SER cc_start: 0.9079 (m) cc_final: 0.8833 (p) REVERT: A 218 ASN cc_start: 0.8554 (t0) cc_final: 0.8264 (t0) REVERT: A 315 ASP cc_start: 0.8097 (p0) cc_final: 0.7776 (p0) REVERT: A 316 GLU cc_start: 0.8195 (tt0) cc_final: 0.7702 (tm-30) REVERT: A 317 MET cc_start: 0.8987 (mtp) cc_final: 0.8743 (mtm) REVERT: A 355 TYR cc_start: 0.8311 (m-80) cc_final: 0.8101 (m-10) REVERT: A 383 SER cc_start: 0.9172 (OUTLIER) cc_final: 0.8484 (t) REVERT: A 406 ASP cc_start: 0.8024 (m-30) cc_final: 0.7380 (t0) REVERT: A 485 ARG cc_start: 0.8224 (mtm-85) cc_final: 0.7722 (mtt90) REVERT: A 493 MET cc_start: 0.8922 (tmm) cc_final: 0.8626 (tmm) REVERT: A 526 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8032 (mm-30) REVERT: A 550 MET cc_start: 0.7774 (mtp) cc_final: 0.7358 (mtp) REVERT: A 603 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7688 (tm-30) REVERT: A 604 ARG cc_start: 0.8558 (tpp80) cc_final: 0.8245 (mmp80) REVERT: A 662 MET cc_start: 0.8469 (mmp) cc_final: 0.8123 (mmp) REVERT: B 27 ASP cc_start: 0.8792 (p0) cc_final: 0.8499 (p0) REVERT: B 31 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8654 (pm20) REVERT: B 109 ASN cc_start: 0.9090 (OUTLIER) cc_final: 0.8738 (m110) REVERT: B 161 ARG cc_start: 0.7921 (mtt180) cc_final: 0.7595 (mtt180) REVERT: B 200 SER cc_start: 0.8974 (t) cc_final: 0.8310 (t) REVERT: B 232 ASN cc_start: 0.8971 (t0) cc_final: 0.8434 (m-40) REVERT: B 246 SER cc_start: 0.7718 (m) cc_final: 0.7280 (p) REVERT: B 250 TYR cc_start: 0.9268 (m-80) cc_final: 0.8091 (m-80) REVERT: B 288 PHE cc_start: 0.9301 (t80) cc_final: 0.9030 (t80) REVERT: B 379 SER cc_start: 0.8871 (t) cc_final: 0.8111 (t) REVERT: B 466 MET cc_start: 0.9097 (ptt) cc_final: 0.8839 (ptm) REVERT: B 480 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8244 (mt-10) REVERT: B 586 TYR cc_start: 0.8529 (m-80) cc_final: 0.8128 (m-80) REVERT: B 599 GLU cc_start: 0.8170 (pt0) cc_final: 0.7891 (pt0) REVERT: B 601 ILE cc_start: 0.9155 (mm) cc_final: 0.8455 (mm) REVERT: B 602 GLU cc_start: 0.8273 (tt0) cc_final: 0.7535 (tt0) REVERT: B 604 ARG cc_start: 0.8990 (mmp80) cc_final: 0.8214 (tpp-160) REVERT: B 626 TYR cc_start: 0.8515 (m-80) cc_final: 0.8296 (m-80) REVERT: B 640 MET cc_start: 0.9119 (tpp) cc_final: 0.8638 (tpp) REVERT: B 667 LEU cc_start: 0.9019 (tt) cc_final: 0.8449 (tt) REVERT: C 23 ASN cc_start: 0.8801 (t0) cc_final: 0.8320 (t0) REVERT: C 24 GLN cc_start: 0.8345 (mt0) cc_final: 0.7949 (mm-40) REVERT: C 178 PHE cc_start: 0.8291 (m-80) cc_final: 0.7662 (m-10) REVERT: C 193 LEU cc_start: 0.8219 (mm) cc_final: 0.7946 (mm) REVERT: C 218 GLU cc_start: 0.9350 (mp0) cc_final: 0.8727 (pp20) REVERT: D 20 MET cc_start: 0.8907 (ptm) cc_final: 0.8643 (ptp) REVERT: D 56 MET cc_start: 0.3116 (mmp) cc_final: 0.2707 (mtt) REVERT: D 131 LEU cc_start: 0.8213 (tt) cc_final: 0.7370 (tt) REVERT: D 174 TYR cc_start: 0.4276 (t80) cc_final: 0.3663 (t80) REVERT: D 189 GLU cc_start: 0.8566 (tp30) cc_final: 0.8005 (mt-10) REVERT: D 204 TYR cc_start: 0.8849 (t80) cc_final: 0.8419 (t80) REVERT: D 212 ILE cc_start: 0.8215 (mt) cc_final: 0.7678 (mt) REVERT: D 216 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7633 (mm110) outliers start: 53 outliers final: 20 residues processed: 679 average time/residue: 0.2843 time to fit residues: 280.9027 Evaluate side-chains 569 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 546 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 191 optimal weight: 0.0980 chunk 52 optimal weight: 0.7980 chunk 175 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 HIS A 608 ASN A 646 GLN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 370 ASN B 588 GLN B 646 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 192 ASN D 214 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.137351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.097114 restraints weight = 33690.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.100488 restraints weight = 16344.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.102754 restraints weight = 9744.563| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16299 Z= 0.139 Angle : 0.633 12.192 22004 Z= 0.333 Chirality : 0.043 0.160 2348 Planarity : 0.004 0.051 2812 Dihedral : 8.781 157.628 2219 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.63 % Allowed : 22.05 % Favored : 75.32 % 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: 1.39 (0.19), residues: 1928 helix: 1.35 (0.15), residues: 1136 sheet: 0.64 (0.39), residues: 116 loop : 0.42 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 30 HIS 0.004 0.001 HIS B 255 PHE 0.051 0.002 PHE C 168 TYR 0.030 0.001 TYR C 22 ARG 0.007 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 896) hydrogen bonds : angle 5.12117 ( 2616) covalent geometry : bond 0.00307 (16298) covalent geometry : angle 0.63315 (22004) Misc. bond : bond 0.00036 ( 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 657 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 612 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LEU cc_start: 0.9234 (mp) cc_final: 0.8899 (mp) REVERT: A 178 SER cc_start: 0.8333 (OUTLIER) cc_final: 0.7979 (p) REVERT: A 179 LEU cc_start: 0.9421 (tp) cc_final: 0.9207 (tp) REVERT: A 218 ASN cc_start: 0.8559 (t0) cc_final: 0.8215 (t0) REVERT: A 355 TYR cc_start: 0.8321 (m-80) cc_final: 0.8070 (m-10) REVERT: A 406 ASP cc_start: 0.8031 (m-30) cc_final: 0.7585 (m-30) REVERT: A 485 ARG cc_start: 0.8230 (mtm-85) cc_final: 0.7613 (mtt90) REVERT: A 493 MET cc_start: 0.8957 (tmm) cc_final: 0.8534 (tmm) REVERT: A 599 GLU cc_start: 0.8497 (mp0) cc_final: 0.8085 (mp0) REVERT: A 683 TYR cc_start: 0.8238 (t80) cc_final: 0.7947 (t80) REVERT: A 684 TYR cc_start: 0.8182 (OUTLIER) cc_final: 0.7446 (m-80) REVERT: B 27 ASP cc_start: 0.8779 (p0) cc_final: 0.8499 (p0) REVERT: B 31 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8592 (pm20) REVERT: B 200 SER cc_start: 0.8949 (t) cc_final: 0.8073 (t) REVERT: B 232 ASN cc_start: 0.8942 (OUTLIER) cc_final: 0.8470 (m-40) REVERT: B 246 SER cc_start: 0.7606 (m) cc_final: 0.7235 (p) REVERT: B 250 TYR cc_start: 0.9216 (m-80) cc_final: 0.8014 (m-80) REVERT: B 276 LYS cc_start: 0.8915 (mtmm) cc_final: 0.8539 (mtmm) REVERT: B 288 PHE cc_start: 0.9198 (t80) cc_final: 0.8810 (t80) REVERT: B 322 MET cc_start: 0.8963 (mmp) cc_final: 0.8600 (mmt) REVERT: B 379 SER cc_start: 0.8795 (t) cc_final: 0.7885 (t) REVERT: B 467 ASN cc_start: 0.9093 (t0) cc_final: 0.8522 (m-40) REVERT: B 494 MET cc_start: 0.8991 (mtp) cc_final: 0.8763 (mtp) REVERT: B 550 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7824 (ttm) REVERT: B 590 SER cc_start: 0.9226 (p) cc_final: 0.8390 (t) REVERT: B 601 ILE cc_start: 0.9200 (mm) cc_final: 0.8402 (mm) REVERT: B 604 ARG cc_start: 0.8926 (mmp80) cc_final: 0.8229 (mmp80) REVERT: B 628 GLU cc_start: 0.7527 (mp0) cc_final: 0.7322 (mp0) REVERT: B 640 MET cc_start: 0.9087 (tpp) cc_final: 0.8485 (tpp) REVERT: B 670 ILE cc_start: 0.9282 (mm) cc_final: 0.9053 (mt) REVERT: C 157 MET cc_start: 0.7676 (mtp) cc_final: 0.7270 (ttt) REVERT: C 172 PHE cc_start: 0.7664 (m-10) cc_final: 0.7398 (m-10) REVERT: C 178 PHE cc_start: 0.8238 (m-80) cc_final: 0.7603 (m-10) REVERT: C 218 GLU cc_start: 0.9379 (mp0) cc_final: 0.9005 (pm20) REVERT: D 18 THR cc_start: 0.6475 (p) cc_final: 0.6244 (p) REVERT: D 46 TYR cc_start: 0.8646 (m-10) cc_final: 0.8220 (m-80) REVERT: D 95 MET cc_start: 0.8919 (tmm) cc_final: 0.8266 (tmm) REVERT: D 103 LYS cc_start: 0.5769 (mptt) cc_final: 0.5557 (tppt) REVERT: D 131 LEU cc_start: 0.8274 (tt) cc_final: 0.8062 (mt) REVERT: D 174 TYR cc_start: 0.4142 (t80) cc_final: 0.3368 (t80) REVERT: D 189 GLU cc_start: 0.8757 (tp30) cc_final: 0.8058 (mt-10) REVERT: D 204 TYR cc_start: 0.8705 (t80) cc_final: 0.8287 (t80) outliers start: 45 outliers final: 19 residues processed: 634 average time/residue: 0.2695 time to fit residues: 250.5511 Evaluate side-chains 589 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 565 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 44 TRP Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 3 optimal weight: 0.0980 chunk 51 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 153 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.132181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.092290 restraints weight = 34295.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.095522 restraints weight = 16939.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.097589 restraints weight = 10325.331| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16299 Z= 0.210 Angle : 0.658 14.692 22004 Z= 0.346 Chirality : 0.044 0.193 2348 Planarity : 0.004 0.052 2812 Dihedral : 8.905 157.239 2217 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.03 % Allowed : 23.10 % Favored : 73.86 % 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: 1.25 (0.15), residues: 1141 sheet: -0.07 (0.40), residues: 138 loop : 0.45 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 30 HIS 0.005 0.001 HIS A 438 PHE 0.046 0.002 PHE C 168 TYR 0.021 0.002 TYR C 22 ARG 0.010 0.001 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.04180 ( 896) hydrogen bonds : angle 5.17001 ( 2616) covalent geometry : bond 0.00472 (16298) covalent geometry : angle 0.65783 (22004) Misc. bond : bond 0.00100 ( 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 622 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 570 time to evaluate : 1.658 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 166 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7949 (mm-30) REVERT: A 172 LEU cc_start: 0.9354 (mp) cc_final: 0.9145 (mp) REVERT: A 178 SER cc_start: 0.8264 (OUTLIER) cc_final: 0.8055 (p) REVERT: A 218 ASN cc_start: 0.8731 (t0) cc_final: 0.8440 (t0) REVERT: A 319 MET cc_start: 0.8599 (tpp) cc_final: 0.8065 (tpp) REVERT: A 322 MET cc_start: 0.8410 (tpp) cc_final: 0.7590 (tpp) REVERT: A 355 TYR cc_start: 0.8295 (m-80) cc_final: 0.8085 (m-10) REVERT: A 383 SER cc_start: 0.9235 (OUTLIER) cc_final: 0.8651 (t) REVERT: A 485 ARG cc_start: 0.8262 (mtm-85) cc_final: 0.7686 (mtt90) REVERT: A 493 MET cc_start: 0.8957 (tmm) cc_final: 0.8519 (tmm) REVERT: A 599 GLU cc_start: 0.8420 (mp0) cc_final: 0.7904 (mp0) REVERT: A 612 TYR cc_start: 0.8971 (m-80) cc_final: 0.8769 (m-80) REVERT: A 640 MET cc_start: 0.8946 (tpp) cc_final: 0.8654 (tpp) REVERT: A 641 ILE cc_start: 0.9685 (mm) cc_final: 0.9469 (mt) REVERT: A 683 TYR cc_start: 0.8442 (t80) cc_final: 0.8071 (t80) REVERT: A 684 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7314 (m-80) REVERT: B 89 PHE cc_start: 0.8788 (t80) cc_final: 0.8525 (t80) REVERT: B 116 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7859 (mt-10) REVERT: B 200 SER cc_start: 0.9006 (t) cc_final: 0.8271 (t) REVERT: B 211 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7849 (mt-10) REVERT: B 246 SER cc_start: 0.7646 (m) cc_final: 0.7393 (p) REVERT: B 250 TYR cc_start: 0.9237 (m-80) cc_final: 0.8142 (m-80) REVERT: B 379 SER cc_start: 0.8841 (t) cc_final: 0.8082 (t) REVERT: B 394 TYR cc_start: 0.9134 (m-80) cc_final: 0.8653 (m-80) REVERT: B 467 ASN cc_start: 0.9091 (t0) cc_final: 0.8495 (t0) REVERT: B 552 ILE cc_start: 0.9452 (mp) cc_final: 0.9179 (mt) REVERT: B 589 SER cc_start: 0.9572 (t) cc_final: 0.9072 (p) REVERT: B 590 SER cc_start: 0.9275 (p) cc_final: 0.8525 (t) REVERT: B 599 GLU cc_start: 0.7929 (pt0) cc_final: 0.7705 (pt0) REVERT: B 601 ILE cc_start: 0.9196 (mm) cc_final: 0.8818 (mm) REVERT: B 639 ASP cc_start: 0.8636 (m-30) cc_final: 0.8087 (m-30) REVERT: B 640 MET cc_start: 0.9089 (tpp) cc_final: 0.8693 (tpp) REVERT: B 686 ARG cc_start: 0.8466 (ttm-80) cc_final: 0.7859 (mtm-85) REVERT: C 157 MET cc_start: 0.7676 (mtp) cc_final: 0.7340 (ttm) REVERT: C 168 PHE cc_start: 0.7805 (m-80) cc_final: 0.7552 (m-80) REVERT: C 172 PHE cc_start: 0.7705 (m-10) cc_final: 0.7374 (m-10) REVERT: C 178 PHE cc_start: 0.8324 (m-80) cc_final: 0.7660 (m-10) REVERT: C 179 TYR cc_start: 0.8428 (t80) cc_final: 0.8082 (t80) REVERT: C 218 GLU cc_start: 0.9295 (mp0) cc_final: 0.8948 (pm20) REVERT: D 18 THR cc_start: 0.6597 (p) cc_final: 0.6223 (p) REVERT: D 46 TYR cc_start: 0.8786 (m-10) cc_final: 0.8371 (m-80) REVERT: D 56 MET cc_start: 0.2575 (mmm) cc_final: 0.2249 (mpp) REVERT: D 131 LEU cc_start: 0.8315 (tt) cc_final: 0.7905 (mt) REVERT: D 149 ASP cc_start: 0.7557 (t0) cc_final: 0.7243 (t0) REVERT: D 174 TYR cc_start: 0.4322 (t80) cc_final: 0.3742 (t80) REVERT: D 204 TYR cc_start: 0.8785 (t80) cc_final: 0.8357 (t80) REVERT: D 242 TYR cc_start: 0.7786 (t80) cc_final: 0.7564 (t80) REVERT: D 281 ASP cc_start: 0.7997 (p0) cc_final: 0.7311 (t70) outliers start: 52 outliers final: 34 residues processed: 593 average time/residue: 0.2645 time to fit residues: 233.1114 Evaluate side-chains 568 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 530 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 44 TRP Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 109 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 188 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 165 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN B 62 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.134978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.094207 restraints weight = 35034.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.097538 restraints weight = 17231.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.099591 restraints weight = 10383.158| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16299 Z= 0.172 Angle : 0.654 13.699 22004 Z= 0.342 Chirality : 0.043 0.144 2348 Planarity : 0.004 0.050 2812 Dihedral : 8.783 153.045 2217 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.27 % Allowed : 24.91 % Favored : 71.82 % 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: 1.09 (0.19), residues: 1928 helix: 1.15 (0.15), residues: 1140 sheet: -0.22 (0.40), residues: 138 loop : 0.39 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 124 HIS 0.006 0.001 HIS C 201 PHE 0.036 0.002 PHE C 168 TYR 0.022 0.001 TYR C 262 ARG 0.007 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 896) hydrogen bonds : angle 5.13833 ( 2616) covalent geometry : bond 0.00384 (16298) covalent geometry : angle 0.65414 (22004) Misc. bond : bond 0.00071 ( 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 616 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 560 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8448 (mp0) REVERT: A 108 THR cc_start: 0.7638 (OUTLIER) cc_final: 0.7395 (p) REVERT: A 164 ARG cc_start: 0.7501 (ptt90) cc_final: 0.7012 (ptt90) REVERT: A 166 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7784 (mm-30) REVERT: A 218 ASN cc_start: 0.8796 (t0) cc_final: 0.8480 (t0) REVERT: A 301 PHE cc_start: 0.9065 (m-10) cc_final: 0.8833 (m-10) REVERT: A 312 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8620 (pt0) REVERT: A 355 TYR cc_start: 0.8219 (m-80) cc_final: 0.8016 (m-10) REVERT: A 383 SER cc_start: 0.9218 (OUTLIER) cc_final: 0.8661 (t) REVERT: A 485 ARG cc_start: 0.8277 (mtm-85) cc_final: 0.7678 (mtt90) REVERT: A 493 MET cc_start: 0.8993 (tmm) cc_final: 0.8554 (tmm) REVERT: A 599 GLU cc_start: 0.8414 (mp0) cc_final: 0.7985 (mp0) REVERT: A 612 TYR cc_start: 0.8898 (m-80) cc_final: 0.8676 (m-80) REVERT: A 640 MET cc_start: 0.8940 (tpp) cc_final: 0.8576 (tpp) REVERT: A 683 TYR cc_start: 0.8377 (t80) cc_final: 0.7650 (t80) REVERT: A 684 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.6982 (m-80) REVERT: B 31 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8645 (pm20) REVERT: B 65 GLU cc_start: 0.8492 (mp0) cc_final: 0.8253 (mp0) REVERT: B 89 PHE cc_start: 0.8772 (t80) cc_final: 0.8570 (t80) REVERT: B 200 SER cc_start: 0.8954 (t) cc_final: 0.8263 (t) REVERT: B 250 TYR cc_start: 0.9191 (m-80) cc_final: 0.8228 (m-80) REVERT: B 290 GLU cc_start: 0.8496 (pp20) cc_final: 0.8272 (pp20) REVERT: B 379 SER cc_start: 0.8850 (t) cc_final: 0.7833 (t) REVERT: B 394 TYR cc_start: 0.9068 (m-80) cc_final: 0.8678 (m-80) REVERT: B 467 ASN cc_start: 0.9004 (t0) cc_final: 0.8395 (t0) REVERT: B 494 MET cc_start: 0.8899 (mtp) cc_final: 0.8654 (mtp) REVERT: B 515 ASP cc_start: 0.8981 (m-30) cc_final: 0.8717 (m-30) REVERT: B 590 SER cc_start: 0.9269 (OUTLIER) cc_final: 0.8589 (t) REVERT: B 599 GLU cc_start: 0.8027 (pt0) cc_final: 0.7375 (pt0) REVERT: B 601 ILE cc_start: 0.9102 (mm) cc_final: 0.8607 (mm) REVERT: B 639 ASP cc_start: 0.8578 (m-30) cc_final: 0.8043 (m-30) REVERT: B 640 MET cc_start: 0.9038 (tpp) cc_final: 0.8684 (tpp) REVERT: B 686 ARG cc_start: 0.8399 (ttm-80) cc_final: 0.7865 (mtm-85) REVERT: C 157 MET cc_start: 0.7629 (mtp) cc_final: 0.7129 (ttt) REVERT: C 172 PHE cc_start: 0.7859 (m-10) cc_final: 0.7478 (m-10) REVERT: C 178 PHE cc_start: 0.8382 (m-80) cc_final: 0.7771 (m-10) REVERT: C 179 TYR cc_start: 0.8431 (t80) cc_final: 0.8080 (t80) REVERT: C 181 GLN cc_start: 0.8038 (mm110) cc_final: 0.7799 (mm-40) REVERT: C 261 ARG cc_start: 0.7118 (ptp-170) cc_final: 0.6681 (mtp-110) REVERT: C 269 MET cc_start: 0.8306 (tmm) cc_final: 0.8051 (ppp) REVERT: D 18 THR cc_start: 0.6405 (p) cc_final: 0.6030 (p) REVERT: D 46 TYR cc_start: 0.8791 (m-10) cc_final: 0.8368 (m-80) REVERT: D 131 LEU cc_start: 0.8291 (tt) cc_final: 0.7913 (mt) REVERT: D 138 ILE cc_start: 0.9082 (mm) cc_final: 0.8873 (mm) REVERT: D 149 ASP cc_start: 0.7704 (t0) cc_final: 0.7382 (t0) REVERT: D 174 TYR cc_start: 0.4540 (t80) cc_final: 0.4063 (t80) REVERT: D 204 TYR cc_start: 0.8841 (t80) cc_final: 0.8398 (t80) REVERT: D 211 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8627 (tt0) REVERT: D 281 ASP cc_start: 0.8225 (p0) cc_final: 0.7650 (t0) REVERT: D 287 LEU cc_start: 0.5093 (OUTLIER) cc_final: 0.4869 (mp) outliers start: 56 outliers final: 34 residues processed: 587 average time/residue: 0.2640 time to fit residues: 229.5280 Evaluate side-chains 561 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 520 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 44 TRP Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 143 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 370 ASN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 568 HIS ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.130342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.091050 restraints weight = 34392.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.094248 restraints weight = 17023.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.096304 restraints weight = 10442.344| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.6073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16299 Z= 0.227 Angle : 0.681 13.318 22004 Z= 0.358 Chirality : 0.044 0.199 2348 Planarity : 0.004 0.050 2812 Dihedral : 8.843 150.641 2216 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.97 % Allowed : 24.15 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.19), residues: 1928 helix: 1.04 (0.15), residues: 1139 sheet: -0.63 (0.39), residues: 150 loop : 0.34 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP D 124 HIS 0.006 0.001 HIS C 201 PHE 0.040 0.002 PHE C 168 TYR 0.022 0.002 TYR C 22 ARG 0.012 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 896) hydrogen bonds : angle 5.20980 ( 2616) covalent geometry : bond 0.00505 (16298) covalent geometry : angle 0.68141 (22004) Misc. bond : bond 0.00074 ( 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 593 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 525 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8923 (t0) cc_final: 0.8641 (t0) REVERT: A 286 ASP cc_start: 0.8695 (m-30) cc_final: 0.8290 (p0) REVERT: A 312 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8121 (pt0) REVERT: A 355 TYR cc_start: 0.8200 (m-80) cc_final: 0.7989 (m-10) REVERT: A 383 SER cc_start: 0.9134 (OUTLIER) cc_final: 0.8678 (t) REVERT: A 485 ARG cc_start: 0.8307 (mtm-85) cc_final: 0.7662 (mtt90) REVERT: A 493 MET cc_start: 0.8956 (tmm) cc_final: 0.8503 (tmm) REVERT: A 599 GLU cc_start: 0.8379 (mp0) cc_final: 0.7926 (mp0) REVERT: A 683 TYR cc_start: 0.8359 (t80) cc_final: 0.8090 (t80) REVERT: A 684 TYR cc_start: 0.7990 (OUTLIER) cc_final: 0.7215 (m-80) REVERT: B 31 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8604 (pm20) REVERT: B 65 GLU cc_start: 0.8552 (mp0) cc_final: 0.8290 (mp0) REVERT: B 89 PHE cc_start: 0.8946 (t80) cc_final: 0.8654 (t80) REVERT: B 200 SER cc_start: 0.9019 (t) cc_final: 0.8388 (t) REVERT: B 228 LYS cc_start: 0.9011 (mmmt) cc_final: 0.8341 (tppt) REVERT: B 250 TYR cc_start: 0.9255 (m-80) cc_final: 0.8217 (m-80) REVERT: B 290 GLU cc_start: 0.8626 (pp20) cc_final: 0.8322 (pp20) REVERT: B 348 MET cc_start: 0.7776 (tpp) cc_final: 0.7546 (tpp) REVERT: B 379 SER cc_start: 0.8843 (t) cc_final: 0.8033 (t) REVERT: B 394 TYR cc_start: 0.9046 (m-80) cc_final: 0.8666 (m-80) REVERT: B 515 ASP cc_start: 0.9008 (m-30) cc_final: 0.8737 (m-30) REVERT: B 586 TYR cc_start: 0.8779 (m-80) cc_final: 0.8576 (m-80) REVERT: B 590 SER cc_start: 0.9272 (OUTLIER) cc_final: 0.8784 (t) REVERT: B 599 GLU cc_start: 0.8246 (pt0) cc_final: 0.7835 (pt0) REVERT: B 636 LYS cc_start: 0.9396 (mmtm) cc_final: 0.8991 (mmtp) REVERT: B 639 ASP cc_start: 0.8601 (m-30) cc_final: 0.7775 (m-30) REVERT: B 640 MET cc_start: 0.9080 (tpp) cc_final: 0.8772 (tpp) REVERT: B 686 ARG cc_start: 0.8425 (ttm-80) cc_final: 0.7952 (mtm-85) REVERT: C 172 PHE cc_start: 0.7842 (m-10) cc_final: 0.7426 (m-10) REVERT: C 178 PHE cc_start: 0.8421 (m-10) cc_final: 0.7886 (m-10) REVERT: C 179 TYR cc_start: 0.8606 (t80) cc_final: 0.8205 (t80) REVERT: C 210 GLN cc_start: 0.5298 (tp40) cc_final: 0.5093 (tp40) REVERT: C 218 GLU cc_start: 0.9297 (mp0) cc_final: 0.8774 (pp20) REVERT: C 269 MET cc_start: 0.8281 (tmm) cc_final: 0.8027 (ptt) REVERT: D 18 THR cc_start: 0.6677 (p) cc_final: 0.6216 (p) REVERT: D 46 TYR cc_start: 0.8792 (m-10) cc_final: 0.8421 (m-80) REVERT: D 149 ASP cc_start: 0.7722 (t0) cc_final: 0.7403 (t0) REVERT: D 174 TYR cc_start: 0.4761 (t80) cc_final: 0.4230 (t80) REVERT: D 179 TYR cc_start: 0.8297 (t80) cc_final: 0.7943 (t80) REVERT: D 204 TYR cc_start: 0.8941 (t80) cc_final: 0.8515 (t80) REVERT: D 211 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8653 (tt0) REVERT: D 235 LEU cc_start: 0.8934 (mt) cc_final: 0.8716 (pp) REVERT: D 287 LEU cc_start: 0.4826 (OUTLIER) cc_final: 0.4400 (mt) outliers start: 68 outliers final: 48 residues processed: 560 average time/residue: 0.2669 time to fit residues: 221.1010 Evaluate side-chains 546 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 492 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 44 TRP Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 7 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 133 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 185 optimal weight: 10.0000 chunk 34 optimal weight: 0.3980 chunk 52 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 370 ASN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 HIS ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN D 201 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.135770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.096562 restraints weight = 34864.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.099951 restraints weight = 17246.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.102194 restraints weight = 10451.895| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.6302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16299 Z= 0.140 Angle : 0.668 14.994 22004 Z= 0.346 Chirality : 0.043 0.290 2348 Planarity : 0.004 0.058 2812 Dihedral : 8.591 146.714 2216 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.33 % Allowed : 27.07 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.19), residues: 1928 helix: 1.06 (0.15), residues: 1124 sheet: -0.46 (0.39), residues: 134 loop : 0.16 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 124 HIS 0.005 0.001 HIS D 201 PHE 0.038 0.002 PHE C 168 TYR 0.020 0.001 TYR A 612 ARG 0.012 0.001 ARG B 274 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 896) hydrogen bonds : angle 5.16084 ( 2616) covalent geometry : bond 0.00316 (16298) covalent geometry : angle 0.66777 (22004) Misc. bond : bond 0.00065 ( 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 575 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 535 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 ARG cc_start: 0.7610 (ptt90) cc_final: 0.6987 (ptt90) REVERT: A 166 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7617 (mm-30) REVERT: A 218 ASN cc_start: 0.8884 (t0) cc_final: 0.8628 (t0) REVERT: A 375 LYS cc_start: 0.9248 (mmtm) cc_final: 0.8847 (mmtm) REVERT: A 383 SER cc_start: 0.9153 (OUTLIER) cc_final: 0.8695 (t) REVERT: A 493 MET cc_start: 0.9014 (tmm) cc_final: 0.8333 (tmm) REVERT: A 599 GLU cc_start: 0.8416 (mp0) cc_final: 0.7879 (mp0) REVERT: A 668 ASN cc_start: 0.8805 (m110) cc_final: 0.8504 (m110) REVERT: A 684 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.7548 (m-80) REVERT: B 31 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8599 (pm20) REVERT: B 65 GLU cc_start: 0.8584 (mp0) cc_final: 0.8305 (mp0) REVERT: B 116 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8026 (mt-10) REVERT: B 200 SER cc_start: 0.8999 (t) cc_final: 0.8281 (t) REVERT: B 228 LYS cc_start: 0.8986 (mmmt) cc_final: 0.8362 (mmtt) REVERT: B 250 TYR cc_start: 0.9217 (m-80) cc_final: 0.8247 (m-80) REVERT: B 290 GLU cc_start: 0.8558 (pp20) cc_final: 0.8269 (pp20) REVERT: B 322 MET cc_start: 0.9085 (mmp) cc_final: 0.8856 (mmt) REVERT: B 344 GLU cc_start: 0.8652 (tt0) cc_final: 0.8447 (tp30) REVERT: B 379 SER cc_start: 0.8818 (t) cc_final: 0.7987 (t) REVERT: B 394 TYR cc_start: 0.9021 (m-80) cc_final: 0.8650 (m-80) REVERT: B 467 ASN cc_start: 0.9042 (t0) cc_final: 0.8480 (t0) REVERT: B 471 TYR cc_start: 0.8564 (t80) cc_final: 0.7827 (t80) REVERT: B 494 MET cc_start: 0.8972 (mtp) cc_final: 0.8721 (mtp) REVERT: B 515 ASP cc_start: 0.8982 (m-30) cc_final: 0.8721 (m-30) REVERT: B 546 LEU cc_start: 0.9141 (mm) cc_final: 0.8852 (tt) REVERT: B 586 TYR cc_start: 0.8836 (m-80) cc_final: 0.8175 (m-80) REVERT: B 590 SER cc_start: 0.9141 (OUTLIER) cc_final: 0.8753 (t) REVERT: B 599 GLU cc_start: 0.8206 (pt0) cc_final: 0.7906 (pt0) REVERT: B 664 THR cc_start: 0.8888 (p) cc_final: 0.8418 (p) REVERT: B 677 ARG cc_start: 0.8860 (mmm-85) cc_final: 0.8166 (ttm-80) REVERT: B 686 ARG cc_start: 0.8327 (ttm-80) cc_final: 0.7980 (mtm-85) REVERT: C 172 PHE cc_start: 0.7809 (m-10) cc_final: 0.7347 (m-10) REVERT: C 178 PHE cc_start: 0.8435 (m-10) cc_final: 0.7964 (m-10) REVERT: C 179 TYR cc_start: 0.8548 (t80) cc_final: 0.8180 (t80) REVERT: C 181 GLN cc_start: 0.8120 (mm110) cc_final: 0.7887 (mm-40) REVERT: D 18 THR cc_start: 0.6665 (p) cc_final: 0.6365 (p) REVERT: D 20 MET cc_start: 0.8845 (ppp) cc_final: 0.8643 (ppp) REVERT: D 46 TYR cc_start: 0.8783 (m-10) cc_final: 0.8382 (m-80) REVERT: D 137 MET cc_start: 0.8374 (mmp) cc_final: 0.7629 (mtp) REVERT: D 149 ASP cc_start: 0.7718 (t0) cc_final: 0.7482 (t0) REVERT: D 174 TYR cc_start: 0.4642 (t80) cc_final: 0.4270 (t80) REVERT: D 179 TYR cc_start: 0.8378 (t80) cc_final: 0.7982 (t80) REVERT: D 204 TYR cc_start: 0.8882 (t80) cc_final: 0.8387 (t80) REVERT: D 211 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8634 (tt0) REVERT: D 263 ASN cc_start: 0.7275 (m-40) cc_final: 0.6790 (p0) REVERT: D 281 ASP cc_start: 0.8097 (p0) cc_final: 0.7408 (t70) REVERT: D 287 LEU cc_start: 0.5160 (OUTLIER) cc_final: 0.4739 (mt) outliers start: 40 outliers final: 23 residues processed: 555 average time/residue: 0.2891 time to fit residues: 234.9302 Evaluate side-chains 533 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 505 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 146 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.133427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.094235 restraints weight = 34582.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.097625 restraints weight = 17336.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.099807 restraints weight = 10488.533| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.6519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16299 Z= 0.159 Angle : 0.680 17.624 22004 Z= 0.351 Chirality : 0.044 0.361 2348 Planarity : 0.004 0.047 2812 Dihedral : 8.532 143.811 2216 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.63 % Allowed : 27.71 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.19), residues: 1928 helix: 1.04 (0.15), residues: 1128 sheet: -0.45 (0.41), residues: 134 loop : 0.14 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP C 30 HIS 0.005 0.001 HIS C 201 PHE 0.039 0.002 PHE B 89 TYR 0.021 0.001 TYR B 149 ARG 0.006 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 896) hydrogen bonds : angle 5.13630 ( 2616) covalent geometry : bond 0.00362 (16298) covalent geometry : angle 0.68032 (22004) Misc. bond : bond 0.00068 ( 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 573 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 528 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8495 (mp0) REVERT: A 164 ARG cc_start: 0.7616 (ptt90) cc_final: 0.7079 (ptt90) REVERT: A 166 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7660 (mm-30) REVERT: A 218 ASN cc_start: 0.8911 (t0) cc_final: 0.8668 (t0) REVERT: A 312 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.7959 (pt0) REVERT: A 375 LYS cc_start: 0.9246 (mmtm) cc_final: 0.8837 (mmtm) REVERT: A 383 SER cc_start: 0.9054 (OUTLIER) cc_final: 0.8709 (t) REVERT: A 493 MET cc_start: 0.8943 (tmm) cc_final: 0.8652 (tmm) REVERT: A 599 GLU cc_start: 0.8381 (mp0) cc_final: 0.7851 (mp0) REVERT: A 668 ASN cc_start: 0.8813 (m-40) cc_final: 0.8518 (m110) REVERT: B 31 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8629 (pm20) REVERT: B 65 GLU cc_start: 0.8529 (mp0) cc_final: 0.8252 (mp0) REVERT: B 106 LEU cc_start: 0.9045 (tp) cc_final: 0.8781 (tt) REVERT: B 116 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8054 (mt-10) REVERT: B 200 SER cc_start: 0.8955 (t) cc_final: 0.8332 (t) REVERT: B 228 LYS cc_start: 0.8997 (mmmt) cc_final: 0.8341 (mmtt) REVERT: B 250 TYR cc_start: 0.9229 (m-80) cc_final: 0.8329 (m-80) REVERT: B 290 GLU cc_start: 0.8619 (pp20) cc_final: 0.8309 (pp20) REVERT: B 322 MET cc_start: 0.9070 (mmp) cc_final: 0.8852 (mmt) REVERT: B 379 SER cc_start: 0.8914 (t) cc_final: 0.7944 (t) REVERT: B 394 TYR cc_start: 0.8990 (m-80) cc_final: 0.8621 (m-80) REVERT: B 399 GLU cc_start: 0.8110 (mp0) cc_final: 0.7822 (mp0) REVERT: B 467 ASN cc_start: 0.9073 (t0) cc_final: 0.8492 (t0) REVERT: B 494 MET cc_start: 0.9034 (mtp) cc_final: 0.8824 (mtp) REVERT: B 515 ASP cc_start: 0.9003 (m-30) cc_final: 0.8709 (m-30) REVERT: B 548 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8115 (mm-30) REVERT: B 590 SER cc_start: 0.9095 (OUTLIER) cc_final: 0.8712 (t) REVERT: B 599 GLU cc_start: 0.8279 (pt0) cc_final: 0.7931 (pt0) REVERT: B 640 MET cc_start: 0.9187 (tpp) cc_final: 0.8889 (tpp) REVERT: B 672 LEU cc_start: 0.9351 (mt) cc_final: 0.9131 (mt) REVERT: B 677 ARG cc_start: 0.8826 (mmm-85) cc_final: 0.8086 (ttm-80) REVERT: B 686 ARG cc_start: 0.8338 (ttm-80) cc_final: 0.7946 (mtm-85) REVERT: C 24 GLN cc_start: 0.8595 (mt0) cc_final: 0.8357 (mp10) REVERT: C 172 PHE cc_start: 0.7878 (m-10) cc_final: 0.7409 (m-80) REVERT: C 178 PHE cc_start: 0.8457 (m-10) cc_final: 0.8022 (m-10) REVERT: C 179 TYR cc_start: 0.8631 (t80) cc_final: 0.8258 (t80) REVERT: D 18 THR cc_start: 0.6735 (p) cc_final: 0.6391 (p) REVERT: D 20 MET cc_start: 0.8835 (ppp) cc_final: 0.8613 (ppp) REVERT: D 46 TYR cc_start: 0.8803 (m-10) cc_final: 0.8404 (m-80) REVERT: D 74 MET cc_start: 0.5776 (OUTLIER) cc_final: 0.4431 (tmm) REVERT: D 131 LEU cc_start: 0.8553 (tt) cc_final: 0.8313 (mt) REVERT: D 137 MET cc_start: 0.8457 (mmp) cc_final: 0.7767 (mtp) REVERT: D 142 TYR cc_start: 0.8244 (m-80) cc_final: 0.7921 (t80) REVERT: D 149 ASP cc_start: 0.7761 (t0) cc_final: 0.7537 (t0) REVERT: D 174 TYR cc_start: 0.4817 (t80) cc_final: 0.4599 (t80) REVERT: D 179 TYR cc_start: 0.8376 (t80) cc_final: 0.7987 (t80) REVERT: D 204 TYR cc_start: 0.8901 (t80) cc_final: 0.8419 (t80) REVERT: D 211 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8601 (tt0) REVERT: D 252 LEU cc_start: 0.7080 (mm) cc_final: 0.6698 (mm) REVERT: D 263 ASN cc_start: 0.7502 (m-40) cc_final: 0.7004 (p0) outliers start: 45 outliers final: 31 residues processed: 549 average time/residue: 0.2637 time to fit residues: 214.0625 Evaluate side-chains 521 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 485 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 140 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 162 optimal weight: 20.0000 chunk 168 optimal weight: 20.0000 chunk 16 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN C 28 GLN C 52 GLN C 216 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.131951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.091585 restraints weight = 34975.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.094849 restraints weight = 17763.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.096942 restraints weight = 11071.122| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.6710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 16299 Z= 0.269 Angle : 0.759 21.241 22004 Z= 0.392 Chirality : 0.047 0.401 2348 Planarity : 0.004 0.047 2812 Dihedral : 8.842 145.596 2216 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.86 % Allowed : 28.18 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.19), residues: 1928 helix: 0.88 (0.15), residues: 1126 sheet: -1.03 (0.39), residues: 156 loop : 0.12 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP C 30 HIS 0.006 0.001 HIS A 438 PHE 0.036 0.002 PHE C 168 TYR 0.038 0.002 TYR B 471 ARG 0.008 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04291 ( 896) hydrogen bonds : angle 5.27280 ( 2616) covalent geometry : bond 0.00599 (16298) covalent geometry : angle 0.75910 (22004) Misc. bond : bond 0.00108 ( 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 536 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 487 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8989 (t0) cc_final: 0.8736 (t0) REVERT: A 312 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.7866 (pt0) REVERT: A 383 SER cc_start: 0.9065 (OUTLIER) cc_final: 0.8684 (t) REVERT: A 493 MET cc_start: 0.8919 (tmm) cc_final: 0.8551 (tmm) REVERT: A 599 GLU cc_start: 0.8298 (mp0) cc_final: 0.7876 (mp0) REVERT: A 684 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.7490 (m-80) REVERT: B 65 GLU cc_start: 0.8595 (mp0) cc_final: 0.8304 (mp0) REVERT: B 116 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8028 (mt-10) REVERT: B 200 SER cc_start: 0.8950 (t) cc_final: 0.8319 (t) REVERT: B 228 LYS cc_start: 0.9056 (mmmt) cc_final: 0.8385 (tppt) REVERT: B 250 TYR cc_start: 0.9255 (m-80) cc_final: 0.8291 (m-80) REVERT: B 370 ASN cc_start: 0.9198 (m-40) cc_final: 0.8979 (m-40) REVERT: B 379 SER cc_start: 0.8846 (t) cc_final: 0.7903 (t) REVERT: B 394 TYR cc_start: 0.9045 (m-80) cc_final: 0.8573 (m-80) REVERT: B 399 GLU cc_start: 0.8090 (mp0) cc_final: 0.7844 (mp0) REVERT: B 515 ASP cc_start: 0.9042 (m-30) cc_final: 0.8742 (m-30) REVERT: B 586 TYR cc_start: 0.8921 (m-80) cc_final: 0.8363 (m-80) REVERT: B 590 SER cc_start: 0.9196 (OUTLIER) cc_final: 0.8804 (t) REVERT: B 599 GLU cc_start: 0.8400 (pt0) cc_final: 0.8113 (pt0) REVERT: B 640 MET cc_start: 0.9087 (tpp) cc_final: 0.8782 (tpp) REVERT: B 686 ARG cc_start: 0.8374 (ttm-80) cc_final: 0.7956 (mtm-85) REVERT: C 24 GLN cc_start: 0.8707 (mt0) cc_final: 0.8427 (mp10) REVERT: C 137 MET cc_start: 0.4040 (mmm) cc_final: 0.3806 (mpp) REVERT: C 172 PHE cc_start: 0.7909 (m-10) cc_final: 0.7505 (m-80) REVERT: C 178 PHE cc_start: 0.8476 (m-10) cc_final: 0.8055 (m-10) REVERT: C 179 TYR cc_start: 0.8812 (t80) cc_final: 0.8469 (t80) REVERT: C 210 GLN cc_start: 0.5271 (tp40) cc_final: 0.4994 (tp-100) REVERT: D 18 THR cc_start: 0.6801 (p) cc_final: 0.6480 (p) REVERT: D 20 MET cc_start: 0.8863 (ppp) cc_final: 0.8651 (ppp) REVERT: D 74 MET cc_start: 0.6104 (OUTLIER) cc_final: 0.5734 (tmm) REVERT: D 137 MET cc_start: 0.8631 (mmp) cc_final: 0.8101 (mtp) REVERT: D 149 ASP cc_start: 0.7902 (t0) cc_final: 0.7638 (t0) REVERT: D 179 TYR cc_start: 0.8341 (t80) cc_final: 0.7682 (t80) REVERT: D 189 GLU cc_start: 0.8829 (tp30) cc_final: 0.7840 (mt-10) REVERT: D 196 ARG cc_start: 0.8922 (mmm160) cc_final: 0.8560 (tpt90) REVERT: D 204 TYR cc_start: 0.8984 (t80) cc_final: 0.8540 (t80) outliers start: 49 outliers final: 38 residues processed: 508 average time/residue: 0.2768 time to fit residues: 208.0893 Evaluate side-chains 521 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 478 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 44 TRP Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 311 THR 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: 0.8980 chunk 51 optimal weight: 7.9990 chunk 165 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 164 optimal weight: 8.9990 chunk 190 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.133655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.094473 restraints weight = 34821.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.097828 restraints weight = 17411.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.100025 restraints weight = 10608.957| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.6867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16299 Z= 0.183 Angle : 0.745 21.855 22004 Z= 0.382 Chirality : 0.046 0.400 2348 Planarity : 0.004 0.047 2812 Dihedral : 8.691 143.765 2216 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.28 % Allowed : 29.23 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.19), residues: 1928 helix: 0.87 (0.15), residues: 1122 sheet: -0.69 (0.41), residues: 138 loop : -0.04 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP C 30 HIS 0.005 0.001 HIS C 201 PHE 0.036 0.002 PHE A 128 TYR 0.042 0.002 TYR C 142 ARG 0.007 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 896) hydrogen bonds : angle 5.22774 ( 2616) covalent geometry : bond 0.00418 (16298) covalent geometry : angle 0.74549 (22004) Misc. bond : bond 0.00092 ( 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 525 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 486 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8950 (t0) cc_final: 0.8722 (t0) REVERT: A 312 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8149 (pt0) REVERT: A 383 SER cc_start: 0.9019 (OUTLIER) cc_final: 0.8665 (t) REVERT: A 493 MET cc_start: 0.8900 (tmm) cc_final: 0.8639 (tmm) REVERT: A 599 GLU cc_start: 0.8327 (mp0) cc_final: 0.7878 (mp0) REVERT: A 668 ASN cc_start: 0.9044 (m110) cc_final: 0.8821 (m110) REVERT: A 684 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.7544 (m-80) REVERT: B 65 GLU cc_start: 0.8603 (mp0) cc_final: 0.8322 (mp0) REVERT: B 116 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8128 (mt-10) REVERT: B 200 SER cc_start: 0.8941 (t) cc_final: 0.8330 (t) REVERT: B 250 TYR cc_start: 0.9207 (m-80) cc_final: 0.8394 (m-80) REVERT: B 379 SER cc_start: 0.8815 (t) cc_final: 0.7855 (t) REVERT: B 399 GLU cc_start: 0.8173 (mp0) cc_final: 0.7916 (mp0) REVERT: B 467 ASN cc_start: 0.9126 (t0) cc_final: 0.8544 (t0) REVERT: B 515 ASP cc_start: 0.9012 (m-30) cc_final: 0.8648 (m-30) REVERT: B 546 LEU cc_start: 0.9251 (mm) cc_final: 0.8986 (tt) REVERT: B 586 TYR cc_start: 0.8904 (m-80) cc_final: 0.8408 (m-80) REVERT: B 590 SER cc_start: 0.9042 (OUTLIER) cc_final: 0.8766 (t) REVERT: B 599 GLU cc_start: 0.8364 (pt0) cc_final: 0.8047 (pt0) REVERT: B 627 LYS cc_start: 0.9147 (tttp) cc_final: 0.8809 (tttp) REVERT: B 640 MET cc_start: 0.9137 (tpp) cc_final: 0.8868 (tpp) REVERT: B 646 GLN cc_start: 0.9125 (pt0) cc_final: 0.8812 (pm20) REVERT: B 686 ARG cc_start: 0.8362 (ttm-80) cc_final: 0.7930 (mtm-85) REVERT: C 23 ASN cc_start: 0.8965 (t0) cc_final: 0.8730 (t0) REVERT: C 24 GLN cc_start: 0.8680 (mt0) cc_final: 0.8370 (mp10) REVERT: C 172 PHE cc_start: 0.7887 (m-10) cc_final: 0.7460 (m-80) REVERT: C 178 PHE cc_start: 0.8473 (m-10) cc_final: 0.8060 (m-10) REVERT: C 179 TYR cc_start: 0.8816 (t80) cc_final: 0.8463 (t80) REVERT: C 269 MET cc_start: 0.8207 (tmm) cc_final: 0.7938 (ppp) REVERT: D 18 THR cc_start: 0.6884 (p) cc_final: 0.6618 (p) REVERT: D 20 MET cc_start: 0.8912 (ppp) cc_final: 0.8677 (ppp) REVERT: D 46 TYR cc_start: 0.8782 (m-10) cc_final: 0.8403 (m-80) REVERT: D 137 MET cc_start: 0.8712 (mmp) cc_final: 0.8166 (mtp) REVERT: D 149 ASP cc_start: 0.7919 (t0) cc_final: 0.7682 (t0) REVERT: D 204 TYR cc_start: 0.8934 (t80) cc_final: 0.8471 (t80) REVERT: D 263 ASN cc_start: 0.7429 (m-40) cc_final: 0.7120 (p0) outliers start: 39 outliers final: 28 residues processed: 500 average time/residue: 0.2695 time to fit residues: 199.8106 Evaluate side-chains 500 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 468 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 456 LYS Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 597 ILE Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 113 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 186 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 140 optimal weight: 10.0000 chunk 168 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN D 238 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.136162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.097193 restraints weight = 34627.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.100642 restraints weight = 17285.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.102905 restraints weight = 10532.323| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.7023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16299 Z= 0.149 Angle : 0.743 20.995 22004 Z= 0.379 Chirality : 0.045 0.414 2348 Planarity : 0.004 0.047 2812 Dihedral : 8.500 142.049 2216 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.98 % Allowed : 29.99 % Favored : 68.03 % 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: 0.57 (0.18), residues: 1928 helix: 0.90 (0.15), residues: 1117 sheet: -0.75 (0.41), residues: 134 loop : -0.07 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP C 30 HIS 0.005 0.001 HIS A 255 PHE 0.035 0.002 PHE A 128 TYR 0.029 0.001 TYR B 471 ARG 0.006 0.001 ARG B 274 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 896) hydrogen bonds : angle 5.20173 ( 2616) covalent geometry : bond 0.00341 (16298) covalent geometry : angle 0.74301 (22004) Misc. bond : bond 0.00072 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6134.74 seconds wall clock time: 108 minutes 18.57 seconds (6498.57 seconds total)