Starting phenix.real_space_refine on Wed May 14 18:28:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bxt_45011/05_2025/9bxt_45011.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bxt_45011/05_2025/9bxt_45011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bxt_45011/05_2025/9bxt_45011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bxt_45011/05_2025/9bxt_45011.map" model { file = "/net/cci-nas-00/data/ceres_data/9bxt_45011/05_2025/9bxt_45011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bxt_45011/05_2025/9bxt_45011.cif" } resolution = 2.88 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= 0.001 sd= 0.026 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 2 5.21 5 S 65 5.16 5 C 7715 2.51 5 N 2002 2.21 5 O 2364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12164 Number of models: 1 Model: "" Number of chains: 7 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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "D" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "E" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 668 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 80} Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 8.08, per 1000 atoms: 0.66 Number of scatterers: 12164 At special positions: 0 Unit cell: (90.246, 92.274, 145.002, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 65 16.00 P 16 15.00 Mg 2 11.99 O 2364 8.00 N 2002 7.00 C 7715 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 170 " - pdb=" SG CYS A 409 " distance=2.03 Simple disulfide: pdb=" SG CYS B 170 " - pdb=" SG CYS B 409 " distance=2.03 Simple disulfide: pdb=" SG CYS E 29 " - pdb=" SG CYS E 32 " distance=2.66 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=0, symmetry=0 Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.6 seconds 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2812 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 11 sheets defined 53.1% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 7 through 14 Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 27 through 40 removed outlier: 3.770A 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 71 removed outlier: 4.259A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.787A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.639A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 removed outlier: 3.524A pdb=" N ASN A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) 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 194 Processing helix chain 'A' and resid 222 through 237 removed outlier: 4.065A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 257 through 264 removed outlier: 3.528A pdb=" N THR A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.661A 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 328 removed outlier: 5.965A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.666A 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 367 removed outlier: 4.231A pdb=" N VAL A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 443 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 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: 3.568A 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 582 through 588 removed outlier: 4.060A pdb=" N TYR A 586 " --> pdb=" O GLY A 582 " (cutoff:3.500A) removed outlier: 4.103A 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 40 removed outlier: 3.612A 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 71 removed outlier: 4.044A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 86 Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.633A 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 221 through 237 removed outlier: 3.880A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.235A 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 removed outlier: 3.513A pdb=" N THR B 264 " --> pdb=" O ASP B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.647A 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 328 removed outlier: 5.482A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 4.600A 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 366 Processing helix chain 'B' and resid 416 through 422 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 475 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: 3.563A pdb=" N LEU B 546 " --> pdb=" O LYS B 542 " (cutoff:3.500A) removed outlier: 3.657A 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 588 removed outlier: 4.255A 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 678 Processing helix chain 'C' and resid 316 through 320 removed outlier: 3.811A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 47 Proline residue: E 37 - end of helix Processing helix chain 'E' and resid 60 through 67 Processing helix chain 'E' and resid 92 through 102 removed outlier: 3.528A pdb=" N LYS E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.234A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 removed outlier: 6.022A pdb=" N PHE A 171 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ASN A 202 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU A 173 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (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 659 Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.817A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.878A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (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 605 Processing sheet with id=AB1, first strand: chain 'B' and resid 655 through 659 Processing sheet with id=AB2, first strand: chain 'E' and resid 51 through 56 removed outlier: 6.468A pdb=" N LYS E 79 " --> pdb=" O VAL E 83 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N VAL E 83 " --> pdb=" O LYS E 79 " (cutoff:3.500A) 556 hydrogen bonds defined for protein. 1602 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.10 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3862 1.34 - 1.46: 2298 1.46 - 1.58: 6122 1.58 - 1.70: 26 1.70 - 1.82: 120 Bond restraints: 12428 Sorted by residual: bond pdb=" CA ILE E 72 " pdb=" C ILE E 72 " ideal model delta sigma weight residual 1.516 1.543 -0.028 1.11e-02 8.12e+03 6.16e+00 bond pdb=" CA ALA E 26 " pdb=" C ALA E 26 " ideal model delta sigma weight residual 1.519 1.542 -0.022 9.50e-03 1.11e+04 5.60e+00 bond pdb=" CB THR E 63 " pdb=" OG1 THR E 63 " ideal model delta sigma weight residual 1.433 1.396 0.037 1.60e-02 3.91e+03 5.43e+00 bond pdb=" CA ALA E 36 " pdb=" C ALA E 36 " ideal model delta sigma weight residual 1.521 1.548 -0.027 1.17e-02 7.31e+03 5.35e+00 bond pdb=" ND1 HIS E 103 " pdb=" CE1 HIS E 103 " ideal model delta sigma weight residual 1.321 1.342 -0.021 1.00e-02 1.00e+04 4.32e+00 ... (remaining 12423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 16174 1.52 - 3.03: 472 3.03 - 4.55: 116 4.55 - 6.06: 24 6.06 - 7.58: 4 Bond angle restraints: 16790 Sorted by residual: angle pdb=" CB HIS E 103 " pdb=" CG HIS E 103 " pdb=" CD2 HIS E 103 " ideal model delta sigma weight residual 131.20 125.33 5.87 1.30e+00 5.92e-01 2.04e+01 angle pdb=" OE1 GLN E 44 " pdb=" CD GLN E 44 " pdb=" NE2 GLN E 44 " ideal model delta sigma weight residual 122.60 118.51 4.09 1.00e+00 1.00e+00 1.67e+01 angle pdb=" C ALA E 26 " pdb=" N PRO E 27 " pdb=" CA PRO E 27 " ideal model delta sigma weight residual 119.19 123.47 -4.28 1.06e+00 8.90e-01 1.63e+01 angle pdb=" N VAL A 273 " pdb=" CA VAL A 273 " pdb=" C VAL A 273 " ideal model delta sigma weight residual 113.71 109.96 3.75 9.50e-01 1.11e+00 1.56e+01 angle pdb=" CA ASP E 43 " pdb=" CB ASP E 43 " pdb=" CG ASP E 43 " ideal model delta sigma weight residual 112.60 108.97 3.63 1.00e+00 1.00e+00 1.32e+01 ... (remaining 16785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.73: 7009 29.73 - 59.46: 466 59.46 - 89.19: 38 89.19 - 118.92: 3 118.92 - 148.65: 4 Dihedral angle restraints: 7520 sinusoidal: 3150 harmonic: 4370 Sorted by residual: dihedral pdb=" CB CYS B 170 " pdb=" SG CYS B 170 " pdb=" SG CYS B 409 " pdb=" CB CYS B 409 " ideal model delta sinusoidal sigma weight residual -86.00 -170.22 84.22 1 1.00e+01 1.00e-02 8.63e+01 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 301.68 153.03 148.65 1 2.00e+01 2.50e-03 4.45e+01 dihedral pdb=" C2 TTP B 802 " pdb=" C1' TTP B 802 " pdb=" N1 TTP B 802 " pdb=" O4' TTP B 802 " ideal model delta sinusoidal sigma weight residual 301.68 156.40 145.28 1 2.00e+01 2.50e-03 4.37e+01 ... (remaining 7517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1276 0.040 - 0.081: 380 0.081 - 0.121: 116 0.121 - 0.162: 17 0.162 - 0.202: 5 Chirality restraints: 1794 Sorted by residual: chirality pdb=" CA PRO E 31 " pdb=" N PRO E 31 " pdb=" C PRO E 31 " pdb=" CB PRO E 31 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CG LEU E 99 " pdb=" CB LEU E 99 " pdb=" CD1 LEU E 99 " pdb=" CD2 LEU E 99 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 9.82e-01 chirality pdb=" CG LEU E 21 " pdb=" CB LEU E 21 " pdb=" CD1 LEU E 21 " pdb=" CD2 LEU E 21 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.30e-01 ... (remaining 1791 not shown) Planarity restraints: 2131 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 25 " 0.078 2.00e-02 2.50e+03 3.71e-02 3.44e+01 pdb=" CG TRP E 25 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP E 25 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP E 25 " -0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP E 25 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP E 25 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP E 25 " -0.041 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 25 " 0.035 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 25 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP E 25 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 58 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" CG ASP E 58 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASP E 58 " 0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP E 58 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 28 " -0.027 2.00e-02 2.50e+03 1.57e-02 6.20e+00 pdb=" CG TRP E 28 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TRP E 28 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP E 28 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP E 28 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP E 28 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 28 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 28 " -0.028 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 28 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP E 28 " -0.009 2.00e-02 2.50e+03 ... (remaining 2128 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 272 2.67 - 3.23: 11695 3.23 - 3.79: 21538 3.79 - 4.34: 30329 4.34 - 4.90: 48552 Nonbonded interactions: 112386 Sorted by model distance: nonbonded pdb=" O2A TTP A 801 " pdb="MG MG A 802 " model vdw 2.118 2.170 nonbonded pdb=" O PRO B 616 " pdb=" OH TYR B 626 " model vdw 2.132 3.040 nonbonded pdb=" O PRO A 616 " pdb=" OH TYR A 626 " model vdw 2.153 3.040 nonbonded pdb=" O GLU A 119 " pdb=" OG SER A 123 " model vdw 2.175 3.040 nonbonded pdb=" NE2 HIS A 372 " pdb=" O GLN A 516 " model vdw 2.202 3.120 ... (remaining 112381 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 688 or resid 803 through 804)) selection = (chain 'B' and (resid 6 through 688 or resid 803 through 804)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.450 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 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:12.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 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 : 0.007 0.630 12431 Z= 0.341 Angle : 0.657 13.529 16796 Z= 0.372 Chirality : 0.043 0.202 1794 Planarity : 0.004 0.040 2131 Dihedral : 18.267 148.652 4699 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.99 % Allowed : 20.73 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.82 (0.22), residues: 1466 helix: 1.01 (0.20), residues: 686 sheet: -0.31 (0.37), residues: 179 loop : 0.48 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.006 TRP E 25 HIS 0.004 0.001 HIS B 255 PHE 0.019 0.002 PHE E 90 TYR 0.029 0.001 TYR E 67 ARG 0.007 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.15669 ( 554) hydrogen bonds : angle 6.85610 ( 1602) SS BOND : bond 0.36358 ( 3) SS BOND : angle 6.08767 ( 6) covalent geometry : bond 0.00379 (12428) covalent geometry : angle 0.64654 (16790) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 412 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.7823 (tttt) cc_final: 0.7614 (ttmm) REVERT: A 14 ASN cc_start: 0.7844 (m110) cc_final: 0.7604 (m110) REVERT: A 23 LYS cc_start: 0.7513 (mmmm) cc_final: 0.7109 (mtmm) REVERT: A 31 GLU cc_start: 0.6619 (mt-10) cc_final: 0.6348 (mt-10) REVERT: A 47 PHE cc_start: 0.7461 (t80) cc_final: 0.7118 (t80) REVERT: A 52 LYS cc_start: 0.7812 (tptm) cc_final: 0.7435 (ttpt) REVERT: A 56 ASP cc_start: 0.7378 (m-30) cc_final: 0.7101 (m-30) REVERT: A 79 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6876 (mm-30) REVERT: A 119 GLU cc_start: 0.7114 (mp0) cc_final: 0.6866 (mp0) REVERT: A 152 SER cc_start: 0.8289 (p) cc_final: 0.8058 (t) REVERT: A 187 ASP cc_start: 0.7934 (t70) cc_final: 0.7618 (t0) REVERT: A 209 LYS cc_start: 0.8247 (ttpp) cc_final: 0.7972 (ttmm) REVERT: A 211 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6881 (mt-10) REVERT: A 218 ASN cc_start: 0.8133 (t0) cc_final: 0.7753 (t160) REVERT: A 286 ASP cc_start: 0.7020 (m-30) cc_final: 0.6785 (m-30) REVERT: A 316 GLU cc_start: 0.7344 (mp0) cc_final: 0.6988 (mp0) REVERT: A 322 MET cc_start: 0.8106 (mmt) cc_final: 0.7665 (mtp) REVERT: A 341 LYS cc_start: 0.8183 (tptt) cc_final: 0.7834 (mmmm) REVERT: A 384 GLU cc_start: 0.7683 (pp20) cc_final: 0.7453 (pp20) REVERT: A 394 TYR cc_start: 0.7957 (m-80) cc_final: 0.7698 (m-80) REVERT: A 458 MET cc_start: 0.8304 (mmm) cc_final: 0.8099 (mmm) REVERT: A 480 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7693 (mp0) REVERT: A 515 ASP cc_start: 0.7883 (m-30) cc_final: 0.7671 (m-30) REVERT: A 548 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7195 (tm-30) REVERT: A 556 GLU cc_start: 0.6773 (pp20) cc_final: 0.5906 (pp20) REVERT: A 560 LYS cc_start: 0.8368 (mmtm) cc_final: 0.8118 (mppt) REVERT: A 590 SER cc_start: 0.8474 (p) cc_final: 0.8159 (p) REVERT: A 599 GLU cc_start: 0.7260 (pt0) cc_final: 0.7016 (pt0) REVERT: A 612 TYR cc_start: 0.7644 (m-80) cc_final: 0.6655 (m-80) REVERT: A 632 MET cc_start: 0.8376 (mtt) cc_final: 0.8018 (mtt) REVERT: A 634 MET cc_start: 0.8185 (mmp) cc_final: 0.7961 (mmm) REVERT: A 679 ILE cc_start: 0.8982 (mm) cc_final: 0.8758 (mm) REVERT: B 18 ILE cc_start: 0.8166 (mm) cc_final: 0.7925 (OUTLIER) REVERT: B 52 LYS cc_start: 0.8242 (tptm) cc_final: 0.7997 (tppp) REVERT: B 117 ARG cc_start: 0.8131 (mmm160) cc_final: 0.7929 (mtp180) REVERT: B 128 PHE cc_start: 0.7967 (t80) cc_final: 0.7759 (t80) REVERT: B 131 ASN cc_start: 0.8223 (t0) cc_final: 0.8004 (t0) REVERT: B 133 ASP cc_start: 0.7809 (t0) cc_final: 0.7597 (t0) REVERT: B 178 SER cc_start: 0.8089 (p) cc_final: 0.7879 (t) REVERT: B 184 ARG cc_start: 0.8028 (tpp-160) cc_final: 0.7809 (tpt-90) REVERT: B 217 GLU cc_start: 0.7032 (mp0) cc_final: 0.6748 (mp0) REVERT: B 227 MET cc_start: 0.8239 (mtp) cc_final: 0.7942 (mtm) REVERT: B 295 ASP cc_start: 0.7838 (t0) cc_final: 0.7469 (t0) REVERT: B 315 ASP cc_start: 0.7434 (p0) cc_final: 0.7119 (p0) REVERT: B 420 MET cc_start: 0.8484 (mmm) cc_final: 0.8070 (mmm) REVERT: B 436 LEU cc_start: 0.8676 (mt) cc_final: 0.8446 (mp) REVERT: B 550 MET cc_start: 0.8411 (mtm) cc_final: 0.8190 (mtp) REVERT: B 559 LYS cc_start: 0.7980 (mttp) cc_final: 0.7724 (mttm) REVERT: B 581 THR cc_start: 0.8034 (p) cc_final: 0.7163 (t) REVERT: B 598 MET cc_start: 0.7430 (mtp) cc_final: 0.7119 (mtm) REVERT: B 612 TYR cc_start: 0.7908 (m-80) cc_final: 0.7606 (m-80) REVERT: B 631 ASP cc_start: 0.7589 (m-30) cc_final: 0.7332 (m-30) REVERT: B 639 ASP cc_start: 0.7406 (m-30) cc_final: 0.7195 (m-30) REVERT: B 660 ASP cc_start: 0.7020 (m-30) cc_final: 0.6814 (m-30) outliers start: 13 outliers final: 7 residues processed: 418 average time/residue: 1.3552 time to fit residues: 609.5291 Evaluate side-chains 352 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 346 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 409 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 329 ASN A 410 ASN A 676 HIS B 34 HIS B 180 ASN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN B 422 HIS B 621 ASN B 645 GLN B 676 HIS E 60 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.122468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.108665 restraints weight = 16929.987| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.71 r_work: 0.3302 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 12431 Z= 0.287 Angle : 0.636 7.845 16796 Z= 0.330 Chirality : 0.047 0.184 1794 Planarity : 0.004 0.064 2131 Dihedral : 12.244 164.390 1747 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.75 % Allowed : 21.50 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.51 (0.21), residues: 1466 helix: 0.80 (0.19), residues: 693 sheet: -0.23 (0.39), residues: 161 loop : 0.15 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 25 HIS 0.011 0.002 HIS A 676 PHE 0.021 0.002 PHE B 492 TYR 0.017 0.002 TYR A 140 ARG 0.006 0.001 ARG A 677 Details of bonding type rmsd hydrogen bonds : bond 0.04172 ( 554) hydrogen bonds : angle 5.37326 ( 1602) SS BOND : bond 0.00919 ( 3) SS BOND : angle 2.40342 ( 6) covalent geometry : bond 0.00658 (12428) covalent geometry : angle 0.63414 (16790) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 364 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8137 (tttt) cc_final: 0.7811 (ttmm) REVERT: A 23 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7603 (mtmm) REVERT: A 31 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6988 (mt-10) REVERT: A 47 PHE cc_start: 0.7935 (t80) cc_final: 0.7572 (t80) REVERT: A 52 LYS cc_start: 0.7994 (tptm) cc_final: 0.7368 (tppp) REVERT: A 56 ASP cc_start: 0.7715 (m-30) cc_final: 0.7356 (m-30) REVERT: A 119 GLU cc_start: 0.7582 (mp0) cc_final: 0.7254 (mp0) REVERT: A 121 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7702 (tpp-160) REVERT: A 174 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7663 (mm-30) REVERT: A 187 ASP cc_start: 0.8133 (t70) cc_final: 0.7843 (t0) REVERT: A 200 SER cc_start: 0.8353 (t) cc_final: 0.8133 (m) REVERT: A 209 LYS cc_start: 0.8242 (ttpp) cc_final: 0.7893 (ttmm) REVERT: A 211 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7290 (mt-10) REVERT: A 286 ASP cc_start: 0.7555 (m-30) cc_final: 0.7160 (m-30) REVERT: A 312 GLN cc_start: 0.8133 (mt0) cc_final: 0.7846 (mt0) REVERT: A 316 GLU cc_start: 0.7786 (mp0) cc_final: 0.7509 (mp0) REVERT: A 341 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8149 (mptt) REVERT: A 384 GLU cc_start: 0.7846 (pp20) cc_final: 0.7215 (pp20) REVERT: A 406 ASP cc_start: 0.7375 (m-30) cc_final: 0.7001 (t0) REVERT: A 452 ARG cc_start: 0.8421 (ttm-80) cc_final: 0.8181 (ttm-80) REVERT: A 458 MET cc_start: 0.8326 (mmm) cc_final: 0.8068 (mmm) REVERT: A 480 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8060 (mt-10) REVERT: A 515 ASP cc_start: 0.8126 (m-30) cc_final: 0.7897 (m-30) REVERT: A 541 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6829 (tm-30) REVERT: A 548 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7698 (tm-30) REVERT: A 599 GLU cc_start: 0.7961 (pt0) cc_final: 0.7751 (pt0) REVERT: A 610 LYS cc_start: 0.7676 (ttpp) cc_final: 0.7445 (ttpp) REVERT: A 612 TYR cc_start: 0.7884 (m-80) cc_final: 0.7622 (m-80) REVERT: B 18 ILE cc_start: 0.8467 (mm) cc_final: 0.8256 (mt) REVERT: B 44 ASN cc_start: 0.8250 (m-40) cc_final: 0.7811 (m-40) REVERT: B 65 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7357 (mm-30) REVERT: B 82 LYS cc_start: 0.8444 (mmmt) cc_final: 0.8242 (mtpt) REVERT: B 117 ARG cc_start: 0.8211 (mmm160) cc_final: 0.7902 (mtp180) REVERT: B 120 ASP cc_start: 0.8288 (m-30) cc_final: 0.8078 (m-30) REVERT: B 133 ASP cc_start: 0.8067 (t0) cc_final: 0.7767 (t0) REVERT: B 217 GLU cc_start: 0.7774 (mp0) cc_final: 0.7401 (mp0) REVERT: B 240 MET cc_start: 0.1281 (ppp) cc_final: 0.1063 (ppp) REVERT: B 243 ARG cc_start: 0.2495 (OUTLIER) cc_final: 0.1801 (ptm-80) REVERT: B 295 ASP cc_start: 0.8174 (t0) cc_final: 0.7817 (t0) REVERT: B 318 ASP cc_start: 0.8003 (t0) cc_final: 0.7653 (t0) REVERT: B 319 MET cc_start: 0.8478 (tpp) cc_final: 0.8156 (tpt) REVERT: B 358 ILE cc_start: 0.8751 (mm) cc_final: 0.8517 (mt) REVERT: B 384 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7473 (pm20) REVERT: B 406 ASP cc_start: 0.7266 (m-30) cc_final: 0.6916 (t0) REVERT: B 420 MET cc_start: 0.8693 (mmm) cc_final: 0.8055 (mmm) REVERT: B 494 MET cc_start: 0.8345 (mtp) cc_final: 0.8131 (mtp) REVERT: B 518 GLU cc_start: 0.7751 (mp0) cc_final: 0.7520 (mm-30) REVERT: B 526 GLU cc_start: 0.7762 (tp30) cc_final: 0.7530 (tp30) REVERT: B 550 MET cc_start: 0.8656 (mtm) cc_final: 0.8364 (mtp) REVERT: B 552 ILE cc_start: 0.8817 (mt) cc_final: 0.8599 (mm) REVERT: B 556 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7600 (mm-30) REVERT: B 581 THR cc_start: 0.8221 (p) cc_final: 0.7772 (t) REVERT: B 598 MET cc_start: 0.8083 (mtp) cc_final: 0.7336 (mtm) REVERT: B 599 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8011 (mt-10) REVERT: B 620 SER cc_start: 0.8536 (m) cc_final: 0.8186 (t) REVERT: B 621 ASN cc_start: 0.8222 (p0) cc_final: 0.8014 (p0) REVERT: B 631 ASP cc_start: 0.8150 (m-30) cc_final: 0.7811 (m-30) REVERT: B 660 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7511 (m-30) REVERT: B 686 ARG cc_start: 0.7501 (mtp85) cc_final: 0.6867 (mtp85) outliers start: 49 outliers final: 18 residues processed: 387 average time/residue: 1.3197 time to fit residues: 549.9599 Evaluate side-chains 362 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 338 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 99 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 142 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 145 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 338 ASN A 410 ASN A 455 ASN A 676 HIS B 11 GLN B 14 ASN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN B 676 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.123791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.109903 restraints weight = 17286.889| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.75 r_work: 0.3321 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12431 Z= 0.192 Angle : 0.560 7.181 16796 Z= 0.290 Chirality : 0.044 0.174 1794 Planarity : 0.004 0.052 2131 Dihedral : 11.817 162.569 1742 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.36 % Allowed : 21.65 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.48 (0.21), residues: 1466 helix: 0.82 (0.19), residues: 700 sheet: -0.28 (0.40), residues: 161 loop : 0.06 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 9 HIS 0.010 0.001 HIS A 676 PHE 0.016 0.002 PHE A 492 TYR 0.019 0.001 TYR A 140 ARG 0.007 0.001 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 554) hydrogen bonds : angle 5.13964 ( 1602) SS BOND : bond 0.00150 ( 3) SS BOND : angle 2.12714 ( 6) covalent geometry : bond 0.00437 (12428) covalent geometry : angle 0.55915 (16790) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 339 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8128 (tttt) cc_final: 0.7801 (ttmm) REVERT: A 13 ASN cc_start: 0.8709 (t0) cc_final: 0.8495 (t0) REVERT: A 14 ASN cc_start: 0.8310 (m110) cc_final: 0.8024 (m-40) REVERT: A 23 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7558 (mtmm) REVERT: A 31 GLU cc_start: 0.7241 (mt-10) cc_final: 0.7039 (mt-10) REVERT: A 47 PHE cc_start: 0.7987 (t80) cc_final: 0.7625 (t80) REVERT: A 52 LYS cc_start: 0.7929 (tptm) cc_final: 0.7302 (tppp) REVERT: A 56 ASP cc_start: 0.7698 (m-30) cc_final: 0.7316 (m-30) REVERT: A 66 GLU cc_start: 0.7398 (tp30) cc_final: 0.7157 (tp30) REVERT: A 119 GLU cc_start: 0.7533 (mp0) cc_final: 0.7211 (mp0) REVERT: A 144 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8068 (mtp) REVERT: A 162 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7899 (ttmt) REVERT: A 174 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7707 (mm-30) REVERT: A 187 ASP cc_start: 0.8128 (t70) cc_final: 0.7850 (t0) REVERT: A 209 LYS cc_start: 0.8196 (ttpp) cc_final: 0.7831 (ttmm) REVERT: A 211 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7284 (mt-10) REVERT: A 286 ASP cc_start: 0.7566 (m-30) cc_final: 0.7198 (m-30) REVERT: A 312 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7809 (mt0) REVERT: A 316 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: A 341 LYS cc_start: 0.8463 (mptt) cc_final: 0.8119 (mptt) REVERT: A 362 ASP cc_start: 0.7932 (m-30) cc_final: 0.7197 (m-30) REVERT: A 384 GLU cc_start: 0.7688 (pp20) cc_final: 0.7132 (pp20) REVERT: A 406 ASP cc_start: 0.7406 (m-30) cc_final: 0.7143 (t0) REVERT: A 458 MET cc_start: 0.8266 (mmm) cc_final: 0.8016 (mmm) REVERT: A 480 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8025 (mt-10) REVERT: A 530 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8008 (ptpp) REVERT: A 545 ASN cc_start: 0.8298 (m-40) cc_final: 0.8068 (m110) REVERT: A 548 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7745 (tm-30) REVERT: A 610 LYS cc_start: 0.7632 (ttpp) cc_final: 0.7346 (ttpp) REVERT: B 18 ILE cc_start: 0.8400 (mm) cc_final: 0.8187 (mt) REVERT: B 46 VAL cc_start: 0.8802 (p) cc_final: 0.8566 (m) REVERT: B 47 PHE cc_start: 0.8205 (t80) cc_final: 0.7867 (t80) REVERT: B 65 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7288 (mm-30) REVERT: B 120 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.8057 (m-30) REVERT: B 133 ASP cc_start: 0.8058 (t0) cc_final: 0.7754 (t0) REVERT: B 217 GLU cc_start: 0.7744 (mp0) cc_final: 0.7338 (mp0) REVERT: B 218 ASN cc_start: 0.8067 (t0) cc_final: 0.7860 (t0) REVERT: B 240 MET cc_start: 0.1309 (ppp) cc_final: 0.0879 (ppp) REVERT: B 295 ASP cc_start: 0.8190 (t0) cc_final: 0.7882 (t0) REVERT: B 318 ASP cc_start: 0.7938 (t0) cc_final: 0.7591 (t0) REVERT: B 319 MET cc_start: 0.8489 (tpp) cc_final: 0.8167 (tpt) REVERT: B 358 ILE cc_start: 0.8686 (mm) cc_final: 0.8459 (mt) REVERT: B 406 ASP cc_start: 0.7319 (m-30) cc_final: 0.7115 (m-30) REVERT: B 420 MET cc_start: 0.8708 (mmm) cc_final: 0.8079 (mmm) REVERT: B 494 MET cc_start: 0.8371 (mtp) cc_final: 0.8097 (mtp) REVERT: B 518 GLU cc_start: 0.7726 (mp0) cc_final: 0.7500 (mm-30) REVERT: B 534 THR cc_start: 0.8574 (m) cc_final: 0.8190 (p) REVERT: B 550 MET cc_start: 0.8674 (mtm) cc_final: 0.8358 (mtp) REVERT: B 556 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7550 (mm-30) REVERT: B 570 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8792 (mtp) REVERT: B 581 THR cc_start: 0.8249 (p) cc_final: 0.7804 (t) REVERT: B 598 MET cc_start: 0.8052 (mtp) cc_final: 0.7108 (mtm) REVERT: B 599 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7931 (mt-10) REVERT: B 620 SER cc_start: 0.8490 (m) cc_final: 0.8258 (p) REVERT: B 621 ASN cc_start: 0.8192 (p0) cc_final: 0.7987 (p0) REVERT: B 686 ARG cc_start: 0.7443 (mtp85) cc_final: 0.6790 (mtp85) outliers start: 57 outliers final: 24 residues processed: 366 average time/residue: 1.3868 time to fit residues: 546.3631 Evaluate side-chains 347 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 315 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 40 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 127 optimal weight: 0.1980 chunk 67 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 14 ASN B 361 GLN B 676 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.124989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.111169 restraints weight = 17107.306| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.73 r_work: 0.3323 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12431 Z= 0.163 Angle : 0.542 6.845 16796 Z= 0.281 Chirality : 0.042 0.169 1794 Planarity : 0.004 0.046 2131 Dihedral : 11.613 163.576 1736 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.52 % Allowed : 22.11 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.21), residues: 1466 helix: 0.98 (0.19), residues: 698 sheet: -0.28 (0.41), residues: 161 loop : 0.03 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 9 HIS 0.008 0.001 HIS B 676 PHE 0.015 0.002 PHE A 261 TYR 0.020 0.001 TYR A 140 ARG 0.006 0.001 ARG B 677 Details of bonding type rmsd hydrogen bonds : bond 0.03413 ( 554) hydrogen bonds : angle 5.06042 ( 1602) SS BOND : bond 0.00180 ( 3) SS BOND : angle 2.20363 ( 6) covalent geometry : bond 0.00373 (12428) covalent geometry : angle 0.54037 (16790) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 337 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8102 (tttt) cc_final: 0.7775 (ttmm) REVERT: A 11 GLN cc_start: 0.7554 (tt0) cc_final: 0.7123 (tm-30) REVERT: A 23 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7597 (mtmm) REVERT: A 31 GLU cc_start: 0.7249 (mt-10) cc_final: 0.7047 (mt-10) REVERT: A 47 PHE cc_start: 0.7969 (t80) cc_final: 0.7620 (t80) REVERT: A 52 LYS cc_start: 0.7909 (tptm) cc_final: 0.7280 (tppp) REVERT: A 56 ASP cc_start: 0.7697 (m-30) cc_final: 0.7311 (m-30) REVERT: A 79 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7281 (mt-10) REVERT: A 119 GLU cc_start: 0.7492 (mp0) cc_final: 0.7240 (mp0) REVERT: A 144 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8068 (mtp) REVERT: A 162 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7909 (ttmt) REVERT: A 187 ASP cc_start: 0.8104 (t70) cc_final: 0.7829 (t0) REVERT: A 209 LYS cc_start: 0.8193 (ttpp) cc_final: 0.7890 (ttmm) REVERT: A 211 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7263 (mt-10) REVERT: A 229 LEU cc_start: 0.8469 (mt) cc_final: 0.8240 (mp) REVERT: A 235 ARG cc_start: 0.8028 (mtm-85) cc_final: 0.7105 (mtm-85) REVERT: A 286 ASP cc_start: 0.7559 (m-30) cc_final: 0.6896 (m-30) REVERT: A 294 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7407 (mp0) REVERT: A 312 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7869 (mt0) REVERT: A 316 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: A 319 MET cc_start: 0.8608 (tpp) cc_final: 0.8328 (tpt) REVERT: A 321 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7604 (tm-30) REVERT: A 341 LYS cc_start: 0.8465 (mptt) cc_final: 0.8106 (mptt) REVERT: A 344 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7422 (mp0) REVERT: A 352 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7577 (mt-10) REVERT: A 362 ASP cc_start: 0.7939 (m-30) cc_final: 0.7007 (m-30) REVERT: A 406 ASP cc_start: 0.7364 (m-30) cc_final: 0.7084 (t0) REVERT: A 458 MET cc_start: 0.8263 (mmm) cc_final: 0.8013 (mmm) REVERT: A 466 MET cc_start: 0.8289 (ptt) cc_final: 0.8069 (ptp) REVERT: A 530 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8015 (ptpp) REVERT: A 545 ASN cc_start: 0.8248 (m-40) cc_final: 0.8017 (m110) REVERT: A 548 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7763 (tm-30) REVERT: A 595 MET cc_start: 0.8350 (mmm) cc_final: 0.8001 (mmm) REVERT: A 610 LYS cc_start: 0.7639 (ttpp) cc_final: 0.7308 (ttpp) REVERT: A 671 ASP cc_start: 0.7488 (m-30) cc_final: 0.7183 (m-30) REVERT: B 18 ILE cc_start: 0.8394 (mm) cc_final: 0.8166 (mt) REVERT: B 46 VAL cc_start: 0.8797 (p) cc_final: 0.8565 (m) REVERT: B 47 PHE cc_start: 0.8178 (t80) cc_final: 0.7849 (t80) REVERT: B 65 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7244 (mm-30) REVERT: B 120 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7997 (m-30) REVERT: B 131 ASN cc_start: 0.8592 (t0) cc_final: 0.8266 (t0) REVERT: B 138 LYS cc_start: 0.7886 (mtpt) cc_final: 0.7660 (mttt) REVERT: B 184 ARG cc_start: 0.8319 (tpp-160) cc_final: 0.7846 (tpt90) REVERT: B 209 LYS cc_start: 0.7933 (ttpt) cc_final: 0.7704 (ttpp) REVERT: B 217 GLU cc_start: 0.7690 (mp0) cc_final: 0.7293 (mp0) REVERT: B 218 ASN cc_start: 0.8100 (t0) cc_final: 0.7850 (t0) REVERT: B 240 MET cc_start: 0.1391 (ppp) cc_final: 0.0945 (ppp) REVERT: B 260 ASP cc_start: 0.8163 (m-30) cc_final: 0.7936 (m-30) REVERT: B 295 ASP cc_start: 0.8209 (t0) cc_final: 0.7896 (t0) REVERT: B 312 GLN cc_start: 0.8359 (mt0) cc_final: 0.8064 (pt0) REVERT: B 318 ASP cc_start: 0.7951 (t0) cc_final: 0.7582 (t0) REVERT: B 319 MET cc_start: 0.8482 (tpp) cc_final: 0.8114 (tpt) REVERT: B 358 ILE cc_start: 0.8701 (mm) cc_final: 0.8492 (mt) REVERT: B 406 ASP cc_start: 0.7344 (m-30) cc_final: 0.7130 (m-30) REVERT: B 420 MET cc_start: 0.8720 (mmm) cc_final: 0.8110 (mmm) REVERT: B 494 MET cc_start: 0.8357 (mtp) cc_final: 0.8091 (mtp) REVERT: B 518 GLU cc_start: 0.7739 (mp0) cc_final: 0.7514 (mm-30) REVERT: B 550 MET cc_start: 0.8638 (mtm) cc_final: 0.8311 (mtp) REVERT: B 556 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7512 (mm-30) REVERT: B 560 LYS cc_start: 0.8235 (mtmm) cc_final: 0.8030 (mtmm) REVERT: B 570 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8804 (mtp) REVERT: B 586 TYR cc_start: 0.8425 (m-80) cc_final: 0.7713 (m-80) REVERT: B 598 MET cc_start: 0.7784 (mtp) cc_final: 0.7103 (mtm) REVERT: B 620 SER cc_start: 0.8461 (m) cc_final: 0.8230 (p) REVERT: B 631 ASP cc_start: 0.8183 (m-30) cc_final: 0.7817 (m-30) REVERT: B 681 THR cc_start: 0.8690 (m) cc_final: 0.8387 (p) REVERT: B 686 ARG cc_start: 0.7440 (mtp85) cc_final: 0.6789 (mtp85) outliers start: 46 outliers final: 23 residues processed: 355 average time/residue: 1.3254 time to fit residues: 507.3411 Evaluate side-chains 354 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 322 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 121 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 47 optimal weight: 0.1980 chunk 143 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 53 optimal weight: 0.0370 chunk 63 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 14 ASN B 361 GLN B 676 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.125593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.111721 restraints weight = 17194.889| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.75 r_work: 0.3332 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12431 Z= 0.144 Angle : 0.533 6.337 16796 Z= 0.276 Chirality : 0.042 0.168 1794 Planarity : 0.003 0.043 2131 Dihedral : 11.353 164.593 1732 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.44 % Allowed : 22.65 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.63 (0.22), residues: 1466 helix: 1.07 (0.19), residues: 700 sheet: -0.29 (0.42), residues: 161 loop : -0.00 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 9 HIS 0.009 0.001 HIS B 676 PHE 0.016 0.001 PHE A 492 TYR 0.018 0.001 TYR A 140 ARG 0.007 0.001 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.03250 ( 554) hydrogen bonds : angle 4.95055 ( 1602) SS BOND : bond 0.00133 ( 3) SS BOND : angle 2.11182 ( 6) covalent geometry : bond 0.00327 (12428) covalent geometry : angle 0.53137 (16790) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 337 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8104 (tttt) cc_final: 0.7747 (ttmm) REVERT: A 23 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7589 (mppt) REVERT: A 31 GLU cc_start: 0.7254 (mt-10) cc_final: 0.7040 (mt-10) REVERT: A 47 PHE cc_start: 0.7972 (t80) cc_final: 0.7627 (t80) REVERT: A 52 LYS cc_start: 0.7889 (tptm) cc_final: 0.7266 (tppp) REVERT: A 56 ASP cc_start: 0.7658 (m-30) cc_final: 0.7259 (m-30) REVERT: A 79 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7269 (mt-10) REVERT: A 119 GLU cc_start: 0.7496 (mp0) cc_final: 0.7232 (mp0) REVERT: A 144 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.8018 (mtp) REVERT: A 162 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7858 (ttmm) REVERT: A 187 ASP cc_start: 0.8023 (t70) cc_final: 0.7763 (t0) REVERT: A 209 LYS cc_start: 0.8166 (ttpp) cc_final: 0.7861 (ttmm) REVERT: A 211 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7288 (mt-10) REVERT: A 235 ARG cc_start: 0.8035 (mtm-85) cc_final: 0.7152 (mtm-85) REVERT: A 286 ASP cc_start: 0.7542 (m-30) cc_final: 0.6810 (m-30) REVERT: A 294 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7323 (mp0) REVERT: A 312 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7828 (mt0) REVERT: A 316 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: A 319 MET cc_start: 0.8578 (tpp) cc_final: 0.8306 (tpt) REVERT: A 321 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7544 (tm-30) REVERT: A 341 LYS cc_start: 0.8458 (mptt) cc_final: 0.8046 (mptt) REVERT: A 344 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7443 (mp0) REVERT: A 362 ASP cc_start: 0.7930 (m-30) cc_final: 0.6985 (m-30) REVERT: A 406 ASP cc_start: 0.7326 (m-30) cc_final: 0.7049 (t0) REVERT: A 458 MET cc_start: 0.8268 (mmm) cc_final: 0.7999 (mmm) REVERT: A 466 MET cc_start: 0.8242 (ptt) cc_final: 0.7926 (ptp) REVERT: A 530 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8008 (ptpp) REVERT: A 545 ASN cc_start: 0.8275 (m-40) cc_final: 0.8058 (m110) REVERT: A 548 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7781 (tm-30) REVERT: A 567 GLU cc_start: 0.7832 (tp30) cc_final: 0.7512 (tp30) REVERT: A 595 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7890 (mmm) REVERT: B 23 LYS cc_start: 0.7871 (mptm) cc_final: 0.7582 (mmtp) REVERT: B 46 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8538 (m) REVERT: B 47 PHE cc_start: 0.8177 (t80) cc_final: 0.7867 (t80) REVERT: B 65 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7215 (mm-30) REVERT: B 120 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7976 (m-30) REVERT: B 131 ASN cc_start: 0.8498 (t0) cc_final: 0.8239 (t0) REVERT: B 138 LYS cc_start: 0.7832 (mtpt) cc_final: 0.7623 (mttm) REVERT: B 184 ARG cc_start: 0.8315 (tpp-160) cc_final: 0.8081 (tpt-90) REVERT: B 209 LYS cc_start: 0.7938 (ttpt) cc_final: 0.7696 (ttpp) REVERT: B 217 GLU cc_start: 0.7688 (mp0) cc_final: 0.7382 (mp0) REVERT: B 218 ASN cc_start: 0.8104 (t0) cc_final: 0.7731 (t0) REVERT: B 240 MET cc_start: 0.1488 (ppp) cc_final: 0.1116 (ppp) REVERT: B 260 ASP cc_start: 0.8131 (m-30) cc_final: 0.7923 (m-30) REVERT: B 295 ASP cc_start: 0.8158 (t0) cc_final: 0.7879 (t0) REVERT: B 312 GLN cc_start: 0.8361 (mt0) cc_final: 0.8117 (pt0) REVERT: B 318 ASP cc_start: 0.7946 (t0) cc_final: 0.7561 (t0) REVERT: B 319 MET cc_start: 0.8482 (tpp) cc_final: 0.8098 (tpt) REVERT: B 406 ASP cc_start: 0.7362 (m-30) cc_final: 0.7139 (m-30) REVERT: B 420 MET cc_start: 0.8684 (mmm) cc_final: 0.8073 (mmm) REVERT: B 444 ASP cc_start: 0.7869 (t70) cc_final: 0.7465 (t0) REVERT: B 494 MET cc_start: 0.8349 (mtp) cc_final: 0.8094 (mtp) REVERT: B 518 GLU cc_start: 0.7759 (mp0) cc_final: 0.7541 (mm-30) REVERT: B 550 MET cc_start: 0.8587 (mtm) cc_final: 0.8323 (mtp) REVERT: B 556 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7501 (mm-30) REVERT: B 570 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8781 (mtp) REVERT: B 581 THR cc_start: 0.8222 (p) cc_final: 0.7819 (t) REVERT: B 598 MET cc_start: 0.7885 (mtp) cc_final: 0.6910 (mtm) REVERT: B 620 SER cc_start: 0.8437 (m) cc_final: 0.8214 (p) REVERT: B 628 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6685 (mm-30) REVERT: B 681 THR cc_start: 0.8697 (m) cc_final: 0.8357 (p) REVERT: B 686 ARG cc_start: 0.7464 (mtp85) cc_final: 0.6884 (mtp85) outliers start: 45 outliers final: 19 residues processed: 355 average time/residue: 1.3052 time to fit residues: 499.9508 Evaluate side-chains 353 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 323 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 684 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 28 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 4 optimal weight: 0.1980 chunk 98 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN B 11 GLN B 361 GLN ** B 415 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 = 0.3643 r_free = 0.3643 target = 0.125312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.111613 restraints weight = 17384.202| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.73 r_work: 0.3342 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12431 Z= 0.148 Angle : 0.533 7.993 16796 Z= 0.274 Chirality : 0.042 0.165 1794 Planarity : 0.003 0.040 2131 Dihedral : 11.198 164.485 1731 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.14 % Allowed : 22.80 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 (0.22), residues: 1466 helix: 1.10 (0.19), residues: 700 sheet: -0.33 (0.42), residues: 161 loop : -0.01 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 9 HIS 0.003 0.001 HIS B 438 PHE 0.016 0.001 PHE B 657 TYR 0.018 0.001 TYR B 612 ARG 0.006 0.001 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.03200 ( 554) hydrogen bonds : angle 4.93365 ( 1602) SS BOND : bond 0.00164 ( 3) SS BOND : angle 2.39843 ( 6) covalent geometry : bond 0.00339 (12428) covalent geometry : angle 0.53115 (16790) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 333 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8100 (tttt) cc_final: 0.7753 (ttpp) REVERT: A 23 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7544 (mtmm) REVERT: A 31 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6994 (mt-10) REVERT: A 47 PHE cc_start: 0.7945 (t80) cc_final: 0.7617 (t80) REVERT: A 52 LYS cc_start: 0.7883 (tptm) cc_final: 0.7236 (tppp) REVERT: A 56 ASP cc_start: 0.7651 (m-30) cc_final: 0.7246 (m-30) REVERT: A 79 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7246 (mt-10) REVERT: A 119 GLU cc_start: 0.7504 (mp0) cc_final: 0.7261 (mp0) REVERT: A 144 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.8020 (mtp) REVERT: A 162 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7878 (ttmm) REVERT: A 187 ASP cc_start: 0.8029 (t70) cc_final: 0.7755 (t0) REVERT: A 209 LYS cc_start: 0.8165 (ttpp) cc_final: 0.7864 (ttmm) REVERT: A 211 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7269 (mt-10) REVERT: A 235 ARG cc_start: 0.8035 (mtm-85) cc_final: 0.7804 (mtm-85) REVERT: A 240 MET cc_start: 0.2145 (tpt) cc_final: 0.1933 (tpt) REVERT: A 286 ASP cc_start: 0.7547 (m-30) cc_final: 0.6834 (m-30) REVERT: A 294 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7320 (mp0) REVERT: A 312 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7822 (mt0) REVERT: A 316 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: A 319 MET cc_start: 0.8570 (tpp) cc_final: 0.8280 (tpt) REVERT: A 321 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7522 (tm-30) REVERT: A 341 LYS cc_start: 0.8454 (mptt) cc_final: 0.8052 (mptt) REVERT: A 344 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7436 (mp0) REVERT: A 362 ASP cc_start: 0.7861 (m-30) cc_final: 0.6879 (m-30) REVERT: A 406 ASP cc_start: 0.7312 (m-30) cc_final: 0.7021 (t0) REVERT: A 458 MET cc_start: 0.8237 (mmm) cc_final: 0.7931 (mmm) REVERT: A 466 MET cc_start: 0.8202 (ptt) cc_final: 0.7918 (ptp) REVERT: A 530 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.8048 (ptpp) REVERT: A 531 TYR cc_start: 0.8343 (m-80) cc_final: 0.7889 (m-80) REVERT: A 545 ASN cc_start: 0.8259 (m-40) cc_final: 0.8050 (m110) REVERT: A 548 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7773 (tm-30) REVERT: A 567 GLU cc_start: 0.7859 (tp30) cc_final: 0.7488 (tp30) REVERT: A 595 MET cc_start: 0.8298 (mmm) cc_final: 0.7895 (mmm) REVERT: A 658 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8087 (mt) REVERT: B 46 VAL cc_start: 0.8730 (OUTLIER) cc_final: 0.8523 (m) REVERT: B 47 PHE cc_start: 0.8151 (t80) cc_final: 0.7873 (t80) REVERT: B 65 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7283 (mm-30) REVERT: B 120 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7986 (m-30) REVERT: B 131 ASN cc_start: 0.8463 (t0) cc_final: 0.8222 (t0) REVERT: B 138 LYS cc_start: 0.7851 (mtpt) cc_final: 0.7649 (mttm) REVERT: B 184 ARG cc_start: 0.8291 (tpp-160) cc_final: 0.8058 (tpt-90) REVERT: B 209 LYS cc_start: 0.7946 (ttpt) cc_final: 0.7706 (ttpp) REVERT: B 260 ASP cc_start: 0.8142 (m-30) cc_final: 0.7937 (m-30) REVERT: B 295 ASP cc_start: 0.8188 (t0) cc_final: 0.7889 (t0) REVERT: B 312 GLN cc_start: 0.8339 (mt0) cc_final: 0.8102 (pt0) REVERT: B 318 ASP cc_start: 0.7964 (t0) cc_final: 0.7585 (t0) REVERT: B 420 MET cc_start: 0.8685 (mmm) cc_final: 0.8083 (mmm) REVERT: B 444 ASP cc_start: 0.7792 (t70) cc_final: 0.7565 (t0) REVERT: B 456 LYS cc_start: 0.8341 (mmtm) cc_final: 0.8031 (mmtm) REVERT: B 494 MET cc_start: 0.8327 (mtp) cc_final: 0.8018 (mtp) REVERT: B 550 MET cc_start: 0.8532 (mtm) cc_final: 0.8288 (mtp) REVERT: B 556 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7484 (mm-30) REVERT: B 560 LYS cc_start: 0.8242 (mtmm) cc_final: 0.8040 (mtmm) REVERT: B 581 THR cc_start: 0.8212 (p) cc_final: 0.7845 (t) REVERT: B 586 TYR cc_start: 0.8393 (m-80) cc_final: 0.7715 (m-80) REVERT: B 598 MET cc_start: 0.7937 (mtp) cc_final: 0.7013 (mtm) REVERT: B 620 SER cc_start: 0.8445 (m) cc_final: 0.8227 (p) REVERT: B 631 ASP cc_start: 0.8070 (m-30) cc_final: 0.7764 (m-30) REVERT: B 681 THR cc_start: 0.8711 (m) cc_final: 0.8340 (p) REVERT: B 686 ARG cc_start: 0.7461 (mtp85) cc_final: 0.6904 (mtp85) outliers start: 41 outliers final: 26 residues processed: 348 average time/residue: 1.2622 time to fit residues: 475.0080 Evaluate side-chains 361 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 325 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 257 ASP Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 684 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 14 ASN B 361 GLN B 415 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.124093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.110350 restraints weight = 17287.752| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.74 r_work: 0.3313 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12431 Z= 0.213 Angle : 0.574 7.959 16796 Z= 0.297 Chirality : 0.044 0.167 1794 Planarity : 0.004 0.042 2131 Dihedral : 11.321 168.461 1731 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.29 % Allowed : 22.95 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.55 (0.22), residues: 1466 helix: 0.97 (0.19), residues: 700 sheet: -0.38 (0.42), residues: 161 loop : 0.02 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 9 HIS 0.004 0.001 HIS E 103 PHE 0.019 0.002 PHE A 564 TYR 0.020 0.002 TYR B 612 ARG 0.006 0.001 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 554) hydrogen bonds : angle 5.08395 ( 1602) SS BOND : bond 0.00228 ( 3) SS BOND : angle 2.40857 ( 6) covalent geometry : bond 0.00489 (12428) covalent geometry : angle 0.57268 (16790) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 332 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8119 (tttt) cc_final: 0.7756 (ttmm) REVERT: A 11 GLN cc_start: 0.7559 (tt0) cc_final: 0.7080 (tm-30) REVERT: A 23 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7462 (mppt) REVERT: A 31 GLU cc_start: 0.7230 (mt-10) cc_final: 0.7022 (mt-10) REVERT: A 47 PHE cc_start: 0.7940 (t80) cc_final: 0.7607 (t80) REVERT: A 52 LYS cc_start: 0.7903 (tptm) cc_final: 0.7228 (tppp) REVERT: A 56 ASP cc_start: 0.7706 (m-30) cc_final: 0.7273 (m-30) REVERT: A 79 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7274 (mt-10) REVERT: A 102 ASN cc_start: 0.8045 (m110) cc_final: 0.7720 (m-40) REVERT: A 119 GLU cc_start: 0.7532 (mp0) cc_final: 0.7288 (mp0) REVERT: A 144 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8044 (mtp) REVERT: A 152 SER cc_start: 0.8386 (p) cc_final: 0.8121 (t) REVERT: A 187 ASP cc_start: 0.8031 (t70) cc_final: 0.7772 (t0) REVERT: A 209 LYS cc_start: 0.8225 (ttpp) cc_final: 0.7866 (ttmm) REVERT: A 211 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7275 (mt-10) REVERT: A 217 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7526 (mm-30) REVERT: A 240 MET cc_start: 0.2156 (tpt) cc_final: 0.1870 (tpt) REVERT: A 286 ASP cc_start: 0.7563 (m-30) cc_final: 0.6821 (m-30) REVERT: A 294 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7443 (mp0) REVERT: A 312 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7866 (mt0) REVERT: A 316 GLU cc_start: 0.7792 (mp0) cc_final: 0.7515 (mp0) REVERT: A 319 MET cc_start: 0.8600 (tpp) cc_final: 0.8349 (tpt) REVERT: A 321 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7516 (tm-30) REVERT: A 322 MET cc_start: 0.7844 (mmm) cc_final: 0.7598 (mtp) REVERT: A 341 LYS cc_start: 0.8471 (mptt) cc_final: 0.8077 (mptt) REVERT: A 344 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7529 (mp0) REVERT: A 352 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7531 (mt-10) REVERT: A 362 ASP cc_start: 0.7868 (m-30) cc_final: 0.6805 (m-30) REVERT: A 406 ASP cc_start: 0.7361 (m-30) cc_final: 0.7086 (t0) REVERT: A 458 MET cc_start: 0.8270 (mmm) cc_final: 0.7999 (mmm) REVERT: A 466 MET cc_start: 0.8237 (ptt) cc_final: 0.7974 (ptp) REVERT: A 530 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8053 (ptpp) REVERT: A 531 TYR cc_start: 0.8351 (m-80) cc_final: 0.7907 (m-80) REVERT: A 545 ASN cc_start: 0.8268 (m-40) cc_final: 0.8056 (m110) REVERT: A 548 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7770 (tm-30) REVERT: A 567 GLU cc_start: 0.7916 (tp30) cc_final: 0.7478 (tp30) REVERT: A 595 MET cc_start: 0.8421 (mmm) cc_final: 0.7942 (mmm) REVERT: B 23 LYS cc_start: 0.7886 (mptm) cc_final: 0.7678 (mmtp) REVERT: B 46 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8504 (m) REVERT: B 47 PHE cc_start: 0.8177 (t80) cc_final: 0.7877 (t80) REVERT: B 65 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7296 (mm-30) REVERT: B 82 LYS cc_start: 0.8365 (mmmt) cc_final: 0.8071 (mtpt) REVERT: B 131 ASN cc_start: 0.8490 (t0) cc_final: 0.8238 (t0) REVERT: B 138 LYS cc_start: 0.7899 (mtpt) cc_final: 0.7671 (mttm) REVERT: B 184 ARG cc_start: 0.8337 (tpp-160) cc_final: 0.7914 (tpt90) REVERT: B 209 LYS cc_start: 0.7940 (ttpt) cc_final: 0.7705 (ttpp) REVERT: B 217 GLU cc_start: 0.7824 (mp0) cc_final: 0.7549 (mp0) REVERT: B 260 ASP cc_start: 0.8193 (m-30) cc_final: 0.7981 (m-30) REVERT: B 295 ASP cc_start: 0.8201 (t0) cc_final: 0.7902 (t0) REVERT: B 312 GLN cc_start: 0.8373 (mt0) cc_final: 0.8064 (pt0) REVERT: B 318 ASP cc_start: 0.7950 (t0) cc_final: 0.7565 (t0) REVERT: B 406 ASP cc_start: 0.7369 (m-30) cc_final: 0.7086 (t0) REVERT: B 420 MET cc_start: 0.8694 (mmm) cc_final: 0.8077 (mmm) REVERT: B 456 LYS cc_start: 0.8355 (mmtm) cc_final: 0.8023 (mmtm) REVERT: B 494 MET cc_start: 0.8353 (mtp) cc_final: 0.8115 (mtp) REVERT: B 550 MET cc_start: 0.8662 (mtm) cc_final: 0.8330 (mtp) REVERT: B 556 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7475 (mm-30) REVERT: B 560 LYS cc_start: 0.8246 (mtmm) cc_final: 0.8011 (mtmm) REVERT: B 598 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7246 (mtm) REVERT: B 631 ASP cc_start: 0.8129 (m-30) cc_final: 0.7850 (m-30) REVERT: B 655 THR cc_start: 0.8315 (m) cc_final: 0.8000 (p) REVERT: B 681 THR cc_start: 0.8752 (m) cc_final: 0.8411 (p) REVERT: B 686 ARG cc_start: 0.7508 (mtp85) cc_final: 0.6921 (mtp85) outliers start: 43 outliers final: 26 residues processed: 350 average time/residue: 1.2518 time to fit residues: 474.9821 Evaluate side-chains 357 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 324 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 684 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 133 optimal weight: 0.9990 chunk 53 optimal weight: 0.0980 chunk 104 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 14 ASN B 218 ASN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.124674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.111132 restraints weight = 17338.867| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.72 r_work: 0.3333 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12431 Z= 0.162 Angle : 0.563 8.843 16796 Z= 0.290 Chirality : 0.043 0.164 1794 Planarity : 0.004 0.041 2131 Dihedral : 11.157 166.613 1731 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.21 % Allowed : 23.49 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.49 (0.22), residues: 1466 helix: 1.00 (0.19), residues: 702 sheet: -0.57 (0.40), residues: 173 loop : -0.05 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 9 HIS 0.003 0.001 HIS E 103 PHE 0.022 0.002 PHE A 68 TYR 0.018 0.001 TYR A 140 ARG 0.008 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03321 ( 554) hydrogen bonds : angle 5.03662 ( 1602) SS BOND : bond 0.00214 ( 3) SS BOND : angle 2.23720 ( 6) covalent geometry : bond 0.00374 (12428) covalent geometry : angle 0.56192 (16790) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 325 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8116 (tttt) cc_final: 0.7769 (ttpp) REVERT: A 23 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7447 (mppt) REVERT: A 31 GLU cc_start: 0.7220 (mt-10) cc_final: 0.7003 (mt-10) REVERT: A 47 PHE cc_start: 0.7989 (t80) cc_final: 0.7685 (t80) REVERT: A 52 LYS cc_start: 0.7905 (tptm) cc_final: 0.7219 (tppp) REVERT: A 56 ASP cc_start: 0.7647 (m-30) cc_final: 0.7236 (m-30) REVERT: A 79 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7269 (mt-10) REVERT: A 102 ASN cc_start: 0.8049 (m110) cc_final: 0.7730 (m-40) REVERT: A 119 GLU cc_start: 0.7498 (mp0) cc_final: 0.7253 (mp0) REVERT: A 144 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.8011 (mtp) REVERT: A 162 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7931 (ttmm) REVERT: A 187 ASP cc_start: 0.8015 (t70) cc_final: 0.7751 (t0) REVERT: A 209 LYS cc_start: 0.8168 (ttpp) cc_final: 0.7830 (ttmm) REVERT: A 211 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7267 (mt-10) REVERT: A 217 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7436 (mm-30) REVERT: A 240 MET cc_start: 0.2097 (tpt) cc_final: 0.1839 (tpt) REVERT: A 286 ASP cc_start: 0.7543 (m-30) cc_final: 0.6774 (m-30) REVERT: A 294 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7479 (mp0) REVERT: A 312 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7849 (mt0) REVERT: A 316 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7427 (mp0) REVERT: A 319 MET cc_start: 0.8582 (tpp) cc_final: 0.8293 (tpt) REVERT: A 321 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7500 (tm-30) REVERT: A 341 LYS cc_start: 0.8469 (mptt) cc_final: 0.8095 (mptt) REVERT: A 344 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7461 (mp0) REVERT: A 352 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7526 (mt-10) REVERT: A 362 ASP cc_start: 0.7840 (m-30) cc_final: 0.6747 (m-30) REVERT: A 406 ASP cc_start: 0.7352 (m-30) cc_final: 0.7079 (t0) REVERT: A 458 MET cc_start: 0.8251 (mmm) cc_final: 0.8003 (mmm) REVERT: A 466 MET cc_start: 0.8191 (ptt) cc_final: 0.7902 (ptp) REVERT: A 530 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.8044 (ptpp) REVERT: A 531 TYR cc_start: 0.8321 (m-80) cc_final: 0.7900 (m-80) REVERT: A 545 ASN cc_start: 0.8263 (m-40) cc_final: 0.8045 (m110) REVERT: A 548 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7740 (tm-30) REVERT: A 567 GLU cc_start: 0.7873 (tp30) cc_final: 0.7418 (tp30) REVERT: A 595 MET cc_start: 0.8436 (mmm) cc_final: 0.7919 (mmm) REVERT: A 598 MET cc_start: 0.7592 (mmm) cc_final: 0.7289 (mmm) REVERT: A 686 ARG cc_start: 0.7321 (mtp85) cc_final: 0.6893 (mtp85) REVERT: B 46 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8506 (m) REVERT: B 47 PHE cc_start: 0.8140 (t80) cc_final: 0.7855 (t80) REVERT: B 48 PHE cc_start: 0.8385 (m-80) cc_final: 0.8167 (m-80) REVERT: B 65 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7299 (mm-30) REVERT: B 131 ASN cc_start: 0.8448 (t0) cc_final: 0.8215 (t0) REVERT: B 184 ARG cc_start: 0.8329 (tpp-160) cc_final: 0.7924 (tpt90) REVERT: B 209 LYS cc_start: 0.7932 (ttpt) cc_final: 0.7706 (ttpp) REVERT: B 217 GLU cc_start: 0.7889 (mp0) cc_final: 0.7430 (mp0) REVERT: B 260 ASP cc_start: 0.8182 (m-30) cc_final: 0.7979 (m-30) REVERT: B 295 ASP cc_start: 0.8179 (t0) cc_final: 0.7929 (t0) REVERT: B 318 ASP cc_start: 0.7857 (t0) cc_final: 0.7440 (t0) REVERT: B 329 ASN cc_start: 0.8137 (t0) cc_final: 0.7911 (t0) REVERT: B 333 LYS cc_start: 0.8322 (ttpp) cc_final: 0.8011 (ttpt) REVERT: B 406 ASP cc_start: 0.7317 (m-30) cc_final: 0.7015 (t0) REVERT: B 420 MET cc_start: 0.8685 (mmm) cc_final: 0.8077 (mmm) REVERT: B 456 LYS cc_start: 0.8329 (mmtm) cc_final: 0.7967 (mmtm) REVERT: B 494 MET cc_start: 0.8354 (mtp) cc_final: 0.8116 (mtp) REVERT: B 550 MET cc_start: 0.8543 (mtm) cc_final: 0.8301 (mtp) REVERT: B 556 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7498 (mm-30) REVERT: B 581 THR cc_start: 0.8381 (p) cc_final: 0.7905 (t) REVERT: B 586 TYR cc_start: 0.8419 (m-80) cc_final: 0.7755 (m-80) REVERT: B 598 MET cc_start: 0.7697 (mtp) cc_final: 0.7053 (mtm) REVERT: B 603 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6811 (tp30) REVERT: B 655 THR cc_start: 0.8320 (m) cc_final: 0.7985 (p) REVERT: B 681 THR cc_start: 0.8724 (m) cc_final: 0.8377 (p) REVERT: B 686 ARG cc_start: 0.7469 (mtp85) cc_final: 0.6835 (mtp85) outliers start: 42 outliers final: 22 residues processed: 341 average time/residue: 1.2908 time to fit residues: 476.3079 Evaluate side-chains 348 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 317 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 603 GLU Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 311 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 129 optimal weight: 0.2980 chunk 76 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 218 ASN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.124355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.110850 restraints weight = 17173.724| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.68 r_work: 0.3337 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12431 Z= 0.165 Angle : 0.574 9.596 16796 Z= 0.294 Chirality : 0.043 0.163 1794 Planarity : 0.004 0.041 2131 Dihedral : 11.089 167.260 1731 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.75 % Allowed : 23.87 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.48 (0.22), residues: 1466 helix: 1.02 (0.19), residues: 698 sheet: -0.58 (0.40), residues: 173 loop : -0.09 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 28 HIS 0.003 0.001 HIS B 438 PHE 0.022 0.002 PHE B 657 TYR 0.019 0.001 TYR A 140 ARG 0.009 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03344 ( 554) hydrogen bonds : angle 5.02711 ( 1602) SS BOND : bond 0.00201 ( 3) SS BOND : angle 2.20577 ( 6) covalent geometry : bond 0.00380 (12428) covalent geometry : angle 0.57279 (16790) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 316 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8130 (tttt) cc_final: 0.7792 (ttpp) REVERT: A 23 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7524 (mtmm) REVERT: A 31 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6985 (mt-10) REVERT: A 38 VAL cc_start: 0.7355 (t) cc_final: 0.7141 (m) REVERT: A 47 PHE cc_start: 0.7967 (t80) cc_final: 0.7657 (t80) REVERT: A 52 LYS cc_start: 0.7913 (tptm) cc_final: 0.7220 (tppp) REVERT: A 56 ASP cc_start: 0.7643 (m-30) cc_final: 0.7225 (m-30) REVERT: A 79 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7263 (mt-10) REVERT: A 102 ASN cc_start: 0.8035 (m110) cc_final: 0.7728 (m-40) REVERT: A 119 GLU cc_start: 0.7469 (mp0) cc_final: 0.7236 (mp0) REVERT: A 144 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8017 (mtp) REVERT: A 162 LYS cc_start: 0.8219 (tttt) cc_final: 0.7945 (ttmm) REVERT: A 187 ASP cc_start: 0.7991 (t70) cc_final: 0.7723 (t0) REVERT: A 209 LYS cc_start: 0.8179 (ttpp) cc_final: 0.7838 (ttmm) REVERT: A 211 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7224 (mt-10) REVERT: A 240 MET cc_start: 0.2067 (tpt) cc_final: 0.1783 (tpt) REVERT: A 286 ASP cc_start: 0.7531 (m-30) cc_final: 0.6732 (m-30) REVERT: A 294 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7487 (mp0) REVERT: A 312 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7834 (mt0) REVERT: A 316 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: A 319 MET cc_start: 0.8575 (tpp) cc_final: 0.8298 (tpt) REVERT: A 321 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7525 (tm-30) REVERT: A 341 LYS cc_start: 0.8438 (mptt) cc_final: 0.8066 (mptt) REVERT: A 344 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7452 (mp0) REVERT: A 362 ASP cc_start: 0.7831 (m-30) cc_final: 0.6718 (m-30) REVERT: A 406 ASP cc_start: 0.7345 (m-30) cc_final: 0.7075 (t0) REVERT: A 458 MET cc_start: 0.8250 (mmm) cc_final: 0.7950 (mmm) REVERT: A 466 MET cc_start: 0.8189 (ptt) cc_final: 0.7883 (ptp) REVERT: A 530 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8051 (ptpp) REVERT: A 531 TYR cc_start: 0.8319 (m-80) cc_final: 0.7851 (m-80) REVERT: A 545 ASN cc_start: 0.8238 (m-40) cc_final: 0.8011 (m110) REVERT: A 548 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7758 (tm-30) REVERT: A 567 GLU cc_start: 0.7871 (tp30) cc_final: 0.7412 (tp30) REVERT: A 595 MET cc_start: 0.8386 (mmm) cc_final: 0.7893 (mmm) REVERT: A 655 THR cc_start: 0.8400 (m) cc_final: 0.7929 (t) REVERT: B 23 LYS cc_start: 0.7859 (mptm) cc_final: 0.7601 (mmtp) REVERT: B 46 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8504 (m) REVERT: B 47 PHE cc_start: 0.8129 (t80) cc_final: 0.7843 (t80) REVERT: B 65 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7292 (mm-30) REVERT: B 82 LYS cc_start: 0.8339 (mmmt) cc_final: 0.8123 (mtpt) REVERT: B 131 ASN cc_start: 0.8439 (t0) cc_final: 0.8219 (t0) REVERT: B 184 ARG cc_start: 0.8333 (tpp-160) cc_final: 0.7904 (tpt90) REVERT: B 209 LYS cc_start: 0.7907 (ttpt) cc_final: 0.7660 (ttpp) REVERT: B 217 GLU cc_start: 0.7902 (mp0) cc_final: 0.7439 (mp0) REVERT: B 295 ASP cc_start: 0.8137 (t0) cc_final: 0.7913 (t0) REVERT: B 318 ASP cc_start: 0.7827 (t0) cc_final: 0.7476 (t0) REVERT: B 329 ASN cc_start: 0.8110 (t0) cc_final: 0.7882 (t0) REVERT: B 406 ASP cc_start: 0.7340 (m-30) cc_final: 0.7006 (t0) REVERT: B 420 MET cc_start: 0.8673 (mmm) cc_final: 0.8049 (mmm) REVERT: B 456 LYS cc_start: 0.8311 (mmtm) cc_final: 0.7943 (mmtm) REVERT: B 494 MET cc_start: 0.8332 (mtp) cc_final: 0.8026 (mtp) REVERT: B 550 MET cc_start: 0.8549 (mtm) cc_final: 0.8307 (mtp) REVERT: B 556 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7454 (mm-30) REVERT: B 560 LYS cc_start: 0.8200 (mtmm) cc_final: 0.7965 (mtmm) REVERT: B 586 TYR cc_start: 0.8393 (m-80) cc_final: 0.7746 (m-80) REVERT: B 598 MET cc_start: 0.7676 (mtp) cc_final: 0.7012 (mtm) REVERT: B 631 ASP cc_start: 0.8138 (m-30) cc_final: 0.7936 (m-30) REVERT: B 655 THR cc_start: 0.8309 (m) cc_final: 0.7990 (p) REVERT: B 681 THR cc_start: 0.8705 (m) cc_final: 0.8411 (p) REVERT: B 686 ARG cc_start: 0.7428 (mtp85) cc_final: 0.6790 (mtp85) outliers start: 36 outliers final: 25 residues processed: 329 average time/residue: 1.2638 time to fit residues: 449.4677 Evaluate side-chains 346 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 314 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 311 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 21 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 14 ASN B 218 ASN B 312 GLN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.123796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.110335 restraints weight = 17271.882| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.69 r_work: 0.3328 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12431 Z= 0.192 Angle : 0.595 9.930 16796 Z= 0.305 Chirality : 0.044 0.180 1794 Planarity : 0.004 0.041 2131 Dihedral : 11.107 167.916 1731 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.68 % Allowed : 24.18 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.42 (0.22), residues: 1466 helix: 0.95 (0.19), residues: 696 sheet: -0.65 (0.41), residues: 173 loop : -0.06 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 28 HIS 0.004 0.001 HIS E 103 PHE 0.022 0.002 PHE B 657 TYR 0.021 0.001 TYR A 140 ARG 0.009 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 554) hydrogen bonds : angle 5.13503 ( 1602) SS BOND : bond 0.00246 ( 3) SS BOND : angle 2.33505 ( 6) covalent geometry : bond 0.00444 (12428) covalent geometry : angle 0.59390 (16790) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 318 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8142 (tttt) cc_final: 0.7817 (ttpp) REVERT: A 23 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7480 (mtmm) REVERT: A 31 GLU cc_start: 0.7222 (mt-10) cc_final: 0.7009 (mt-10) REVERT: A 47 PHE cc_start: 0.7944 (t80) cc_final: 0.7614 (t80) REVERT: A 52 LYS cc_start: 0.7914 (tptm) cc_final: 0.7213 (tppp) REVERT: A 56 ASP cc_start: 0.7669 (m-30) cc_final: 0.7231 (m-30) REVERT: A 79 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7264 (mt-10) REVERT: A 102 ASN cc_start: 0.8072 (m110) cc_final: 0.7740 (m-40) REVERT: A 119 GLU cc_start: 0.7499 (mp0) cc_final: 0.7268 (mp0) REVERT: A 144 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.8013 (mtp) REVERT: A 152 SER cc_start: 0.8399 (p) cc_final: 0.8140 (t) REVERT: A 162 LYS cc_start: 0.8221 (tttt) cc_final: 0.7943 (ttmm) REVERT: A 187 ASP cc_start: 0.8020 (t70) cc_final: 0.7743 (t0) REVERT: A 209 LYS cc_start: 0.8173 (ttpp) cc_final: 0.7835 (ttmm) REVERT: A 211 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7247 (mt-10) REVERT: A 217 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7426 (mm-30) REVERT: A 240 MET cc_start: 0.2040 (tpt) cc_final: 0.1763 (tpt) REVERT: A 286 ASP cc_start: 0.7539 (m-30) cc_final: 0.6750 (m-30) REVERT: A 294 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7525 (mp0) REVERT: A 312 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7822 (mt0) REVERT: A 316 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: A 319 MET cc_start: 0.8606 (tpp) cc_final: 0.8327 (tpt) REVERT: A 321 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7594 (tm-30) REVERT: A 331 ARG cc_start: 0.8140 (mpp80) cc_final: 0.7684 (mtp180) REVERT: A 341 LYS cc_start: 0.8445 (mptt) cc_final: 0.8058 (mptt) REVERT: A 344 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7461 (mp0) REVERT: A 362 ASP cc_start: 0.7825 (m-30) cc_final: 0.6712 (m-30) REVERT: A 406 ASP cc_start: 0.7360 (m-30) cc_final: 0.7093 (t0) REVERT: A 458 MET cc_start: 0.8264 (mmm) cc_final: 0.7967 (mmm) REVERT: A 466 MET cc_start: 0.8163 (ptt) cc_final: 0.7893 (ptp) REVERT: A 530 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.8043 (ptpp) REVERT: A 531 TYR cc_start: 0.8319 (m-80) cc_final: 0.7848 (m-80) REVERT: A 545 ASN cc_start: 0.8253 (m-40) cc_final: 0.8050 (m110) REVERT: A 548 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7764 (tm-30) REVERT: A 567 GLU cc_start: 0.7900 (tp30) cc_final: 0.7457 (tp30) REVERT: A 595 MET cc_start: 0.8433 (mmm) cc_final: 0.7914 (mmm) REVERT: A 655 THR cc_start: 0.8416 (m) cc_final: 0.7730 (t) REVERT: A 657 PHE cc_start: 0.8504 (m-80) cc_final: 0.8043 (m-80) REVERT: A 686 ARG cc_start: 0.7331 (mtp85) cc_final: 0.6932 (mtp85) REVERT: B 23 LYS cc_start: 0.7910 (mptm) cc_final: 0.7650 (mmtp) REVERT: B 46 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8508 (m) REVERT: B 47 PHE cc_start: 0.8153 (t80) cc_final: 0.7889 (t80) REVERT: B 65 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7294 (mm-30) REVERT: B 82 LYS cc_start: 0.8379 (mmmt) cc_final: 0.8099 (mtpt) REVERT: B 131 ASN cc_start: 0.8473 (t0) cc_final: 0.8253 (t0) REVERT: B 184 ARG cc_start: 0.8328 (tpp-160) cc_final: 0.7899 (tpt90) REVERT: B 217 GLU cc_start: 0.7949 (mp0) cc_final: 0.7463 (mp0) REVERT: B 295 ASP cc_start: 0.8151 (t0) cc_final: 0.7931 (t0) REVERT: B 318 ASP cc_start: 0.7880 (t0) cc_final: 0.7461 (t0) REVERT: B 329 ASN cc_start: 0.8129 (t0) cc_final: 0.7895 (t0) REVERT: B 333 LYS cc_start: 0.8326 (ttpp) cc_final: 0.7982 (ttpt) REVERT: B 406 ASP cc_start: 0.7341 (m-30) cc_final: 0.6997 (t0) REVERT: B 420 MET cc_start: 0.8669 (mmm) cc_final: 0.8033 (mmm) REVERT: B 456 LYS cc_start: 0.8295 (mmtm) cc_final: 0.7940 (mmtm) REVERT: B 494 MET cc_start: 0.8349 (mtp) cc_final: 0.8088 (mtp) REVERT: B 550 MET cc_start: 0.8584 (mtm) cc_final: 0.8308 (mtp) REVERT: B 556 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7489 (mm-30) REVERT: B 560 LYS cc_start: 0.8240 (mtmm) cc_final: 0.7994 (mtmm) REVERT: B 586 TYR cc_start: 0.8426 (m-80) cc_final: 0.7758 (m-80) REVERT: B 598 MET cc_start: 0.7718 (mtp) cc_final: 0.7054 (mtm) REVERT: B 655 THR cc_start: 0.8315 (m) cc_final: 0.8022 (p) REVERT: B 681 THR cc_start: 0.8746 (m) cc_final: 0.8452 (p) REVERT: B 686 ARG cc_start: 0.7447 (mtp85) cc_final: 0.6848 (mtp85) outliers start: 35 outliers final: 23 residues processed: 329 average time/residue: 1.3061 time to fit residues: 464.0668 Evaluate side-chains 340 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 310 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 311 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 0.3980 chunk 105 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 129 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 218 ASN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.124666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.111235 restraints weight = 17239.578| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.69 r_work: 0.3343 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12431 Z= 0.152 Angle : 0.580 9.848 16796 Z= 0.297 Chirality : 0.043 0.178 1794 Planarity : 0.004 0.041 2131 Dihedral : 10.968 166.945 1731 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.52 % Allowed : 24.56 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 (0.22), residues: 1466 helix: 1.07 (0.20), residues: 692 sheet: -0.66 (0.41), residues: 173 loop : -0.04 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 28 HIS 0.003 0.001 HIS E 103 PHE 0.026 0.002 PHE A 564 TYR 0.023 0.001 TYR A 140 ARG 0.009 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03288 ( 554) hydrogen bonds : angle 5.08374 ( 1602) SS BOND : bond 0.00215 ( 3) SS BOND : angle 2.12075 ( 6) covalent geometry : bond 0.00350 (12428) covalent geometry : angle 0.57850 (16790) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10340.86 seconds wall clock time: 178 minutes 50.41 seconds (10730.41 seconds total)