Starting phenix.real_space_refine on Sat Jun 14 05:40:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bx3_44992/06_2025/9bx3_44992_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bx3_44992/06_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_44992/06_2025/9bx3_44992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bx3_44992/06_2025/9bx3_44992.map" model { file = "/net/cci-nas-00/data/ceres_data/9bx3_44992/06_2025/9bx3_44992_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bx3_44992/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15954 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {' MG': 1, 'ATP': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 9.93, per 1000 atoms: 0.62 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: 4.69 Conformation dependent library (CDL) restraints added in 2.2 seconds 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3688 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 10 sheets defined 64.3% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 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: 5.96 Time building geometry restraints manager: 5.51 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 40.150 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.590 ------------------------------------------------------------------------------- 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 : 1.792 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: 0.3055 time to fit residues: 381.7433 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 : 1.924 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.137350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.095384 restraints weight = 33172.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.098875 restraints weight = 16603.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.101093 restraints weight = 10156.003| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 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 = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 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 : 1.896 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: 0.9262 (mp) cc_final: 0.8514 (mp) REVERT: A 179 LEU cc_start: 0.9429 (tp) cc_final: 0.9217 (tp) REVERT: A 204 SER cc_start: 0.9080 (m) cc_final: 0.8835 (p) REVERT: A 218 ASN cc_start: 0.8522 (t0) cc_final: 0.8233 (t0) REVERT: A 315 ASP cc_start: 0.8096 (p0) cc_final: 0.7780 (p0) REVERT: A 316 GLU cc_start: 0.8193 (tt0) cc_final: 0.7699 (tm-30) REVERT: A 317 MET cc_start: 0.8991 (mtp) cc_final: 0.8743 (mtm) REVERT: A 355 TYR cc_start: 0.8308 (m-80) cc_final: 0.8103 (m-10) REVERT: A 383 SER cc_start: 0.9175 (OUTLIER) cc_final: 0.8480 (t) REVERT: A 406 ASP cc_start: 0.8017 (m-30) cc_final: 0.7371 (t0) REVERT: A 485 ARG cc_start: 0.8223 (mtm-85) cc_final: 0.7724 (mtt90) REVERT: A 493 MET cc_start: 0.8921 (tmm) cc_final: 0.8626 (tmm) REVERT: A 526 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8028 (mm-30) REVERT: A 550 MET cc_start: 0.7773 (mtp) cc_final: 0.7356 (mtp) REVERT: A 603 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7687 (tm-30) REVERT: A 604 ARG cc_start: 0.8546 (tpp80) cc_final: 0.8233 (mmp80) REVERT: A 662 MET cc_start: 0.8456 (mmp) cc_final: 0.8111 (mmp) REVERT: B 27 ASP cc_start: 0.8781 (p0) cc_final: 0.8490 (p0) REVERT: B 31 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8651 (pm20) REVERT: B 109 ASN cc_start: 0.9083 (OUTLIER) cc_final: 0.8727 (m110) REVERT: B 161 ARG cc_start: 0.7924 (mtt180) cc_final: 0.7592 (mtt180) REVERT: B 200 SER cc_start: 0.8980 (t) cc_final: 0.8319 (t) REVERT: B 232 ASN cc_start: 0.8975 (t0) cc_final: 0.8444 (m-40) REVERT: B 246 SER cc_start: 0.7730 (m) cc_final: 0.7290 (p) REVERT: B 250 TYR cc_start: 0.9265 (m-80) cc_final: 0.8095 (m-80) REVERT: B 288 PHE cc_start: 0.9300 (t80) cc_final: 0.9027 (t80) REVERT: B 379 SER cc_start: 0.8865 (t) cc_final: 0.8105 (t) REVERT: B 466 MET cc_start: 0.9093 (ptt) cc_final: 0.8837 (ptm) REVERT: B 480 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8244 (mt-10) REVERT: B 586 TYR cc_start: 0.8525 (m-80) cc_final: 0.8127 (m-80) REVERT: B 599 GLU cc_start: 0.8158 (pt0) cc_final: 0.7891 (pt0) REVERT: B 601 ILE cc_start: 0.9151 (mm) cc_final: 0.8452 (mm) REVERT: B 602 GLU cc_start: 0.8256 (tt0) cc_final: 0.7517 (tt0) REVERT: B 604 ARG cc_start: 0.8983 (mmp80) cc_final: 0.8209 (tpp-160) REVERT: B 626 TYR cc_start: 0.8515 (m-80) cc_final: 0.8294 (m-80) REVERT: B 640 MET cc_start: 0.9117 (tpp) cc_final: 0.8636 (tpp) REVERT: B 667 LEU cc_start: 0.9025 (tt) cc_final: 0.8455 (tt) REVERT: C 23 ASN cc_start: 0.8797 (t0) cc_final: 0.8319 (t0) REVERT: C 24 GLN cc_start: 0.8335 (mt0) cc_final: 0.7948 (mm-40) REVERT: C 178 PHE cc_start: 0.8287 (m-80) cc_final: 0.7656 (m-10) REVERT: C 193 LEU cc_start: 0.8218 (mm) cc_final: 0.7945 (mm) REVERT: C 218 GLU cc_start: 0.9352 (mp0) cc_final: 0.8729 (pp20) REVERT: D 20 MET cc_start: 0.8907 (ptm) cc_final: 0.8643 (ptp) REVERT: D 56 MET cc_start: 0.3145 (mmp) cc_final: 0.2718 (mtt) REVERT: D 131 LEU cc_start: 0.8217 (tt) cc_final: 0.7375 (tt) REVERT: D 174 TYR cc_start: 0.4260 (t80) cc_final: 0.3648 (t80) REVERT: D 189 GLU cc_start: 0.8554 (tp30) cc_final: 0.8001 (mt-10) REVERT: D 204 TYR cc_start: 0.8851 (t80) cc_final: 0.8419 (t80) REVERT: D 212 ILE cc_start: 0.8219 (mt) cc_final: 0.7670 (mt) REVERT: D 216 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7633 (mm110) outliers start: 53 outliers final: 20 residues processed: 679 average time/residue: 0.2870 time to fit residues: 282.6496 Evaluate side-chains 568 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 545 time to evaluate : 2.009 ------------------------------------------------------------------------------- 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: 6.9990 chunk 52 optimal weight: 0.0370 chunk 175 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 121 optimal weight: 0.0370 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.138155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.097708 restraints weight = 33400.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.101164 restraints weight = 16114.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.103439 restraints weight = 9584.662| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16299 Z= 0.137 Angle : 0.635 12.164 22004 Z= 0.334 Chirality : 0.043 0.154 2348 Planarity : 0.004 0.051 2812 Dihedral : 8.672 157.085 2219 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.51 % Allowed : 22.17 % 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: 1.38 (0.19), residues: 1928 helix: 1.35 (0.15), residues: 1136 sheet: 0.63 (0.39), residues: 116 loop : 0.42 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 30 HIS 0.004 0.001 HIS B 255 PHE 0.047 0.002 PHE C 168 TYR 0.029 0.001 TYR C 22 ARG 0.007 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 896) hydrogen bonds : angle 5.12216 ( 2616) covalent geometry : bond 0.00298 (16298) covalent geometry : angle 0.63504 (22004) Misc. bond : bond 0.00104 ( 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 654 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 611 time to evaluate : 2.054 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 172 LEU cc_start: 0.9230 (mp) cc_final: 0.8887 (mp) REVERT: A 218 ASN cc_start: 0.8582 (t0) cc_final: 0.8244 (t0) REVERT: A 355 TYR cc_start: 0.8321 (m-80) cc_final: 0.8076 (m-10) REVERT: A 406 ASP cc_start: 0.8022 (m-30) cc_final: 0.7575 (m-30) REVERT: A 485 ARG cc_start: 0.8223 (mtm-85) cc_final: 0.7873 (mtt90) REVERT: A 493 MET cc_start: 0.8952 (tmm) cc_final: 0.8528 (tmm) REVERT: A 599 GLU cc_start: 0.8498 (mp0) cc_final: 0.8086 (mp0) REVERT: A 612 TYR cc_start: 0.8976 (m-80) cc_final: 0.8630 (m-80) REVERT: A 662 MET cc_start: 0.8513 (mmp) cc_final: 0.8286 (mmp) REVERT: A 683 TYR cc_start: 0.8232 (t80) cc_final: 0.7918 (t80) REVERT: B 27 ASP cc_start: 0.8791 (p0) cc_final: 0.8588 (p0) REVERT: B 28 LYS cc_start: 0.9231 (mmtm) cc_final: 0.8722 (mmmm) REVERT: B 31 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8560 (pm20) REVERT: B 200 SER cc_start: 0.8952 (t) cc_final: 0.8077 (t) REVERT: B 232 ASN cc_start: 0.8943 (OUTLIER) cc_final: 0.8475 (m-40) REVERT: B 246 SER cc_start: 0.7600 (m) cc_final: 0.7224 (p) REVERT: B 250 TYR cc_start: 0.9230 (m-80) cc_final: 0.8082 (m-80) REVERT: B 276 LYS cc_start: 0.8882 (mtmm) cc_final: 0.8528 (mtmm) REVERT: B 288 PHE cc_start: 0.9193 (t80) cc_final: 0.8808 (t80) REVERT: B 379 SER cc_start: 0.8799 (t) cc_final: 0.7883 (t) REVERT: B 494 MET cc_start: 0.9004 (mtp) cc_final: 0.8764 (mtp) REVERT: B 601 ILE cc_start: 0.9195 (mm) cc_final: 0.8421 (mm) REVERT: B 604 ARG cc_start: 0.8942 (mmp80) cc_final: 0.8267 (mmp80) REVERT: B 628 GLU cc_start: 0.7509 (mp0) cc_final: 0.7303 (mp0) REVERT: B 640 MET cc_start: 0.9085 (tpp) cc_final: 0.8475 (tpp) REVERT: B 670 ILE cc_start: 0.9280 (mm) cc_final: 0.9053 (mt) REVERT: C 157 MET cc_start: 0.7651 (mtp) cc_final: 0.7267 (ttt) REVERT: C 172 PHE cc_start: 0.7636 (m-10) cc_final: 0.7365 (m-10) REVERT: C 178 PHE cc_start: 0.8232 (m-80) cc_final: 0.7574 (m-10) REVERT: C 218 GLU cc_start: 0.9389 (mp0) cc_final: 0.9024 (pm20) REVERT: D 18 THR cc_start: 0.6409 (p) cc_final: 0.6169 (p) REVERT: D 46 TYR cc_start: 0.8619 (m-10) cc_final: 0.8202 (m-80) REVERT: D 95 MET cc_start: 0.8893 (tmm) cc_final: 0.8194 (tmm) REVERT: D 103 LYS cc_start: 0.5804 (mptt) cc_final: 0.5558 (tppt) REVERT: D 131 LEU cc_start: 0.8279 (tt) cc_final: 0.8070 (mt) REVERT: D 174 TYR cc_start: 0.4098 (t80) cc_final: 0.3323 (t80) REVERT: D 189 GLU cc_start: 0.8741 (tp30) cc_final: 0.8051 (mt-10) REVERT: D 204 TYR cc_start: 0.8668 (t80) cc_final: 0.8257 (t80) outliers start: 43 outliers final: 18 residues processed: 633 average time/residue: 0.2948 time to fit residues: 274.0164 Evaluate side-chains 575 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 555 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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: 0.8980 chunk 51 optimal weight: 0.0070 chunk 121 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 overall best weight: 1.9602 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.133391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.093203 restraints weight = 34405.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.096383 restraints weight = 17645.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.098327 restraints weight = 10981.164| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16299 Z= 0.186 Angle : 0.641 9.445 22004 Z= 0.338 Chirality : 0.043 0.191 2348 Planarity : 0.004 0.052 2812 Dihedral : 8.727 156.189 2217 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.63 % Allowed : 23.28 % Favored : 74.10 % 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: 1.24 (0.19), residues: 1928 helix: 1.25 (0.15), residues: 1142 sheet: -0.04 (0.40), residues: 138 loop : 0.47 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 30 HIS 0.007 0.001 HIS C 201 PHE 0.043 0.002 PHE C 168 TYR 0.021 0.002 TYR C 22 ARG 0.014 0.001 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 896) hydrogen bonds : angle 5.11176 ( 2616) covalent geometry : bond 0.00416 (16298) covalent geometry : angle 0.64126 (22004) Misc. bond : bond 0.00092 ( 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 617 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 572 time to evaluate : 1.719 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: 0.7798 (ptt90) cc_final: 0.7376 (ptt90) REVERT: A 172 LEU cc_start: 0.9351 (mp) cc_final: 0.9131 (mp) REVERT: A 218 ASN cc_start: 0.8679 (t0) cc_final: 0.8352 (t0) REVERT: A 317 MET cc_start: 0.8990 (mtp) cc_final: 0.8687 (mtm) REVERT: A 322 MET cc_start: 0.8421 (tpp) cc_final: 0.7651 (tpp) REVERT: A 355 TYR cc_start: 0.8294 (m-80) cc_final: 0.8039 (m-10) REVERT: A 383 SER cc_start: 0.9234 (OUTLIER) cc_final: 0.8623 (t) REVERT: A 485 ARG cc_start: 0.8256 (mtm-85) cc_final: 0.7704 (mtt90) REVERT: A 493 MET cc_start: 0.8965 (tmm) cc_final: 0.8704 (tmm) REVERT: A 550 MET cc_start: 0.7651 (mtm) cc_final: 0.7102 (ptp) REVERT: A 599 GLU cc_start: 0.8436 (mp0) cc_final: 0.7927 (mp0) REVERT: A 604 ARG cc_start: 0.8414 (tpp80) cc_final: 0.8174 (mmp80) REVERT: A 606 TYR cc_start: 0.8637 (m-80) cc_final: 0.8429 (m-80) REVERT: A 612 TYR cc_start: 0.9001 (m-80) cc_final: 0.8744 (m-80) REVERT: A 640 MET cc_start: 0.8905 (tpp) cc_final: 0.8598 (tpp) REVERT: A 641 ILE cc_start: 0.9680 (mm) cc_final: 0.9448 (mt) REVERT: A 654 PHE cc_start: 0.8890 (t80) cc_final: 0.8656 (t80) REVERT: A 662 MET cc_start: 0.8568 (mmp) cc_final: 0.8354 (mmp) REVERT: A 665 ARG cc_start: 0.8864 (ttp-170) cc_final: 0.8597 (ptm-80) REVERT: B 89 PHE cc_start: 0.8832 (t80) cc_final: 0.8550 (t80) REVERT: B 200 SER cc_start: 0.8987 (t) cc_final: 0.8134 (t) REVERT: B 246 SER cc_start: 0.7663 (m) cc_final: 0.7426 (p) REVERT: B 250 TYR cc_start: 0.9236 (m-80) cc_final: 0.8088 (m-80) REVERT: B 379 SER cc_start: 0.8846 (t) cc_final: 0.8016 (t) REVERT: B 394 TYR cc_start: 0.9132 (m-80) cc_final: 0.8650 (m-80) REVERT: B 420 MET cc_start: 0.9098 (mmm) cc_final: 0.8875 (mmp) REVERT: B 467 ASN cc_start: 0.9102 (t0) cc_final: 0.8572 (m-40) REVERT: B 471 TYR cc_start: 0.8530 (t80) cc_final: 0.8215 (t80) REVERT: B 494 MET cc_start: 0.9015 (mtp) cc_final: 0.8784 (mtp) REVERT: B 590 SER cc_start: 0.9162 (p) cc_final: 0.8652 (t) REVERT: B 599 GLU cc_start: 0.7899 (pt0) cc_final: 0.7674 (pt0) REVERT: B 601 ILE cc_start: 0.9171 (mm) cc_final: 0.8787 (mm) REVERT: B 639 ASP cc_start: 0.8624 (m-30) cc_final: 0.8086 (m-30) REVERT: B 640 MET cc_start: 0.9077 (tpp) cc_final: 0.8644 (tpp) REVERT: B 686 ARG cc_start: 0.8463 (ttm-80) cc_final: 0.7863 (mtm-85) REVERT: C 30 TRP cc_start: 0.7186 (p-90) cc_final: 0.6884 (p-90) REVERT: C 157 MET cc_start: 0.7595 (mtp) cc_final: 0.7310 (ttm) REVERT: C 168 PHE cc_start: 0.7789 (m-80) cc_final: 0.7562 (m-80) REVERT: C 172 PHE cc_start: 0.7713 (m-10) cc_final: 0.7399 (m-10) REVERT: C 178 PHE cc_start: 0.8291 (m-80) cc_final: 0.7661 (m-10) REVERT: C 179 TYR cc_start: 0.8413 (t80) cc_final: 0.8081 (t80) REVERT: C 181 GLN cc_start: 0.8044 (mm110) cc_final: 0.7810 (mm-40) REVERT: D 18 THR cc_start: 0.6363 (p) cc_final: 0.6019 (p) REVERT: D 46 TYR cc_start: 0.8779 (m-10) cc_final: 0.8349 (m-80) REVERT: D 131 LEU cc_start: 0.8304 (tt) cc_final: 0.7848 (tp) REVERT: D 149 ASP cc_start: 0.7611 (t0) cc_final: 0.7310 (t0) REVERT: D 174 TYR cc_start: 0.4279 (t80) cc_final: 0.3766 (t80) REVERT: D 204 TYR cc_start: 0.8783 (t80) cc_final: 0.8338 (t80) REVERT: D 281 ASP cc_start: 0.8150 (p0) cc_final: 0.7450 (t70) outliers start: 45 outliers final: 33 residues processed: 592 average time/residue: 0.2703 time to fit residues: 237.8413 Evaluate side-chains 567 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 533 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 153 THR 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 B residue 37 PHE 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 342 LEU 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 584 ILE 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 87 LYS 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: 2.9990 chunk 29 optimal weight: 7.9990 chunk 188 optimal weight: 7.9990 chunk 102 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 HIS ** 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** D 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.128944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.089064 restraints weight = 35262.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.092309 restraints weight = 17631.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.094335 restraints weight = 10707.952| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.5833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16299 Z= 0.287 Angle : 0.717 13.351 22004 Z= 0.379 Chirality : 0.046 0.383 2348 Planarity : 0.004 0.052 2812 Dihedral : 9.082 154.204 2217 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 4.14 % Allowed : 23.34 % Favored : 72.52 % 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: 1.00 (0.15), residues: 1140 sheet: -0.73 (0.38), residues: 156 loop : 0.46 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP D 124 HIS 0.006 0.001 HIS A 438 PHE 0.032 0.002 PHE C 168 TYR 0.023 0.002 TYR C 262 ARG 0.007 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04395 ( 896) hydrogen bonds : angle 5.29220 ( 2616) covalent geometry : bond 0.00628 (16298) covalent geometry : angle 0.71739 (22004) Misc. bond : bond 0.00051 ( 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 604 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 533 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8036 (mm-30) REVERT: A 178 SER cc_start: 0.8326 (OUTLIER) cc_final: 0.8080 (p) REVERT: A 218 ASN cc_start: 0.8938 (t0) cc_final: 0.8666 (t0) REVERT: A 286 ASP cc_start: 0.8759 (m-30) cc_final: 0.8543 (m-30) REVERT: A 355 TYR cc_start: 0.8253 (m-80) cc_final: 0.8023 (m-10) REVERT: A 383 SER cc_start: 0.9170 (OUTLIER) cc_final: 0.8698 (t) REVERT: A 485 ARG cc_start: 0.8355 (mtm-85) cc_final: 0.7666 (mtt90) REVERT: A 493 MET cc_start: 0.8916 (tmm) cc_final: 0.8533 (tmm) REVERT: A 599 GLU cc_start: 0.8364 (mp0) cc_final: 0.7896 (mp0) REVERT: A 612 TYR cc_start: 0.8914 (m-80) cc_final: 0.8634 (m-80) REVERT: A 640 MET cc_start: 0.9064 (tpp) cc_final: 0.8735 (tpp) REVERT: A 647 HIS cc_start: 0.8836 (OUTLIER) cc_final: 0.8525 (m90) REVERT: A 684 TYR cc_start: 0.8172 (OUTLIER) cc_final: 0.7261 (m-80) REVERT: B 31 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8627 (pm20) REVERT: B 65 GLU cc_start: 0.8508 (mp0) cc_final: 0.8276 (mp0) REVERT: B 116 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8036 (mt-10) REVERT: B 200 SER cc_start: 0.9010 (t) cc_final: 0.8470 (t) REVERT: B 250 TYR cc_start: 0.9249 (m-80) cc_final: 0.8388 (m-80) REVERT: B 379 SER cc_start: 0.8846 (t) cc_final: 0.8038 (t) REVERT: B 394 TYR cc_start: 0.9097 (m-80) cc_final: 0.8644 (m-80) REVERT: B 399 GLU cc_start: 0.8294 (mp0) cc_final: 0.7987 (mp0) REVERT: B 515 ASP cc_start: 0.9023 (m-30) cc_final: 0.8768 (m-30) REVERT: B 590 SER cc_start: 0.9269 (OUTLIER) cc_final: 0.8785 (t) REVERT: B 599 GLU cc_start: 0.8107 (pt0) cc_final: 0.7276 (pt0) REVERT: B 639 ASP cc_start: 0.8680 (m-30) cc_final: 0.8142 (m-30) REVERT: B 640 MET cc_start: 0.9078 (tpp) cc_final: 0.8751 (tpp) REVERT: B 686 ARG cc_start: 0.8393 (ttm-80) cc_final: 0.7838 (mtm-85) REVERT: C 24 GLN cc_start: 0.8664 (mt0) cc_final: 0.8249 (mm110) REVERT: C 168 PHE cc_start: 0.8088 (m-80) cc_final: 0.7823 (m-80) REVERT: C 172 PHE cc_start: 0.7933 (m-10) cc_final: 0.7530 (m-10) REVERT: C 178 PHE cc_start: 0.8364 (m-80) cc_final: 0.7873 (m-10) REVERT: C 179 TYR cc_start: 0.8578 (t80) cc_final: 0.8198 (t80) REVERT: C 218 GLU cc_start: 0.9295 (mp0) cc_final: 0.8755 (pp20) REVERT: C 269 MET cc_start: 0.8260 (tmm) cc_final: 0.8031 (ptt) REVERT: D 18 THR cc_start: 0.6467 (p) cc_final: 0.6068 (p) REVERT: D 149 ASP cc_start: 0.7760 (t0) cc_final: 0.7427 (t0) REVERT: D 174 TYR cc_start: 0.4914 (t80) cc_final: 0.4404 (t80) REVERT: D 179 TYR cc_start: 0.8243 (t80) cc_final: 0.7903 (t80) REVERT: D 204 TYR cc_start: 0.8916 (t80) cc_final: 0.8477 (t80) REVERT: D 212 ILE cc_start: 0.8393 (mt) cc_final: 0.8089 (mt) REVERT: D 281 ASP cc_start: 0.8054 (p0) cc_final: 0.7665 (t70) outliers start: 71 outliers final: 39 residues processed: 561 average time/residue: 0.2837 time to fit residues: 233.3940 Evaluate side-chains 547 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 502 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL 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 178 SER Chi-restraints excluded: chain A residue 199 VAL 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 440 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 647 HIS 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 183 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 342 LEU 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 590 SER 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 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 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 Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 143 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 106 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.133488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.094462 restraints weight = 34486.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.097774 restraints weight = 17162.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.099963 restraints weight = 10416.292| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 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 = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.6095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16299 Z= 0.142 Angle : 0.645 10.010 22004 Z= 0.338 Chirality : 0.042 0.137 2348 Planarity : 0.004 0.055 2812 Dihedral : 8.644 149.152 2216 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.63 % Allowed : 25.55 % 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: 0.95 (0.19), residues: 1928 helix: 1.05 (0.15), residues: 1139 sheet: -0.42 (0.39), residues: 140 loop : 0.34 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 124 HIS 0.005 0.001 HIS C 201 PHE 0.029 0.002 PHE D 168 TYR 0.022 0.001 TYR C 262 ARG 0.008 0.001 ARG A 665 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 896) hydrogen bonds : angle 5.14820 ( 2616) covalent geometry : bond 0.00318 (16298) covalent geometry : angle 0.64540 (22004) Misc. bond : bond 0.00072 ( 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 622 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 577 time to evaluate : 1.774 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 128 PHE cc_start: 0.8898 (t80) cc_final: 0.8682 (t80) REVERT: A 218 ASN cc_start: 0.8954 (t0) cc_final: 0.8614 (t0) REVERT: A 257 ASP cc_start: 0.8630 (m-30) cc_final: 0.8309 (m-30) REVERT: A 286 ASP cc_start: 0.8688 (m-30) cc_final: 0.8376 (p0) REVERT: A 350 ARG cc_start: 0.8250 (mtp180) cc_final: 0.8015 (mtp180) REVERT: A 383 SER cc_start: 0.9169 (OUTLIER) cc_final: 0.8635 (t) REVERT: A 493 MET cc_start: 0.8996 (tmm) cc_final: 0.8665 (tmm) REVERT: A 599 GLU cc_start: 0.8430 (mp0) cc_final: 0.7705 (mp0) REVERT: A 604 ARG cc_start: 0.8468 (tpp80) cc_final: 0.8141 (mmp80) REVERT: A 612 TYR cc_start: 0.8888 (m-80) cc_final: 0.8596 (m-80) REVERT: A 615 MET cc_start: 0.9086 (mmp) cc_final: 0.8881 (mmp) REVERT: A 646 GLN cc_start: 0.9218 (mt0) cc_final: 0.8962 (mt0) REVERT: A 668 ASN cc_start: 0.8841 (m110) cc_final: 0.8603 (m110) REVERT: A 683 TYR cc_start: 0.8249 (t80) cc_final: 0.7955 (t80) REVERT: A 684 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.6982 (m-80) REVERT: B 31 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8592 (pm20) REVERT: B 65 GLU cc_start: 0.8558 (mp0) cc_final: 0.8295 (mp0) REVERT: B 89 PHE cc_start: 0.8964 (t80) cc_final: 0.8733 (t80) REVERT: B 200 SER cc_start: 0.9002 (t) cc_final: 0.8166 (t) REVERT: B 228 LYS cc_start: 0.9024 (mmmt) cc_final: 0.8508 (tppt) REVERT: B 250 TYR cc_start: 0.9219 (m-80) cc_final: 0.8195 (m-80) REVERT: B 276 LYS cc_start: 0.8494 (mmtt) cc_final: 0.8072 (mmmt) REVERT: B 290 GLU cc_start: 0.8529 (pp20) cc_final: 0.8253 (pp20) REVERT: B 379 SER cc_start: 0.8774 (t) cc_final: 0.7837 (t) REVERT: B 394 TYR cc_start: 0.9102 (m-80) cc_final: 0.8802 (m-80) REVERT: B 399 GLU cc_start: 0.8270 (mp0) cc_final: 0.7960 (mp0) REVERT: B 467 ASN cc_start: 0.9078 (t0) cc_final: 0.8465 (t0) REVERT: B 494 MET cc_start: 0.8949 (mtp) cc_final: 0.8693 (mtp) REVERT: B 515 ASP cc_start: 0.8999 (m-30) cc_final: 0.8736 (m-30) REVERT: B 586 TYR cc_start: 0.8806 (m-80) cc_final: 0.8298 (m-80) REVERT: B 590 SER cc_start: 0.9106 (OUTLIER) cc_final: 0.8672 (t) REVERT: B 601 ILE cc_start: 0.9151 (mm) cc_final: 0.8609 (mm) REVERT: B 639 ASP cc_start: 0.8643 (m-30) cc_final: 0.7870 (m-30) REVERT: B 640 MET cc_start: 0.9101 (tpp) cc_final: 0.8727 (tpp) REVERT: B 686 ARG cc_start: 0.8446 (ttm-80) cc_final: 0.8033 (mtm-85) REVERT: C 24 GLN cc_start: 0.8656 (mt0) cc_final: 0.8345 (mm110) REVERT: C 172 PHE cc_start: 0.7744 (m-10) cc_final: 0.7343 (m-10) REVERT: C 178 PHE cc_start: 0.8361 (m-10) cc_final: 0.7878 (m-10) REVERT: C 179 TYR cc_start: 0.8488 (t80) cc_final: 0.8105 (t80) REVERT: D 18 THR cc_start: 0.6491 (p) cc_final: 0.6152 (p) REVERT: D 46 TYR cc_start: 0.8786 (m-10) cc_final: 0.8340 (m-80) REVERT: D 131 LEU cc_start: 0.8409 (tt) cc_final: 0.8203 (tp) REVERT: D 149 ASP cc_start: 0.7667 (t0) cc_final: 0.7400 (t0) REVERT: D 174 TYR cc_start: 0.4730 (t80) cc_final: 0.4331 (t80) REVERT: D 204 TYR cc_start: 0.8908 (t80) cc_final: 0.8404 (t80) REVERT: D 215 LYS cc_start: 0.7969 (ptmm) cc_final: 0.7697 (pttt) REVERT: D 252 LEU cc_start: 0.6593 (mm) cc_final: 0.5651 (mm) REVERT: D 281 ASP cc_start: 0.8163 (p0) cc_final: 0.7864 (t70) outliers start: 45 outliers final: 26 residues processed: 596 average time/residue: 0.2768 time to fit residues: 243.8195 Evaluate side-chains 541 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 511 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 201 LEU 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 58 LEU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 410 ASN 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 18 THR Chi-restraints excluded: chain C residue 174 TYR 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 145 ILE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 226 GLU 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: 0.8980 chunk 79 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 185 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 370 ASN B 568 HIS ** B 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 HIS ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.135291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.096820 restraints weight = 34535.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.100205 restraints weight = 16953.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.102485 restraints weight = 10206.775| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 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 = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.6335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16299 Z= 0.148 Angle : 0.685 13.207 22004 Z= 0.351 Chirality : 0.043 0.227 2348 Planarity : 0.004 0.049 2812 Dihedral : 8.582 145.436 2216 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.45 % Allowed : 27.01 % Favored : 70.54 % 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: 0.73 (0.18), residues: 1928 helix: 0.91 (0.15), residues: 1135 sheet: -0.44 (0.41), residues: 134 loop : 0.16 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP D 124 HIS 0.004 0.001 HIS C 201 PHE 0.039 0.002 PHE C 168 TYR 0.019 0.001 TYR C 262 ARG 0.009 0.001 ARG B 274 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 896) hydrogen bonds : angle 5.19181 ( 2616) covalent geometry : bond 0.00337 (16298) covalent geometry : angle 0.68472 (22004) Misc. bond : bond 0.00068 ( 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 583 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 541 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8519 (mp0) REVERT: A 128 PHE cc_start: 0.8877 (t80) cc_final: 0.8666 (t80) REVERT: A 164 ARG cc_start: 0.7461 (ptt90) cc_final: 0.6987 (ptt90) REVERT: A 218 ASN cc_start: 0.8901 (t0) cc_final: 0.8599 (t0) REVERT: A 350 ARG cc_start: 0.8241 (mtp180) cc_final: 0.7960 (mtp180) REVERT: A 355 TYR cc_start: 0.8191 (m-10) cc_final: 0.7969 (m-10) REVERT: A 379 SER cc_start: 0.9293 (t) cc_final: 0.9025 (t) REVERT: A 383 SER cc_start: 0.9093 (OUTLIER) cc_final: 0.8486 (t) REVERT: A 493 MET cc_start: 0.8972 (tmm) cc_final: 0.8656 (tmm) REVERT: A 599 GLU cc_start: 0.8543 (mp0) cc_final: 0.7818 (mp0) REVERT: A 683 TYR cc_start: 0.8235 (t80) cc_final: 0.7925 (t80) REVERT: A 684 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.7142 (m-80) REVERT: B 15 GLU cc_start: 0.8401 (tp30) cc_final: 0.8148 (tp30) REVERT: B 31 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8598 (pm20) REVERT: B 65 GLU cc_start: 0.8580 (mp0) cc_final: 0.8296 (mp0) REVERT: B 116 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7965 (mt-10) REVERT: B 200 SER cc_start: 0.8945 (t) cc_final: 0.8223 (t) REVERT: B 207 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7369 (mtt180) REVERT: B 228 LYS cc_start: 0.9027 (mmmt) cc_final: 0.8540 (tppt) REVERT: B 250 TYR cc_start: 0.9206 (m-80) cc_final: 0.8260 (m-80) REVERT: B 290 GLU cc_start: 0.8546 (pp20) cc_final: 0.8252 (pp20) REVERT: B 379 SER cc_start: 0.8855 (t) cc_final: 0.7744 (t) REVERT: B 394 TYR cc_start: 0.9119 (m-80) cc_final: 0.8820 (m-80) REVERT: B 399 GLU cc_start: 0.8244 (mp0) cc_final: 0.7950 (mp0) REVERT: B 467 ASN cc_start: 0.9026 (t0) cc_final: 0.8467 (t0) REVERT: B 480 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8200 (mm-30) REVERT: B 515 ASP cc_start: 0.8977 (m-30) cc_final: 0.8738 (m-30) REVERT: B 548 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8137 (mm-30) REVERT: B 586 TYR cc_start: 0.8791 (m-80) cc_final: 0.8095 (m-80) REVERT: B 590 SER cc_start: 0.9043 (OUTLIER) cc_final: 0.8615 (t) REVERT: B 640 MET cc_start: 0.9164 (tpp) cc_final: 0.8766 (tpp) REVERT: B 672 LEU cc_start: 0.9329 (mt) cc_final: 0.9083 (mt) REVERT: B 686 ARG cc_start: 0.8338 (ttm-80) cc_final: 0.8017 (mtm-85) REVERT: C 24 GLN cc_start: 0.8725 (mt0) cc_final: 0.8328 (mm110) REVERT: C 172 PHE cc_start: 0.7778 (m-10) cc_final: 0.7299 (m-10) REVERT: C 178 PHE cc_start: 0.8375 (m-10) cc_final: 0.7860 (m-10) REVERT: C 179 TYR cc_start: 0.8560 (t80) cc_final: 0.8174 (t80) REVERT: C 269 MET cc_start: 0.8268 (tmm) cc_final: 0.7887 (ptt) REVERT: D 18 THR cc_start: 0.6660 (p) cc_final: 0.6325 (p) REVERT: D 20 MET cc_start: 0.8852 (ppp) cc_final: 0.8633 (ppp) REVERT: D 46 TYR cc_start: 0.8800 (m-10) cc_final: 0.8402 (m-80) REVERT: D 137 MET cc_start: 0.8362 (mmp) cc_final: 0.7652 (mtp) REVERT: D 149 ASP cc_start: 0.7731 (t0) cc_final: 0.7456 (t0) REVERT: D 204 TYR cc_start: 0.8906 (t80) cc_final: 0.8461 (t80) outliers start: 42 outliers final: 26 residues processed: 561 average time/residue: 0.2690 time to fit residues: 223.7133 Evaluate side-chains 539 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 508 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 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 58 LEU 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 207 ARG Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 314 MET 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 C residue 72 THR 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 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 211 GLU 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: 0.3980 chunk 80 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN ** C 238 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 = 0.3755 r_free = 0.3755 target = 0.134658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.096032 restraints weight = 34448.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.099383 restraints weight = 17124.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.101541 restraints weight = 10326.298| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 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 = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.6543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16299 Z= 0.161 Angle : 0.706 13.990 22004 Z= 0.363 Chirality : 0.044 0.318 2348 Planarity : 0.004 0.049 2812 Dihedral : 8.563 144.020 2216 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.57 % Allowed : 27.83 % Favored : 69.60 % 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: 0.71 (0.19), residues: 1928 helix: 0.91 (0.15), residues: 1128 sheet: -0.39 (0.42), residues: 132 loop : 0.11 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 30 HIS 0.005 0.001 HIS C 201 PHE 0.040 0.002 PHE B 89 TYR 0.022 0.001 TYR B 149 ARG 0.013 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 896) hydrogen bonds : angle 5.23759 ( 2616) covalent geometry : bond 0.00368 (16298) covalent geometry : angle 0.70575 (22004) Misc. bond : bond 0.00061 ( 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 571 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 527 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8499 (mp0) REVERT: A 128 PHE cc_start: 0.8934 (t80) cc_final: 0.8647 (t80) REVERT: A 164 ARG cc_start: 0.7639 (ptt90) cc_final: 0.7426 (ptt90) REVERT: A 166 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7611 (mm-30) REVERT: A 218 ASN cc_start: 0.8952 (t0) cc_final: 0.8660 (t0) REVERT: A 301 PHE cc_start: 0.9082 (m-10) cc_final: 0.8734 (m-10) REVERT: A 350 ARG cc_start: 0.8296 (mtp180) cc_final: 0.7996 (mtp180) REVERT: A 383 SER cc_start: 0.9059 (OUTLIER) cc_final: 0.8561 (t) REVERT: A 458 MET cc_start: 0.9030 (mmm) cc_final: 0.8816 (mmm) REVERT: A 493 MET cc_start: 0.8807 (tmm) cc_final: 0.8530 (tmm) REVERT: A 599 GLU cc_start: 0.8463 (mp0) cc_final: 0.7916 (mp0) REVERT: A 683 TYR cc_start: 0.8240 (t80) cc_final: 0.7793 (t80) REVERT: A 684 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.7107 (m-80) REVERT: B 31 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8622 (pm20) REVERT: B 65 GLU cc_start: 0.8567 (mp0) cc_final: 0.8267 (mp0) REVERT: B 116 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8160 (mt-10) REVERT: B 200 SER cc_start: 0.8946 (t) cc_final: 0.8280 (t) REVERT: B 207 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7322 (mtt180) REVERT: B 228 LYS cc_start: 0.9035 (mmmt) cc_final: 0.8443 (mmtt) REVERT: B 250 TYR cc_start: 0.9233 (m-80) cc_final: 0.8405 (m-80) REVERT: B 286 ASP cc_start: 0.8184 (m-30) cc_final: 0.7869 (m-30) REVERT: B 290 GLU cc_start: 0.8544 (pp20) cc_final: 0.8242 (pp20) REVERT: B 379 SER cc_start: 0.8837 (t) cc_final: 0.7809 (t) REVERT: B 394 TYR cc_start: 0.9114 (m-80) cc_final: 0.8804 (m-80) REVERT: B 399 GLU cc_start: 0.8306 (mp0) cc_final: 0.7979 (mp0) REVERT: B 467 ASN cc_start: 0.8985 (t0) cc_final: 0.8392 (t0) REVERT: B 515 ASP cc_start: 0.9008 (m-30) cc_final: 0.8716 (m-30) REVERT: B 548 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8091 (mm-30) REVERT: B 590 SER cc_start: 0.9032 (OUTLIER) cc_final: 0.8517 (t) REVERT: B 640 MET cc_start: 0.9178 (tpp) cc_final: 0.8769 (tpp) REVERT: B 677 ARG cc_start: 0.9012 (mmm-85) cc_final: 0.8768 (mmm160) REVERT: B 686 ARG cc_start: 0.8323 (ttm-80) cc_final: 0.8017 (mtm-85) REVERT: C 24 GLN cc_start: 0.8714 (mt0) cc_final: 0.8505 (mt0) REVERT: C 172 PHE cc_start: 0.7814 (m-10) cc_final: 0.7318 (m-80) REVERT: C 178 PHE cc_start: 0.8381 (m-10) cc_final: 0.7874 (m-10) REVERT: C 179 TYR cc_start: 0.8653 (t80) cc_final: 0.8245 (t80) REVERT: D 18 THR cc_start: 0.6888 (p) cc_final: 0.6673 (p) REVERT: D 20 MET cc_start: 0.8882 (ppp) cc_final: 0.8680 (ppp) REVERT: D 137 MET cc_start: 0.8443 (mmp) cc_final: 0.7763 (mtp) REVERT: D 142 TYR cc_start: 0.8339 (m-80) cc_final: 0.7952 (t80) REVERT: D 149 ASP cc_start: 0.7762 (t0) cc_final: 0.7531 (t0) REVERT: D 204 TYR cc_start: 0.8973 (t80) cc_final: 0.8509 (t80) REVERT: D 215 LYS cc_start: 0.7658 (pttt) cc_final: 0.7237 (ptmm) REVERT: D 281 ASP cc_start: 0.8279 (p0) cc_final: 0.7615 (t70) outliers start: 44 outliers final: 29 residues processed: 543 average time/residue: 0.2748 time to fit residues: 220.7975 Evaluate side-chains 538 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 504 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 320 ASN 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 143 LEU Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 342 LEU 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 597 ILE 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 316 LYS Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 211 GLU 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: 1.9990 chunk 83 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 168 optimal weight: 20.0000 chunk 16 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 76 optimal weight: 0.0970 chunk 27 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.136290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.097718 restraints weight = 34465.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.101058 restraints weight = 17029.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.103316 restraints weight = 10305.915| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 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 = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.6770 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= 0.147 Angle : 0.720 15.951 22004 Z= 0.367 Chirality : 0.044 0.332 2348 Planarity : 0.004 0.050 2812 Dihedral : 8.453 141.656 2216 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.45 % Allowed : 29.00 % Favored : 68.55 % 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: 0.65 (0.19), residues: 1928 helix: 0.87 (0.15), residues: 1140 sheet: -0.41 (0.43), residues: 130 loop : 0.06 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP D 124 HIS 0.006 0.001 HIS C 201 PHE 0.036 0.002 PHE C 168 TYR 0.027 0.001 TYR C 142 ARG 0.011 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 896) hydrogen bonds : angle 5.20589 ( 2616) covalent geometry : bond 0.00335 (16298) covalent geometry : angle 0.71992 (22004) Misc. bond : bond 0.00058 ( 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 562 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 520 time to evaluate : 1.773 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 31 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8498 (mp0) REVERT: A 128 PHE cc_start: 0.8896 (t80) cc_final: 0.8668 (t80) REVERT: A 218 ASN cc_start: 0.8878 (t0) cc_final: 0.8594 (t0) REVERT: A 257 ASP cc_start: 0.8728 (m-30) cc_final: 0.8390 (m-30) REVERT: A 312 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8144 (pt0) REVERT: A 350 ARG cc_start: 0.8265 (mtp180) cc_final: 0.7971 (mtp180) REVERT: A 383 SER cc_start: 0.9052 (OUTLIER) cc_final: 0.8555 (t) REVERT: A 385 VAL cc_start: 0.9157 (t) cc_final: 0.8744 (p) REVERT: A 458 MET cc_start: 0.9032 (mmm) cc_final: 0.8787 (mmm) REVERT: A 493 MET cc_start: 0.8813 (tmm) cc_final: 0.8582 (tmm) REVERT: A 599 GLU cc_start: 0.8539 (mp0) cc_final: 0.8027 (mp0) REVERT: A 612 TYR cc_start: 0.8865 (m-80) cc_final: 0.8373 (m-80) REVERT: B 65 GLU cc_start: 0.8560 (mp0) cc_final: 0.8252 (mp0) REVERT: B 116 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8067 (mt-10) REVERT: B 161 ARG cc_start: 0.7925 (mtt180) cc_final: 0.7722 (mtt180) REVERT: B 200 SER cc_start: 0.8932 (t) cc_final: 0.8293 (t) REVERT: B 207 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7392 (mtt180) REVERT: B 228 LYS cc_start: 0.9025 (mmmt) cc_final: 0.8530 (tppt) REVERT: B 250 TYR cc_start: 0.9216 (m-80) cc_final: 0.8393 (m-80) REVERT: B 286 ASP cc_start: 0.8164 (m-30) cc_final: 0.7847 (m-30) REVERT: B 290 GLU cc_start: 0.8581 (pp20) cc_final: 0.8290 (pp20) REVERT: B 379 SER cc_start: 0.8880 (t) cc_final: 0.7881 (t) REVERT: B 394 TYR cc_start: 0.9108 (m-80) cc_final: 0.8812 (m-80) REVERT: B 399 GLU cc_start: 0.8287 (mp0) cc_final: 0.7978 (mp0) REVERT: B 467 ASN cc_start: 0.8875 (t0) cc_final: 0.8257 (t0) REVERT: B 487 PHE cc_start: 0.9374 (t80) cc_final: 0.9047 (t80) REVERT: B 515 ASP cc_start: 0.9008 (m-30) cc_final: 0.8702 (m-30) REVERT: B 590 SER cc_start: 0.9019 (OUTLIER) cc_final: 0.8479 (t) REVERT: B 610 LYS cc_start: 0.8755 (mmmm) cc_final: 0.8191 (mmmm) REVERT: B 640 MET cc_start: 0.9135 (tpp) cc_final: 0.8708 (tpp) REVERT: B 677 ARG cc_start: 0.8971 (mmm-85) cc_final: 0.8753 (mmm160) REVERT: B 686 ARG cc_start: 0.8334 (ttm-80) cc_final: 0.7908 (mtm-85) REVERT: C 24 GLN cc_start: 0.8751 (mt0) cc_final: 0.8451 (mt0) REVERT: C 30 TRP cc_start: 0.6874 (p-90) cc_final: 0.6556 (p-90) REVERT: C 137 MET cc_start: 0.3901 (mmm) cc_final: 0.3641 (mpp) REVERT: C 172 PHE cc_start: 0.7824 (m-10) cc_final: 0.7436 (m-80) REVERT: C 178 PHE cc_start: 0.8361 (m-10) cc_final: 0.7860 (m-10) REVERT: C 179 TYR cc_start: 0.8662 (t80) cc_final: 0.8272 (t80) REVERT: C 269 MET cc_start: 0.8249 (tmm) cc_final: 0.7895 (ptt) REVERT: D 18 THR cc_start: 0.6712 (p) cc_final: 0.6392 (p) REVERT: D 20 MET cc_start: 0.8891 (ppp) cc_final: 0.8668 (ppp) REVERT: D 137 MET cc_start: 0.8503 (mmp) cc_final: 0.7968 (mtp) REVERT: D 149 ASP cc_start: 0.7726 (t0) cc_final: 0.7499 (t0) REVERT: D 204 TYR cc_start: 0.8935 (t80) cc_final: 0.8461 (t80) REVERT: D 241 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7715 (tm-30) REVERT: D 281 ASP cc_start: 0.8243 (p0) cc_final: 0.7592 (t70) outliers start: 42 outliers final: 35 residues processed: 536 average time/residue: 0.2809 time to fit residues: 221.4231 Evaluate side-chains 540 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 501 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 58 LEU 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 207 ARG Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 342 LEU 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 B residue 597 ILE Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain C residue 44 TRP Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 96 MET 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 316 LYS Chi-restraints excluded: chain D residue 24 GLN 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 211 GLU 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: 0.7980 chunk 83 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 165 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 120 optimal weight: 0.0570 chunk 164 optimal weight: 0.9990 chunk 190 optimal weight: 0.4980 chunk 129 optimal weight: 7.9990 overall best weight: 0.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 418 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 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.136952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.098331 restraints weight = 34830.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.101706 restraints weight = 17125.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.103993 restraints weight = 10369.865| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.6979 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= 0.145 Angle : 0.733 16.366 22004 Z= 0.376 Chirality : 0.045 0.319 2348 Planarity : 0.004 0.055 2812 Dihedral : 8.354 139.453 2216 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.45 % Allowed : 29.00 % Favored : 68.55 % 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: 0.61 (0.19), residues: 1928 helix: 0.83 (0.15), residues: 1140 sheet: -0.51 (0.43), residues: 130 loop : 0.05 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 124 HIS 0.004 0.001 HIS C 201 PHE 0.034 0.002 PHE C 168 TYR 0.032 0.001 TYR D 174 ARG 0.009 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 896) hydrogen bonds : angle 5.21668 ( 2616) covalent geometry : bond 0.00331 (16298) covalent geometry : angle 0.73282 (22004) Misc. bond : bond 0.00048 ( 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 565 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 523 time to evaluate : 1.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8625 (mp0) REVERT: A 128 PHE cc_start: 0.8873 (t80) cc_final: 0.8636 (t80) REVERT: A 164 ARG cc_start: 0.7806 (ptt90) cc_final: 0.7213 (ptt90) REVERT: A 166 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7385 (mm-30) REVERT: A 184 ARG cc_start: 0.8737 (tpp-160) cc_final: 0.8380 (tpp80) REVERT: A 218 ASN cc_start: 0.8845 (t0) cc_final: 0.8578 (t0) REVERT: A 312 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8466 (pt0) REVERT: A 350 ARG cc_start: 0.8226 (mtp180) cc_final: 0.7906 (mtp180) REVERT: A 383 SER cc_start: 0.9078 (OUTLIER) cc_final: 0.8555 (t) REVERT: A 385 VAL cc_start: 0.9103 (t) cc_final: 0.8547 (p) REVERT: A 485 ARG cc_start: 0.8530 (mtm-85) cc_final: 0.8270 (ttm-80) REVERT: A 493 MET cc_start: 0.8833 (tmm) cc_final: 0.8563 (tmm) REVERT: A 599 GLU cc_start: 0.8546 (mp0) cc_final: 0.8072 (mp0) REVERT: A 683 TYR cc_start: 0.8222 (t80) cc_final: 0.7870 (t80) REVERT: A 684 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.7350 (m-80) REVERT: B 65 GLU cc_start: 0.8522 (mp0) cc_final: 0.8243 (mp0) REVERT: B 116 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7967 (mt-10) REVERT: B 200 SER cc_start: 0.8941 (t) cc_final: 0.8264 (t) REVERT: B 207 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7504 (mtt180) REVERT: B 228 LYS cc_start: 0.9025 (mmmt) cc_final: 0.8408 (mmtt) REVERT: B 250 TYR cc_start: 0.9184 (m-80) cc_final: 0.8391 (m-80) REVERT: B 286 ASP cc_start: 0.8274 (m-30) cc_final: 0.7983 (m-30) REVERT: B 290 GLU cc_start: 0.8585 (pp20) cc_final: 0.8277 (pp20) REVERT: B 379 SER cc_start: 0.8929 (t) cc_final: 0.7758 (t) REVERT: B 394 TYR cc_start: 0.9098 (m-80) cc_final: 0.8805 (m-80) REVERT: B 399 GLU cc_start: 0.8268 (mp0) cc_final: 0.7980 (mp0) REVERT: B 415 ASN cc_start: 0.9406 (t0) cc_final: 0.9014 (t0) REVERT: B 515 ASP cc_start: 0.8971 (m-30) cc_final: 0.8639 (m-30) REVERT: B 590 SER cc_start: 0.8968 (OUTLIER) cc_final: 0.8533 (t) REVERT: B 610 LYS cc_start: 0.8764 (mmmm) cc_final: 0.8229 (mmmm) REVERT: B 640 MET cc_start: 0.9164 (tpp) cc_final: 0.8701 (tpp) REVERT: B 686 ARG cc_start: 0.8365 (ttm-80) cc_final: 0.7945 (mtm-85) REVERT: C 24 GLN cc_start: 0.8694 (mt0) cc_final: 0.8438 (mt0) REVERT: C 33 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7683 (tp30) REVERT: C 172 PHE cc_start: 0.7827 (m-10) cc_final: 0.7415 (m-80) REVERT: C 178 PHE cc_start: 0.8416 (m-10) cc_final: 0.7926 (m-10) REVERT: C 179 TYR cc_start: 0.8699 (t80) cc_final: 0.8338 (t80) REVERT: C 269 MET cc_start: 0.8164 (tmm) cc_final: 0.7909 (ppp) REVERT: D 18 THR cc_start: 0.6763 (p) cc_final: 0.6487 (p) REVERT: D 20 MET cc_start: 0.8889 (ppp) cc_final: 0.8684 (ppp) REVERT: D 137 MET cc_start: 0.8833 (mmp) cc_final: 0.8466 (mtp) REVERT: D 149 ASP cc_start: 0.7702 (t0) cc_final: 0.7469 (t0) REVERT: D 204 TYR cc_start: 0.8931 (t80) cc_final: 0.8487 (t80) REVERT: D 215 LYS cc_start: 0.7705 (pttt) cc_final: 0.7155 (ptmm) REVERT: D 241 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7732 (tm-30) REVERT: D 242 TYR cc_start: 0.7532 (t80) cc_final: 0.7313 (m-80) REVERT: D 281 ASP cc_start: 0.8199 (p0) cc_final: 0.7556 (t70) outliers start: 42 outliers final: 32 residues processed: 538 average time/residue: 0.2908 time to fit residues: 230.3529 Evaluate side-chains 544 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 506 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 214 LYS Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 58 LEU 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 207 ARG Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 410 ASN 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 33 GLU Chi-restraints excluded: chain C residue 44 TRP 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 316 LYS Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 211 GLU 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: 0.9990 chunk 80 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 186 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 140 optimal weight: 20.0000 chunk 168 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.133763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.094337 restraints weight = 34946.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.097604 restraints weight = 17739.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.099721 restraints weight = 10952.598| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.7034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 16299 Z= 0.217 Angle : 0.764 15.939 22004 Z= 0.396 Chirality : 0.047 0.321 2348 Planarity : 0.004 0.051 2812 Dihedral : 8.601 141.565 2216 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.45 % Allowed : 29.64 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.19), residues: 1928 helix: 0.78 (0.15), residues: 1140 sheet: -0.70 (0.42), residues: 140 loop : 0.03 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP C 30 HIS 0.006 0.001 HIS C 201 PHE 0.032 0.002 PHE C 168 TYR 0.034 0.002 TYR C 142 ARG 0.008 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04303 ( 896) hydrogen bonds : angle 5.34167 ( 2616) covalent geometry : bond 0.00494 (16298) covalent geometry : angle 0.76432 (22004) Misc. bond : bond 0.00069 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6515.31 seconds wall clock time: 113 minutes 39.55 seconds (6819.55 seconds total)