Starting phenix.real_space_refine on Tue Jun 10 22:24:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bxt_45011/06_2025/9bxt_45011.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bxt_45011/06_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_45011/06_2025/9bxt_45011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bxt_45011/06_2025/9bxt_45011.map" model { file = "/net/cci-nas-00/data/ceres_data/9bxt_45011/06_2025/9bxt_45011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bxt_45011/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 7.74, per 1000 atoms: 0.64 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: 3.09 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: 1.46 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: 3.97 Time building geometry restraints manager: 3.50 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: 1.190 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: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 29.570 Find NCS groups from input model: 0.510 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:13.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.480 ------------------------------------------------------------------------------- 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 : 1.381 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: 1.4848 time to fit residues: 666.1239 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 : 1.310 ------------------------------------------------------------------------------- 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 = 0.108664 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: 3.85 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 : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8138 (tttt) cc_final: 0.7811 (ttmm) REVERT: A 23 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7605 (mtmm) REVERT: A 31 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6988 (mt-10) REVERT: A 47 PHE cc_start: 0.7937 (t80) cc_final: 0.7572 (t80) REVERT: A 52 LYS cc_start: 0.7994 (tptm) cc_final: 0.7369 (tppp) REVERT: A 56 ASP cc_start: 0.7717 (m-30) cc_final: 0.7359 (m-30) REVERT: A 119 GLU cc_start: 0.7587 (mp0) cc_final: 0.7259 (mp0) REVERT: A 121 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7703 (tpp-160) REVERT: A 174 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7663 (mm-30) REVERT: A 187 ASP cc_start: 0.8134 (t70) cc_final: 0.7844 (t0) REVERT: A 200 SER cc_start: 0.8352 (t) cc_final: 0.8132 (m) REVERT: A 209 LYS cc_start: 0.8242 (ttpp) cc_final: 0.7893 (ttmm) REVERT: A 211 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7290 (mt-10) REVERT: A 286 ASP cc_start: 0.7555 (m-30) cc_final: 0.7161 (m-30) REVERT: A 312 GLN cc_start: 0.8134 (mt0) cc_final: 0.7846 (mt0) REVERT: A 316 GLU cc_start: 0.7787 (mp0) cc_final: 0.7510 (mp0) REVERT: A 341 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8151 (mptt) REVERT: A 384 GLU cc_start: 0.7849 (pp20) cc_final: 0.7217 (pp20) REVERT: A 406 ASP cc_start: 0.7377 (m-30) cc_final: 0.7001 (t0) REVERT: A 452 ARG cc_start: 0.8420 (ttm-80) cc_final: 0.8180 (ttm-80) REVERT: A 458 MET cc_start: 0.8326 (mmm) cc_final: 0.8068 (mmm) REVERT: A 480 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8063 (mt-10) REVERT: A 515 ASP cc_start: 0.8129 (m-30) cc_final: 0.7901 (m-30) REVERT: A 541 GLU cc_start: 0.7186 (tm-30) cc_final: 0.6832 (tm-30) REVERT: A 548 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7695 (tm-30) REVERT: A 599 GLU cc_start: 0.7962 (pt0) cc_final: 0.7753 (pt0) REVERT: A 610 LYS cc_start: 0.7675 (ttpp) cc_final: 0.7444 (ttpp) REVERT: A 612 TYR cc_start: 0.7883 (m-80) cc_final: 0.7620 (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: 0.7813 (m-40) REVERT: B 65 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7360 (mm-30) REVERT: B 82 LYS cc_start: 0.8445 (mmmt) cc_final: 0.8243 (mtpt) REVERT: B 117 ARG cc_start: 0.8211 (mmm160) cc_final: 0.7902 (mtp180) REVERT: B 120 ASP cc_start: 0.8289 (m-30) cc_final: 0.8081 (m-30) REVERT: B 133 ASP cc_start: 0.8066 (t0) cc_final: 0.7768 (t0) REVERT: B 217 GLU cc_start: 0.7776 (mp0) cc_final: 0.7402 (mp0) REVERT: B 240 MET cc_start: 0.1283 (ppp) cc_final: 0.1065 (ppp) REVERT: B 243 ARG cc_start: 0.2495 (OUTLIER) cc_final: 0.1801 (ptm-80) REVERT: B 295 ASP cc_start: 0.8177 (t0) cc_final: 0.7819 (t0) REVERT: B 318 ASP cc_start: 0.8002 (t0) cc_final: 0.7653 (t0) REVERT: B 319 MET cc_start: 0.8477 (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: 0.8096 (OUTLIER) cc_final: 0.7473 (pm20) REVERT: B 406 ASP cc_start: 0.7270 (m-30) cc_final: 0.6921 (t0) REVERT: B 420 MET cc_start: 0.8692 (mmm) cc_final: 0.8055 (mmm) REVERT: B 494 MET cc_start: 0.8344 (mtp) cc_final: 0.8132 (mtp) REVERT: B 518 GLU cc_start: 0.7755 (mp0) cc_final: 0.7523 (mm-30) REVERT: B 526 GLU cc_start: 0.7765 (tp30) cc_final: 0.7531 (tp30) REVERT: B 550 MET cc_start: 0.8657 (mtm) cc_final: 0.8365 (mtp) REVERT: B 552 ILE cc_start: 0.8817 (mt) cc_final: 0.8599 (mm) REVERT: B 556 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7602 (mm-30) REVERT: B 581 THR cc_start: 0.8223 (p) cc_final: 0.7773 (t) REVERT: B 598 MET cc_start: 0.8088 (mtp) cc_final: 0.7342 (mtm) REVERT: B 599 GLU cc_start: 0.8260 (mt-10) cc_final: 0.8013 (mt-10) REVERT: B 620 SER cc_start: 0.8534 (m) cc_final: 0.8186 (t) REVERT: B 621 ASN cc_start: 0.8222 (p0) cc_final: 0.8015 (p0) REVERT: B 631 ASP cc_start: 0.8153 (m-30) cc_final: 0.7815 (m-30) REVERT: B 660 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7513 (m-30) REVERT: B 686 ARG cc_start: 0.7502 (mtp85) cc_final: 0.6870 (mtp85) outliers start: 49 outliers final: 18 residues processed: 387 average time/residue: 1.4260 time to fit residues: 593.3180 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 : 1.375 ------------------------------------------------------------------------------- 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: 0.7980 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 145 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3625 r_free = 0.3625 target = 0.123425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.109469 restraints weight = 17309.068| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.76 r_work: 0.3323 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2799 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= 0.189 Angle : 0.560 7.244 16796 Z= 0.289 Chirality : 0.044 0.175 1794 Planarity : 0.004 0.052 2131 Dihedral : 11.817 162.420 1742 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.36 % Allowed : 21.73 % 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: 0.48 (0.21), residues: 1466 helix: 0.83 (0.19), residues: 700 sheet: -0.27 (0.40), residues: 161 loop : 0.06 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 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 0.03639 ( 554) hydrogen bonds : angle 5.13810 ( 1602) SS BOND : bond 0.00123 ( 3) SS BOND : angle 2.12112 ( 6) covalent geometry : bond 0.00432 (12428) covalent geometry : angle 0.55888 (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 395 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 338 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8127 (tttt) cc_final: 0.7799 (ttmm) REVERT: A 13 ASN cc_start: 0.8706 (t0) cc_final: 0.8505 (t0) REVERT: A 14 ASN cc_start: 0.8306 (m110) cc_final: 0.8020 (m-40) REVERT: A 23 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7586 (mtmm) REVERT: A 31 GLU cc_start: 0.7240 (mt-10) cc_final: 0.7038 (mt-10) REVERT: A 47 PHE cc_start: 0.7985 (t80) cc_final: 0.7623 (t80) REVERT: A 52 LYS cc_start: 0.7926 (tptm) cc_final: 0.7301 (tppp) REVERT: A 56 ASP cc_start: 0.7690 (m-30) cc_final: 0.7306 (m-30) REVERT: A 66 GLU cc_start: 0.7396 (tp30) cc_final: 0.7144 (tp30) REVERT: A 119 GLU cc_start: 0.7527 (mp0) cc_final: 0.7204 (mp0) REVERT: A 133 ASP cc_start: 0.7906 (t70) cc_final: 0.7704 (t0) REVERT: A 144 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8065 (mtp) REVERT: A 162 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7901 (ttmt) REVERT: A 174 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7700 (mm-30) REVERT: A 187 ASP cc_start: 0.8131 (t70) cc_final: 0.7853 (t0) REVERT: A 209 LYS cc_start: 0.8194 (ttpp) cc_final: 0.7825 (ttmm) REVERT: A 211 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7293 (mt-10) REVERT: A 286 ASP cc_start: 0.7570 (m-30) cc_final: 0.7213 (m-30) REVERT: A 312 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7808 (mt0) REVERT: A 316 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: A 341 LYS cc_start: 0.8464 (mptt) cc_final: 0.8120 (mptt) REVERT: A 362 ASP cc_start: 0.7932 (m-30) cc_final: 0.7208 (m-30) REVERT: A 384 GLU cc_start: 0.7690 (pp20) cc_final: 0.7121 (pp20) REVERT: A 406 ASP cc_start: 0.7352 (m-30) cc_final: 0.7086 (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: 0.8029 (mt-10) REVERT: A 530 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8008 (ptpp) REVERT: A 545 ASN cc_start: 0.8297 (m-40) cc_final: 0.8066 (m110) REVERT: A 548 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7692 (tm-30) REVERT: A 610 LYS cc_start: 0.7631 (ttpp) cc_final: 0.7341 (ttpp) REVERT: B 18 ILE cc_start: 0.8399 (mm) cc_final: 0.8188 (mt) REVERT: B 46 VAL cc_start: 0.8802 (p) cc_final: 0.8566 (m) REVERT: B 47 PHE cc_start: 0.8202 (t80) cc_final: 0.7866 (t80) REVERT: B 65 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7291 (mm-30) REVERT: B 120 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.8050 (m-30) REVERT: B 133 ASP cc_start: 0.8059 (t0) cc_final: 0.7755 (t0) REVERT: B 217 GLU cc_start: 0.7738 (mp0) cc_final: 0.7330 (mp0) REVERT: B 218 ASN cc_start: 0.8064 (t0) cc_final: 0.7857 (t0) REVERT: B 240 MET cc_start: 0.1307 (ppp) cc_final: 0.0877 (ppp) REVERT: B 295 ASP cc_start: 0.8190 (t0) cc_final: 0.7882 (t0) REVERT: B 318 ASP cc_start: 0.7939 (t0) cc_final: 0.7592 (t0) REVERT: B 319 MET cc_start: 0.8492 (tpp) cc_final: 0.8169 (tpt) REVERT: B 358 ILE cc_start: 0.8682 (mm) cc_final: 0.8456 (mt) REVERT: B 406 ASP cc_start: 0.7314 (m-30) cc_final: 0.7108 (m-30) REVERT: B 420 MET cc_start: 0.8710 (mmm) cc_final: 0.8086 (mmm) REVERT: B 494 MET cc_start: 0.8371 (mtp) cc_final: 0.8097 (mtp) REVERT: B 518 GLU cc_start: 0.7733 (mp0) cc_final: 0.7507 (mm-30) REVERT: B 534 THR cc_start: 0.8571 (m) cc_final: 0.8181 (p) REVERT: B 550 MET cc_start: 0.8673 (mtm) cc_final: 0.8358 (mtp) REVERT: B 556 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7551 (mm-30) REVERT: B 570 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8784 (mtp) REVERT: B 581 THR cc_start: 0.8249 (p) cc_final: 0.7803 (t) REVERT: B 598 MET cc_start: 0.8048 (mtp) cc_final: 0.7103 (mtm) REVERT: B 599 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7927 (mt-10) REVERT: B 620 SER cc_start: 0.8486 (m) cc_final: 0.8253 (p) REVERT: B 621 ASN cc_start: 0.8185 (p0) cc_final: 0.7980 (p0) REVERT: B 686 ARG cc_start: 0.7443 (mtp85) cc_final: 0.6788 (mtp85) outliers start: 57 outliers final: 23 residues processed: 365 average time/residue: 1.7086 time to fit residues: 671.1081 Evaluate side-chains 353 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 322 time to evaluate : 1.782 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 56 optimal weight: 3.9990 chunk 127 optimal weight: 0.0770 chunk 67 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 101 optimal weight: 0.0070 chunk 13 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 32 optimal weight: 0.0170 chunk 72 optimal weight: 0.9980 overall best weight: 0.2994 ------------------------------------------------------------------------------- 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 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.126696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.112938 restraints weight = 17052.026| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.74 r_work: 0.3352 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12431 Z= 0.116 Angle : 0.519 6.774 16796 Z= 0.269 Chirality : 0.041 0.168 1794 Planarity : 0.003 0.042 2131 Dihedral : 11.404 160.635 1736 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.29 % Allowed : 22.65 % 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: 0.70 (0.21), residues: 1466 helix: 1.12 (0.19), residues: 700 sheet: -0.22 (0.41), residues: 161 loop : 0.02 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 9 HIS 0.008 0.001 HIS B 676 PHE 0.014 0.001 PHE A 492 TYR 0.018 0.001 TYR A 140 ARG 0.007 0.001 ARG B 677 Details of bonding type rmsd hydrogen bonds : bond 0.03132 ( 554) hydrogen bonds : angle 4.92781 ( 1602) SS BOND : bond 0.00194 ( 3) SS BOND : angle 2.19976 ( 6) covalent geometry : bond 0.00261 (12428) covalent geometry : angle 0.51696 (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 393 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 350 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8113 (tttt) cc_final: 0.7766 (ttmm) REVERT: A 23 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7536 (mtmm) REVERT: A 31 GLU cc_start: 0.7226 (mt-10) cc_final: 0.7025 (mt-10) REVERT: A 47 PHE cc_start: 0.8014 (t80) cc_final: 0.7693 (t80) REVERT: A 52 LYS cc_start: 0.7899 (tptm) cc_final: 0.7284 (tppp) REVERT: A 56 ASP cc_start: 0.7636 (m-30) cc_final: 0.7265 (m-30) REVERT: A 66 GLU cc_start: 0.7399 (tp30) cc_final: 0.7155 (tp30) REVERT: A 119 GLU cc_start: 0.7493 (mp0) cc_final: 0.7236 (mp0) REVERT: A 133 ASP cc_start: 0.7781 (t70) cc_final: 0.7567 (t0) REVERT: A 144 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.8005 (mtp) REVERT: A 152 SER cc_start: 0.8351 (p) cc_final: 0.8048 (t) REVERT: A 162 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7934 (mtmt) REVERT: A 174 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7576 (mm-30) REVERT: A 187 ASP cc_start: 0.8094 (t70) cc_final: 0.7818 (t0) REVERT: A 209 LYS cc_start: 0.8178 (ttpp) cc_final: 0.7809 (ttmm) REVERT: A 211 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7263 (mt-10) REVERT: A 286 ASP cc_start: 0.7548 (m-30) cc_final: 0.7089 (m-30) REVERT: A 309 GLU cc_start: 0.7730 (tp30) cc_final: 0.7422 (mm-30) REVERT: A 312 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7869 (mt0) REVERT: A 316 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: A 321 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7606 (tm-30) REVERT: A 341 LYS cc_start: 0.8472 (mptt) cc_final: 0.8151 (mptt) REVERT: A 362 ASP cc_start: 0.7836 (m-30) cc_final: 0.7003 (m-30) REVERT: A 384 GLU cc_start: 0.7595 (pp20) cc_final: 0.7051 (pp20) REVERT: A 406 ASP cc_start: 0.7303 (m-30) cc_final: 0.7030 (t0) REVERT: A 458 MET cc_start: 0.8247 (mmm) cc_final: 0.7986 (mmm) REVERT: A 480 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8026 (mp0) REVERT: A 530 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8021 (ptpp) REVERT: A 545 ASN cc_start: 0.8271 (m-40) cc_final: 0.8033 (m110) REVERT: A 548 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7591 (tm-30) REVERT: A 595 MET cc_start: 0.8293 (mmm) cc_final: 0.7827 (mmm) REVERT: A 605 THR cc_start: 0.8142 (m) cc_final: 0.7919 (p) REVERT: A 610 LYS cc_start: 0.7623 (ttpp) cc_final: 0.7309 (ttpp) REVERT: B 18 ILE cc_start: 0.8403 (mm) cc_final: 0.8181 (mt) REVERT: B 46 VAL cc_start: 0.8770 (p) cc_final: 0.8558 (m) REVERT: B 47 PHE cc_start: 0.8150 (t80) cc_final: 0.7831 (t80) REVERT: B 65 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7229 (mm-30) REVERT: B 120 ASP cc_start: 0.8157 (m-30) cc_final: 0.7920 (m-30) REVERT: B 209 LYS cc_start: 0.7895 (ttpt) cc_final: 0.7597 (ttpp) REVERT: B 217 GLU cc_start: 0.7638 (mp0) cc_final: 0.7251 (mp0) REVERT: B 218 ASN cc_start: 0.8092 (t0) cc_final: 0.7839 (t0) REVERT: B 240 MET cc_start: 0.1364 (ppp) cc_final: 0.0911 (ppp) REVERT: B 295 ASP cc_start: 0.8145 (t0) cc_final: 0.7872 (t0) REVERT: B 312 GLN cc_start: 0.8345 (mt0) cc_final: 0.8034 (pt0) REVERT: B 318 ASP cc_start: 0.7899 (t0) cc_final: 0.7531 (t0) REVERT: B 319 MET cc_start: 0.8482 (tpp) cc_final: 0.8151 (tpt) REVERT: B 358 ILE cc_start: 0.8615 (mm) cc_final: 0.8411 (mt) REVERT: B 406 ASP cc_start: 0.7301 (m-30) cc_final: 0.7077 (m-30) REVERT: B 420 MET cc_start: 0.8711 (mmm) cc_final: 0.8111 (mmm) REVERT: B 444 ASP cc_start: 0.7777 (t70) cc_final: 0.7428 (t0) REVERT: B 456 LYS cc_start: 0.8422 (mmtm) cc_final: 0.8153 (mmtm) REVERT: B 494 MET cc_start: 0.8345 (mtp) cc_final: 0.8036 (mtp) REVERT: B 518 GLU cc_start: 0.7747 (mp0) cc_final: 0.7525 (mm-30) REVERT: B 550 MET cc_start: 0.8588 (mtm) cc_final: 0.8219 (mtp) REVERT: B 556 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7536 (mm-30) REVERT: B 581 THR cc_start: 0.8218 (p) cc_final: 0.7772 (t) REVERT: B 586 TYR cc_start: 0.8412 (m-80) cc_final: 0.7656 (m-80) REVERT: B 598 MET cc_start: 0.7772 (mtp) cc_final: 0.7113 (mtm) REVERT: B 612 TYR cc_start: 0.7942 (m-80) cc_final: 0.7686 (m-80) REVERT: B 620 SER cc_start: 0.8442 (m) cc_final: 0.8208 (p) REVERT: B 621 ASN cc_start: 0.8130 (p0) cc_final: 0.7922 (p0) REVERT: B 631 ASP cc_start: 0.8155 (m-30) cc_final: 0.7778 (m-30) REVERT: B 681 THR cc_start: 0.8655 (m) cc_final: 0.8308 (p) REVERT: B 686 ARG cc_start: 0.7423 (mtp85) cc_final: 0.6771 (mtp85) outliers start: 43 outliers final: 18 residues processed: 368 average time/residue: 1.4653 time to fit residues: 580.0095 Evaluate side-chains 346 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 321 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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 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 684 TYR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 73 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 409 CYS Chi-restraints excluded: chain B residue 410 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 121 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 143 optimal weight: 0.0050 chunk 86 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 72 optimal weight: 0.0010 chunk 10 optimal weight: 0.2980 overall best weight: 0.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 361 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.126991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.113219 restraints weight = 17227.630| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.74 r_work: 0.3354 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3200 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= 0.124 Angle : 0.526 7.172 16796 Z= 0.271 Chirality : 0.041 0.166 1794 Planarity : 0.003 0.039 2131 Dihedral : 11.180 162.823 1732 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.75 % Allowed : 22.72 % Favored : 73.53 % 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: 0.76 (0.22), residues: 1466 helix: 1.23 (0.20), residues: 700 sheet: -0.23 (0.42), residues: 161 loop : 0.00 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 9 HIS 0.003 0.001 HIS B 438 PHE 0.014 0.001 PHE A 261 TYR 0.017 0.001 TYR A 140 ARG 0.008 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03081 ( 554) hydrogen bonds : angle 4.85076 ( 1602) SS BOND : bond 0.00139 ( 3) SS BOND : angle 2.08631 ( 6) covalent geometry : bond 0.00281 (12428) covalent geometry : angle 0.52467 (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 393 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 344 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8143 (tttt) cc_final: 0.7760 (ttmm) REVERT: A 23 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7613 (mtmm) REVERT: A 31 GLU cc_start: 0.7241 (mt-10) cc_final: 0.7033 (mt-10) REVERT: A 47 PHE cc_start: 0.8006 (t80) cc_final: 0.7694 (t80) REVERT: A 52 LYS cc_start: 0.7887 (tptm) cc_final: 0.7242 (tppp) REVERT: A 56 ASP cc_start: 0.7514 (m-30) cc_final: 0.7125 (m-30) REVERT: A 66 GLU cc_start: 0.7382 (tp30) cc_final: 0.7165 (tp30) REVERT: A 79 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7256 (mt-10) REVERT: A 119 GLU cc_start: 0.7482 (mp0) cc_final: 0.7232 (mp0) REVERT: A 133 ASP cc_start: 0.7783 (t0) cc_final: 0.7572 (t0) REVERT: A 144 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7983 (mtp) REVERT: A 152 SER cc_start: 0.8372 (p) cc_final: 0.8073 (t) REVERT: A 161 ARG cc_start: 0.7736 (mtp180) cc_final: 0.7459 (mtm180) REVERT: A 162 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8033 (ttmt) REVERT: A 187 ASP cc_start: 0.8076 (t70) cc_final: 0.7862 (t0) REVERT: A 209 LYS cc_start: 0.8140 (ttpp) cc_final: 0.7902 (ttmm) REVERT: A 211 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7299 (mt-10) REVERT: A 286 ASP cc_start: 0.7565 (m-30) cc_final: 0.7047 (m-30) REVERT: A 312 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7849 (mt0) REVERT: A 316 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: A 319 MET cc_start: 0.8558 (tpp) cc_final: 0.8326 (tpt) REVERT: A 321 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7570 (tm-30) REVERT: A 341 LYS cc_start: 0.8456 (mptt) cc_final: 0.8123 (mptt) REVERT: A 362 ASP cc_start: 0.7848 (m-30) cc_final: 0.7013 (m-30) REVERT: A 406 ASP cc_start: 0.7235 (m-30) cc_final: 0.6970 (t0) REVERT: A 458 MET cc_start: 0.8250 (mmm) cc_final: 0.7951 (mmm) REVERT: A 530 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8022 (ptpp) REVERT: A 531 TYR cc_start: 0.8316 (m-80) cc_final: 0.7900 (m-80) REVERT: A 545 ASN cc_start: 0.8300 (m-40) cc_final: 0.8065 (m110) REVERT: A 548 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7604 (tm-30) REVERT: A 595 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7854 (mmm) REVERT: A 599 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7624 (pm20) REVERT: A 667 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7785 (tp) REVERT: A 671 ASP cc_start: 0.7472 (m-30) cc_final: 0.7168 (m-30) REVERT: B 46 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8545 (m) REVERT: B 47 PHE cc_start: 0.8145 (t80) cc_final: 0.7826 (t80) REVERT: B 65 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7218 (mm-30) REVERT: B 120 ASP cc_start: 0.8168 (m-30) cc_final: 0.7936 (m-30) REVERT: B 176 ASN cc_start: 0.8125 (t0) cc_final: 0.7908 (t0) REVERT: B 184 ARG cc_start: 0.8304 (tpp-160) cc_final: 0.8057 (tpt-90) REVERT: B 217 GLU cc_start: 0.7635 (mp0) cc_final: 0.7362 (mp0) REVERT: B 218 ASN cc_start: 0.8065 (t0) cc_final: 0.7722 (t0) REVERT: B 227 MET cc_start: 0.8367 (mtp) cc_final: 0.8059 (mtm) REVERT: B 240 MET cc_start: 0.1503 (ppp) cc_final: 0.1093 (ppp) REVERT: B 295 ASP cc_start: 0.8144 (t0) cc_final: 0.7851 (t0) REVERT: B 318 ASP cc_start: 0.7818 (t0) cc_final: 0.7403 (t0) REVERT: B 319 MET cc_start: 0.8479 (tpp) cc_final: 0.8145 (tpt) REVERT: B 420 MET cc_start: 0.8705 (mmm) cc_final: 0.8084 (mmm) REVERT: B 456 LYS cc_start: 0.8401 (mmtm) cc_final: 0.8056 (mmtm) REVERT: B 494 MET cc_start: 0.8351 (mtp) cc_final: 0.8130 (mtp) REVERT: B 518 GLU cc_start: 0.7687 (mp0) cc_final: 0.7477 (mm-30) REVERT: B 550 MET cc_start: 0.8548 (mtm) cc_final: 0.8275 (mtp) REVERT: B 556 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7490 (mm-30) REVERT: B 581 THR cc_start: 0.8195 (p) cc_final: 0.7764 (t) REVERT: B 586 TYR cc_start: 0.8392 (m-80) cc_final: 0.7681 (m-80) REVERT: B 598 MET cc_start: 0.7923 (mtp) cc_final: 0.6931 (mtm) REVERT: B 604 ARG cc_start: 0.7551 (mmt-90) cc_final: 0.7310 (mmt-90) REVERT: B 620 SER cc_start: 0.8448 (m) cc_final: 0.8243 (p) REVERT: B 628 GLU cc_start: 0.6950 (mm-30) cc_final: 0.6738 (mm-30) REVERT: B 681 THR cc_start: 0.8673 (m) cc_final: 0.8323 (p) REVERT: B 686 ARG cc_start: 0.7480 (mtp85) cc_final: 0.6884 (mtp85) outliers start: 49 outliers final: 18 residues processed: 363 average time/residue: 1.5218 time to fit residues: 594.4123 Evaluate side-chains 359 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 330 time to evaluate : 1.460 ------------------------------------------------------------------------------- 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 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 595 MET Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 8 LYS Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 168 VAL 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 410 ASN 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: 0.6980 chunk 91 optimal weight: 0.0010 chunk 99 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 57 optimal weight: 0.2980 chunk 94 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 14 ASN B 361 GLN ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.125730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.111950 restraints weight = 17391.229| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.73 r_work: 0.3353 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3354 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= 0.143 Angle : 0.536 7.220 16796 Z= 0.276 Chirality : 0.042 0.165 1794 Planarity : 0.003 0.040 2131 Dihedral : 11.063 162.832 1731 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.14 % Allowed : 23.72 % 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: 0.68 (0.22), residues: 1466 helix: 1.19 (0.19), residues: 702 sheet: -0.47 (0.40), residues: 173 loop : -0.01 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 9 HIS 0.003 0.001 HIS B 568 PHE 0.016 0.001 PHE A 492 TYR 0.019 0.001 TYR A 140 ARG 0.009 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03151 ( 554) hydrogen bonds : angle 4.87911 ( 1602) SS BOND : bond 0.00248 ( 3) SS BOND : angle 2.37501 ( 6) covalent geometry : bond 0.00328 (12428) covalent geometry : angle 0.53401 (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 375 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 334 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8111 (tttt) cc_final: 0.7773 (ttpp) REVERT: A 20 LYS cc_start: 0.8130 (ptmm) cc_final: 0.7893 (ptmm) REVERT: A 23 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7608 (mppt) REVERT: A 31 GLU cc_start: 0.7262 (mt-10) cc_final: 0.7047 (mt-10) REVERT: A 47 PHE cc_start: 0.7979 (t80) cc_final: 0.7656 (t80) REVERT: A 52 LYS cc_start: 0.7890 (tptm) cc_final: 0.7236 (tppp) REVERT: A 56 ASP cc_start: 0.7541 (m-30) cc_final: 0.7148 (m-30) REVERT: A 66 GLU cc_start: 0.7328 (tp30) cc_final: 0.7125 (tp30) REVERT: A 79 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7229 (mt-10) REVERT: A 119 GLU cc_start: 0.7501 (mp0) cc_final: 0.7253 (mp0) REVERT: A 133 ASP cc_start: 0.7786 (t0) cc_final: 0.7555 (t0) REVERT: A 144 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7986 (mtp) REVERT: A 152 SER cc_start: 0.8359 (p) cc_final: 0.8091 (t) REVERT: A 162 LYS cc_start: 0.8311 (tttt) cc_final: 0.7888 (ttmm) REVERT: A 187 ASP cc_start: 0.8144 (t70) cc_final: 0.7889 (t0) REVERT: A 209 LYS cc_start: 0.8152 (ttpp) cc_final: 0.7823 (ttmm) REVERT: A 211 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7269 (mt-10) REVERT: A 240 MET cc_start: 0.2125 (tpt) cc_final: 0.1913 (tpt) REVERT: A 286 ASP cc_start: 0.7555 (m-30) cc_final: 0.6842 (m-30) REVERT: A 294 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7268 (mp0) REVERT: A 312 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7880 (pt0) REVERT: A 316 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: A 319 MET cc_start: 0.8549 (tpp) cc_final: 0.8324 (tpt) REVERT: A 321 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7544 (tm-30) REVERT: A 341 LYS cc_start: 0.8446 (mptt) cc_final: 0.8096 (mptt) REVERT: A 344 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7424 (mp0) REVERT: A 362 ASP cc_start: 0.7911 (m-30) cc_final: 0.6990 (m-30) REVERT: A 386 LEU cc_start: 0.8639 (mt) cc_final: 0.8364 (mt) REVERT: A 406 ASP cc_start: 0.7273 (m-30) cc_final: 0.6993 (t0) REVERT: A 458 MET cc_start: 0.8185 (mmm) cc_final: 0.7877 (mmm) REVERT: A 530 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.8033 (ptpp) REVERT: A 531 TYR cc_start: 0.8317 (m-80) cc_final: 0.7893 (m-80) REVERT: A 545 ASN cc_start: 0.8282 (m-40) cc_final: 0.8055 (m110) REVERT: A 548 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7693 (tm-30) REVERT: A 567 GLU cc_start: 0.7825 (tp30) cc_final: 0.7547 (tp30) REVERT: A 595 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7856 (mmm) REVERT: A 599 GLU cc_start: 0.7751 (pt0) cc_final: 0.7549 (pm20) REVERT: A 667 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7772 (tp) REVERT: A 671 ASP cc_start: 0.7456 (m-30) cc_final: 0.7116 (m-30) REVERT: B 46 VAL cc_start: 0.8722 (OUTLIER) cc_final: 0.8502 (m) REVERT: B 47 PHE cc_start: 0.8156 (t80) cc_final: 0.7843 (t80) REVERT: B 65 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7208 (mm-30) REVERT: B 120 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7966 (m-30) REVERT: B 136 LYS cc_start: 0.8205 (mmmm) cc_final: 0.7983 (tppp) REVERT: B 176 ASN cc_start: 0.8137 (t0) cc_final: 0.7925 (t0) REVERT: B 184 ARG cc_start: 0.8312 (tpp-160) cc_final: 0.8073 (tpt-90) REVERT: B 256 ARG cc_start: 0.8389 (ttp80) cc_final: 0.8188 (tpt90) REVERT: B 295 ASP cc_start: 0.8136 (t0) cc_final: 0.7860 (t0) REVERT: B 318 ASP cc_start: 0.7813 (t0) cc_final: 0.7404 (t0) REVERT: B 319 MET cc_start: 0.8464 (tpp) cc_final: 0.8129 (tpt) REVERT: B 406 ASP cc_start: 0.7308 (m-30) cc_final: 0.6989 (t0) REVERT: B 420 MET cc_start: 0.8671 (mmm) cc_final: 0.8020 (mmm) REVERT: B 456 LYS cc_start: 0.8358 (mmtm) cc_final: 0.7995 (mmtm) REVERT: B 494 MET cc_start: 0.8356 (mtp) cc_final: 0.8104 (mtp) REVERT: B 550 MET cc_start: 0.8523 (mtm) cc_final: 0.8215 (mtp) REVERT: B 556 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7456 (mm-30) REVERT: B 581 THR cc_start: 0.8198 (p) cc_final: 0.7822 (t) REVERT: B 586 TYR cc_start: 0.8374 (m-80) cc_final: 0.7714 (m-80) REVERT: B 598 MET cc_start: 0.7911 (mtp) cc_final: 0.6876 (mtm) REVERT: B 620 SER cc_start: 0.8456 (m) cc_final: 0.8243 (p) REVERT: B 628 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6756 (mm-30) REVERT: B 631 ASP cc_start: 0.8055 (m-30) cc_final: 0.7781 (m-30) REVERT: B 681 THR cc_start: 0.8680 (m) cc_final: 0.8352 (p) REVERT: B 686 ARG cc_start: 0.7480 (mtp85) cc_final: 0.6922 (mtp85) outliers start: 41 outliers final: 19 residues processed: 349 average time/residue: 1.3444 time to fit residues: 505.3825 Evaluate side-chains 360 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 331 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 224 VAL 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 595 MET Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 8 LYS 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 178 SER 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 584 ILE Chi-restraints excluded: chain B residue 589 SER 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: 0.4980 chunk 20 optimal weight: 0.0060 chunk 16 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 312 GLN ** B 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.126112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.112355 restraints weight = 17253.476| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.73 r_work: 0.3363 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12431 Z= 0.132 Angle : 0.537 8.644 16796 Z= 0.276 Chirality : 0.042 0.166 1794 Planarity : 0.003 0.039 2131 Dihedral : 10.924 163.786 1731 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.75 % Allowed : 24.18 % Favored : 73.07 % 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: 0.69 (0.22), residues: 1466 helix: 1.20 (0.19), residues: 702 sheet: -0.53 (0.40), residues: 173 loop : 0.01 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 9 HIS 0.003 0.001 HIS B 438 PHE 0.015 0.001 PHE A 564 TYR 0.016 0.001 TYR B 612 ARG 0.008 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03067 ( 554) hydrogen bonds : angle 4.86825 ( 1602) SS BOND : bond 0.00202 ( 3) SS BOND : angle 2.11387 ( 6) covalent geometry : bond 0.00304 (12428) covalent geometry : angle 0.53552 (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 373 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 337 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8121 (tttt) cc_final: 0.7770 (ttpp) REVERT: A 23 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7589 (mtmm) REVERT: A 31 GLU cc_start: 0.7266 (mt-10) cc_final: 0.7052 (mt-10) REVERT: A 38 VAL cc_start: 0.7289 (t) cc_final: 0.7062 (m) REVERT: A 47 PHE cc_start: 0.7968 (t80) cc_final: 0.7658 (t80) REVERT: A 52 LYS cc_start: 0.7869 (tptm) cc_final: 0.7220 (tppp) REVERT: A 56 ASP cc_start: 0.7524 (m-30) cc_final: 0.7122 (m-30) REVERT: A 79 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7190 (mt-10) REVERT: A 102 ASN cc_start: 0.7916 (m110) cc_final: 0.7598 (m-40) REVERT: A 119 GLU cc_start: 0.7493 (mp0) cc_final: 0.7253 (mp0) REVERT: A 133 ASP cc_start: 0.7815 (t0) cc_final: 0.7595 (t0) REVERT: A 144 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7959 (mtp) REVERT: A 152 SER cc_start: 0.8381 (p) cc_final: 0.8123 (t) REVERT: A 162 LYS cc_start: 0.8324 (tttt) cc_final: 0.7880 (ttmm) REVERT: A 187 ASP cc_start: 0.8118 (t70) cc_final: 0.7871 (t0) REVERT: A 209 LYS cc_start: 0.8144 (ttpp) cc_final: 0.7826 (ttmm) REVERT: A 211 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7249 (mt-10) REVERT: A 231 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7549 (OUTLIER) REVERT: A 240 MET cc_start: 0.2064 (tpt) cc_final: 0.1776 (tpt) REVERT: A 286 ASP cc_start: 0.7560 (m-30) cc_final: 0.6832 (m-30) REVERT: A 294 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7236 (mp0) REVERT: A 316 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: A 319 MET cc_start: 0.8534 (tpp) cc_final: 0.8293 (tpt) REVERT: A 321 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7577 (tm-30) REVERT: A 341 LYS cc_start: 0.8423 (mptt) cc_final: 0.8074 (mptt) REVERT: A 344 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7425 (mp0) REVERT: A 362 ASP cc_start: 0.7852 (m-30) cc_final: 0.6835 (m-30) REVERT: A 386 LEU cc_start: 0.8606 (mt) cc_final: 0.8331 (mt) REVERT: A 406 ASP cc_start: 0.7284 (m-30) cc_final: 0.7054 (t0) REVERT: A 458 MET cc_start: 0.8180 (mmm) cc_final: 0.7867 (mmm) REVERT: A 466 MET cc_start: 0.8125 (ptt) cc_final: 0.7877 (ptp) REVERT: A 530 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.8032 (ptpp) REVERT: A 531 TYR cc_start: 0.8312 (m-80) cc_final: 0.7847 (m-80) REVERT: A 545 ASN cc_start: 0.8267 (m-40) cc_final: 0.8032 (m110) REVERT: A 548 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7739 (tm-30) REVERT: A 567 GLU cc_start: 0.7872 (tp30) cc_final: 0.7540 (tp30) REVERT: A 595 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7862 (mmm) REVERT: A 599 GLU cc_start: 0.7693 (pt0) cc_final: 0.7485 (pm20) REVERT: A 667 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7718 (tp) REVERT: A 671 ASP cc_start: 0.7438 (m-30) cc_final: 0.7106 (m-30) REVERT: B 46 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8494 (m) REVERT: B 47 PHE cc_start: 0.8151 (t80) cc_final: 0.7856 (t80) REVERT: B 65 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7300 (mm-30) REVERT: B 75 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6927 (mm-30) REVERT: B 120 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7971 (m-30) REVERT: B 176 ASN cc_start: 0.8146 (t0) cc_final: 0.7911 (t0) REVERT: B 184 ARG cc_start: 0.8293 (tpp-160) cc_final: 0.8048 (tpt-90) REVERT: B 295 ASP cc_start: 0.8112 (t0) cc_final: 0.7855 (t0) REVERT: B 312 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8087 (pt0) REVERT: B 316 GLU cc_start: 0.7009 (tm-30) cc_final: 0.6571 (tm-30) REVERT: B 318 ASP cc_start: 0.7791 (t0) cc_final: 0.7390 (t0) REVERT: B 319 MET cc_start: 0.8475 (tpp) cc_final: 0.8134 (tpt) REVERT: B 406 ASP cc_start: 0.7316 (m-30) cc_final: 0.6987 (t0) REVERT: B 420 MET cc_start: 0.8665 (mmm) cc_final: 0.8031 (mmm) REVERT: B 456 LYS cc_start: 0.8363 (mmtm) cc_final: 0.7961 (mmtm) REVERT: B 494 MET cc_start: 0.8332 (mtp) cc_final: 0.8067 (mtp) REVERT: B 550 MET cc_start: 0.8548 (mtm) cc_final: 0.8241 (mtp) REVERT: B 556 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7566 (mm-30) REVERT: B 581 THR cc_start: 0.8193 (p) cc_final: 0.7816 (t) REVERT: B 586 TYR cc_start: 0.8359 (m-80) cc_final: 0.7664 (m-80) REVERT: B 598 MET cc_start: 0.7879 (mtp) cc_final: 0.6973 (mtm) REVERT: B 620 SER cc_start: 0.8465 (m) cc_final: 0.8249 (p) REVERT: B 628 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6829 (mm-30) REVERT: B 681 THR cc_start: 0.8699 (m) cc_final: 0.8321 (p) REVERT: B 686 ARG cc_start: 0.7438 (mtp85) cc_final: 0.6892 (mtp85) outliers start: 36 outliers final: 17 residues processed: 352 average time/residue: 1.3890 time to fit residues: 526.8293 Evaluate side-chains 354 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 327 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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 231 ASP Chi-restraints excluded: chain A residue 300 VAL 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 385 VAL 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 A residue 667 LEU Chi-restraints excluded: chain A residue 670 ILE 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 178 SER Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 399 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 133 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 140 optimal weight: 0.0980 chunk 59 optimal weight: 0.2980 chunk 145 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 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 = 0.3658 r_free = 0.3658 target = 0.126048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.112299 restraints weight = 17328.387| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.73 r_work: 0.3356 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12431 Z= 0.135 Angle : 0.549 8.879 16796 Z= 0.280 Chirality : 0.042 0.163 1794 Planarity : 0.003 0.040 2131 Dihedral : 10.831 163.253 1731 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.91 % Allowed : 24.79 % Favored : 72.30 % 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: 0.68 (0.22), residues: 1466 helix: 1.19 (0.19), residues: 702 sheet: -0.56 (0.40), residues: 173 loop : 0.01 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 9 HIS 0.003 0.001 HIS B 438 PHE 0.023 0.001 PHE A 564 TYR 0.018 0.001 TYR A 140 ARG 0.008 0.000 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03054 ( 554) hydrogen bonds : angle 4.85495 ( 1602) SS BOND : bond 0.00207 ( 3) SS BOND : angle 2.11563 ( 6) covalent geometry : bond 0.00312 (12428) covalent geometry : angle 0.54767 (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 373 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 335 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8124 (tttt) cc_final: 0.7770 (ttpp) REVERT: A 23 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7581 (mppt) REVERT: A 31 GLU cc_start: 0.7267 (mt-10) cc_final: 0.7053 (mt-10) REVERT: A 38 VAL cc_start: 0.7268 (t) cc_final: 0.7046 (m) REVERT: A 47 PHE cc_start: 0.7981 (t80) cc_final: 0.7670 (t80) REVERT: A 52 LYS cc_start: 0.7877 (tptm) cc_final: 0.7214 (tppp) REVERT: A 56 ASP cc_start: 0.7498 (m-30) cc_final: 0.7091 (m-30) REVERT: A 79 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7209 (mt-10) REVERT: A 102 ASN cc_start: 0.7928 (m110) cc_final: 0.7611 (m-40) REVERT: A 119 GLU cc_start: 0.7489 (mp0) cc_final: 0.7253 (mp0) REVERT: A 133 ASP cc_start: 0.7792 (t0) cc_final: 0.7556 (t0) REVERT: A 144 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7951 (mtp) REVERT: A 152 SER cc_start: 0.8364 (p) cc_final: 0.8122 (t) REVERT: A 162 LYS cc_start: 0.8355 (tttt) cc_final: 0.7895 (ttmm) REVERT: A 187 ASP cc_start: 0.8118 (t70) cc_final: 0.7857 (t0) REVERT: A 209 LYS cc_start: 0.8129 (ttpp) cc_final: 0.7815 (ttmm) REVERT: A 211 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7313 (mt-10) REVERT: A 231 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7485 (t0) REVERT: A 240 MET cc_start: 0.2046 (tpt) cc_final: 0.1717 (tpt) REVERT: A 286 ASP cc_start: 0.7543 (m-30) cc_final: 0.6795 (m-30) REVERT: A 294 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7241 (mp0) REVERT: A 312 GLN cc_start: 0.8141 (pt0) cc_final: 0.7846 (pt0) REVERT: A 316 GLU cc_start: 0.7730 (mp0) cc_final: 0.7361 (mp0) REVERT: A 319 MET cc_start: 0.8522 (tpp) cc_final: 0.8281 (tpt) REVERT: A 321 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7584 (tm-30) REVERT: A 341 LYS cc_start: 0.8434 (mptt) cc_final: 0.8082 (mptt) REVERT: A 344 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7436 (mp0) REVERT: A 352 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7500 (mt-10) REVERT: A 362 ASP cc_start: 0.7829 (m-30) cc_final: 0.6796 (m-30) REVERT: A 386 LEU cc_start: 0.8630 (mt) cc_final: 0.8352 (mt) REVERT: A 406 ASP cc_start: 0.7316 (m-30) cc_final: 0.7055 (t0) REVERT: A 458 MET cc_start: 0.8174 (mmm) cc_final: 0.7855 (mmm) REVERT: A 466 MET cc_start: 0.8148 (ptt) cc_final: 0.7915 (ptp) REVERT: A 530 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.8034 (ptpp) REVERT: A 531 TYR cc_start: 0.8309 (m-80) cc_final: 0.7847 (m-80) REVERT: A 545 ASN cc_start: 0.8264 (m-40) cc_final: 0.8016 (m110) REVERT: A 548 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7750 (tm-30) REVERT: A 567 GLU cc_start: 0.7880 (tp30) cc_final: 0.7498 (tp30) REVERT: A 570 MET cc_start: 0.8770 (mmm) cc_final: 0.8569 (ttm) REVERT: A 595 MET cc_start: 0.8289 (mmm) cc_final: 0.7920 (mmm) REVERT: A 599 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7543 (pm20) REVERT: A 655 THR cc_start: 0.8411 (m) cc_final: 0.7927 (t) REVERT: A 667 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7764 (tp) REVERT: A 671 ASP cc_start: 0.7467 (m-30) cc_final: 0.7140 (m-30) REVERT: A 686 ARG cc_start: 0.7263 (mtp85) cc_final: 0.6801 (mtp85) REVERT: B 46 VAL cc_start: 0.8689 (OUTLIER) cc_final: 0.8477 (m) REVERT: B 47 PHE cc_start: 0.8144 (t80) cc_final: 0.7854 (t80) REVERT: B 65 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7300 (mm-30) REVERT: B 115 LEU cc_start: 0.8774 (mt) cc_final: 0.8566 (mp) REVERT: B 120 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7986 (m-30) REVERT: B 136 LYS cc_start: 0.8247 (mmmm) cc_final: 0.8015 (tppp) REVERT: B 176 ASN cc_start: 0.8132 (t0) cc_final: 0.7920 (t0) REVERT: B 184 ARG cc_start: 0.8297 (tpp-160) cc_final: 0.7900 (tpt90) REVERT: B 217 GLU cc_start: 0.7834 (mp0) cc_final: 0.7396 (mp0) REVERT: B 295 ASP cc_start: 0.8125 (t0) cc_final: 0.7882 (t0) REVERT: B 312 GLN cc_start: 0.8482 (pt0) cc_final: 0.8054 (pt0) REVERT: B 316 GLU cc_start: 0.7003 (tm-30) cc_final: 0.6558 (tm-30) REVERT: B 318 ASP cc_start: 0.7840 (t0) cc_final: 0.7422 (t0) REVERT: B 319 MET cc_start: 0.8460 (tpp) cc_final: 0.8103 (tpt) REVERT: B 406 ASP cc_start: 0.7339 (m-30) cc_final: 0.7003 (t0) REVERT: B 420 MET cc_start: 0.8658 (mmm) cc_final: 0.8023 (mmm) REVERT: B 456 LYS cc_start: 0.8372 (mttm) cc_final: 0.7947 (mmtm) REVERT: B 494 MET cc_start: 0.8332 (mtp) cc_final: 0.8009 (mtp) REVERT: B 550 MET cc_start: 0.8563 (mtm) cc_final: 0.8316 (mtp) REVERT: B 556 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7554 (mm-30) REVERT: B 567 GLU cc_start: 0.7998 (tp30) cc_final: 0.7640 (tp30) REVERT: B 586 TYR cc_start: 0.8330 (m-80) cc_final: 0.7640 (m-80) REVERT: B 598 MET cc_start: 0.7901 (mtp) cc_final: 0.6979 (mtm) REVERT: B 620 SER cc_start: 0.8459 (m) cc_final: 0.8246 (p) REVERT: B 628 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6838 (mm-30) REVERT: B 681 THR cc_start: 0.8704 (m) cc_final: 0.8365 (p) REVERT: B 686 ARG cc_start: 0.7429 (mtp85) cc_final: 0.6887 (mtp85) outliers start: 38 outliers final: 23 residues processed: 350 average time/residue: 1.6711 time to fit residues: 630.5382 Evaluate side-chains 359 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 327 time to evaluate : 1.394 ------------------------------------------------------------------------------- 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 224 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 300 VAL 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 599 GLU Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 667 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 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 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 684 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 0.0970 chunk 33 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 129 optimal weight: 0.6980 chunk 76 optimal weight: 0.0170 overall best weight: 0.4216 ------------------------------------------------------------------------------- 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 B 361 GLN B 415 ASN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.126481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.112864 restraints weight = 17150.988| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.72 r_work: 0.3358 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12431 Z= 0.129 Angle : 0.557 9.490 16796 Z= 0.283 Chirality : 0.042 0.163 1794 Planarity : 0.004 0.040 2131 Dihedral : 10.719 163.497 1731 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.60 % Allowed : 25.10 % Favored : 72.30 % 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: 0.68 (0.22), residues: 1466 helix: 1.19 (0.20), residues: 704 sheet: -0.16 (0.43), residues: 153 loop : -0.14 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 9 HIS 0.003 0.001 HIS B 438 PHE 0.020 0.001 PHE B 657 TYR 0.017 0.001 TYR A 140 ARG 0.008 0.001 ARG A 677 Details of bonding type rmsd hydrogen bonds : bond 0.03045 ( 554) hydrogen bonds : angle 4.87441 ( 1602) SS BOND : bond 0.00180 ( 3) SS BOND : angle 1.97497 ( 6) covalent geometry : bond 0.00296 (12428) covalent geometry : angle 0.55623 (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 378 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 344 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8139 (tttt) cc_final: 0.7783 (ttpp) REVERT: A 23 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7595 (mtmm) REVERT: A 31 GLU cc_start: 0.7261 (mt-10) cc_final: 0.7050 (mt-10) REVERT: A 38 VAL cc_start: 0.7251 (t) cc_final: 0.7030 (m) REVERT: A 47 PHE cc_start: 0.7939 (t80) cc_final: 0.7624 (t80) REVERT: A 52 LYS cc_start: 0.7871 (tptm) cc_final: 0.7167 (tppp) REVERT: A 56 ASP cc_start: 0.7496 (m-30) cc_final: 0.7078 (m-30) REVERT: A 79 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7210 (mt-10) REVERT: A 102 ASN cc_start: 0.7908 (m110) cc_final: 0.7605 (m-40) REVERT: A 119 GLU cc_start: 0.7486 (mp0) cc_final: 0.7261 (mp0) REVERT: A 133 ASP cc_start: 0.7776 (t0) cc_final: 0.7543 (t0) REVERT: A 144 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7946 (mtp) REVERT: A 152 SER cc_start: 0.8364 (p) cc_final: 0.8121 (t) REVERT: A 162 LYS cc_start: 0.8383 (tttt) cc_final: 0.7934 (ttmm) REVERT: A 187 ASP cc_start: 0.8114 (t70) cc_final: 0.7852 (t0) REVERT: A 209 LYS cc_start: 0.8132 (ttpp) cc_final: 0.7820 (ttmm) REVERT: A 211 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7304 (mt-10) REVERT: A 231 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7459 (t0) REVERT: A 240 MET cc_start: 0.1992 (tpt) cc_final: 0.1654 (tpt) REVERT: A 286 ASP cc_start: 0.7538 (m-30) cc_final: 0.6792 (m-30) REVERT: A 294 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7211 (mp0) REVERT: A 316 GLU cc_start: 0.7750 (mp0) cc_final: 0.7348 (mp0) REVERT: A 319 MET cc_start: 0.8525 (tpp) cc_final: 0.8285 (tpt) REVERT: A 321 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7604 (tm-30) REVERT: A 331 ARG cc_start: 0.8094 (mpp80) cc_final: 0.7588 (mtp180) REVERT: A 341 LYS cc_start: 0.8435 (mptt) cc_final: 0.8046 (mptt) REVERT: A 344 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7471 (mp0) REVERT: A 352 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7486 (mt-10) REVERT: A 362 ASP cc_start: 0.7800 (m-30) cc_final: 0.6782 (m-30) REVERT: A 386 LEU cc_start: 0.8618 (mt) cc_final: 0.8337 (mt) REVERT: A 406 ASP cc_start: 0.7301 (m-30) cc_final: 0.7040 (t0) REVERT: A 458 MET cc_start: 0.8164 (mmm) cc_final: 0.7854 (mmm) REVERT: A 466 MET cc_start: 0.8169 (ptt) cc_final: 0.7859 (ptp) REVERT: A 530 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7972 (ptpp) REVERT: A 531 TYR cc_start: 0.8293 (m-80) cc_final: 0.7855 (m-80) REVERT: A 534 THR cc_start: 0.8113 (m) cc_final: 0.7642 (p) REVERT: A 545 ASN cc_start: 0.8263 (m-40) cc_final: 0.8018 (m110) REVERT: A 548 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7754 (tm-30) REVERT: A 567 GLU cc_start: 0.7895 (tp30) cc_final: 0.7481 (tp30) REVERT: A 570 MET cc_start: 0.8768 (mmm) cc_final: 0.8538 (ttm) REVERT: A 591 THR cc_start: 0.8578 (m) cc_final: 0.7798 (p) REVERT: A 595 MET cc_start: 0.8333 (mmm) cc_final: 0.7839 (mmm) REVERT: A 599 GLU cc_start: 0.7766 (pt0) cc_final: 0.7531 (pm20) REVERT: A 655 THR cc_start: 0.8414 (m) cc_final: 0.7947 (t) REVERT: A 667 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7784 (tp) REVERT: A 671 ASP cc_start: 0.7449 (m-30) cc_final: 0.7123 (m-30) REVERT: A 686 ARG cc_start: 0.7245 (mtp85) cc_final: 0.6798 (mtp85) REVERT: B 23 LYS cc_start: 0.7764 (mptm) cc_final: 0.7557 (mmtp) REVERT: B 46 VAL cc_start: 0.8681 (OUTLIER) cc_final: 0.8479 (m) REVERT: B 47 PHE cc_start: 0.8119 (t80) cc_final: 0.7827 (t80) REVERT: B 65 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7224 (mm-30) REVERT: B 115 LEU cc_start: 0.8778 (mt) cc_final: 0.8554 (mp) REVERT: B 120 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7955 (m-30) REVERT: B 136 LYS cc_start: 0.8232 (mmmm) cc_final: 0.8014 (tppp) REVERT: B 176 ASN cc_start: 0.8145 (t0) cc_final: 0.7937 (t0) REVERT: B 184 ARG cc_start: 0.8290 (tpp-160) cc_final: 0.7899 (tpt90) REVERT: B 217 GLU cc_start: 0.7865 (mp0) cc_final: 0.7438 (mp0) REVERT: B 295 ASP cc_start: 0.8108 (t0) cc_final: 0.7874 (t0) REVERT: B 318 ASP cc_start: 0.7763 (t0) cc_final: 0.7371 (t0) REVERT: B 319 MET cc_start: 0.8479 (tpp) cc_final: 0.8115 (tpt) REVERT: B 406 ASP cc_start: 0.7321 (m-30) cc_final: 0.6989 (t0) REVERT: B 420 MET cc_start: 0.8638 (mmm) cc_final: 0.7982 (mmm) REVERT: B 452 ARG cc_start: 0.8372 (mtp85) cc_final: 0.8061 (mtp180) REVERT: B 456 LYS cc_start: 0.8373 (mttm) cc_final: 0.7963 (mmtm) REVERT: B 494 MET cc_start: 0.8333 (mtp) cc_final: 0.8092 (mtp) REVERT: B 550 MET cc_start: 0.8298 (mtm) cc_final: 0.8069 (mtp) REVERT: B 556 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7604 (mm-30) REVERT: B 586 TYR cc_start: 0.8338 (m-80) cc_final: 0.7609 (m-80) REVERT: B 598 MET cc_start: 0.7841 (mtp) cc_final: 0.6752 (mtm) REVERT: B 620 SER cc_start: 0.8436 (m) cc_final: 0.8221 (p) REVERT: B 628 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6792 (mm-30) REVERT: B 681 THR cc_start: 0.8707 (m) cc_final: 0.8351 (p) REVERT: B 686 ARG cc_start: 0.7408 (mtp85) cc_final: 0.6840 (mtp85) REVERT: E 42 LEU cc_start: 0.8186 (tp) cc_final: 0.7930 (tp) outliers start: 34 outliers final: 21 residues processed: 355 average time/residue: 1.4117 time to fit residues: 543.9649 Evaluate side-chains 362 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 333 time to evaluate : 1.607 ------------------------------------------------------------------------------- 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 224 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 300 VAL 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 667 LEU 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 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 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 684 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 21 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 6 optimal weight: 0.0170 chunk 2 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN B 11 GLN B 218 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.125402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.111731 restraints weight = 17236.789| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.73 r_work: 0.3340 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12431 Z= 0.163 Angle : 0.582 9.953 16796 Z= 0.295 Chirality : 0.043 0.174 1794 Planarity : 0.004 0.041 2131 Dihedral : 10.698 164.538 1731 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.45 % Allowed : 25.86 % Favored : 71.69 % 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: 0.57 (0.22), residues: 1466 helix: 1.09 (0.19), residues: 704 sheet: -0.56 (0.40), residues: 173 loop : -0.04 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 9 HIS 0.003 0.001 HIS E 103 PHE 0.027 0.002 PHE A 564 TYR 0.019 0.001 TYR A 140 ARG 0.008 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03206 ( 554) hydrogen bonds : angle 4.95020 ( 1602) SS BOND : bond 0.00208 ( 3) SS BOND : angle 2.07381 ( 6) covalent geometry : bond 0.00378 (12428) covalent geometry : angle 0.58070 (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 358 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 326 time to evaluate : 2.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8130 (tttt) cc_final: 0.7771 (ttpp) REVERT: A 19 GLN cc_start: 0.8294 (mt0) cc_final: 0.8008 (mt0) REVERT: A 23 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7487 (mtmm) REVERT: A 31 GLU cc_start: 0.7247 (mt-10) cc_final: 0.7037 (mt-10) REVERT: A 38 VAL cc_start: 0.7293 (t) cc_final: 0.7066 (m) REVERT: A 47 PHE cc_start: 0.7964 (t80) cc_final: 0.7653 (t80) REVERT: A 52 LYS cc_start: 0.7862 (tptm) cc_final: 0.7160 (tppp) REVERT: A 56 ASP cc_start: 0.7532 (m-30) cc_final: 0.7100 (m-30) REVERT: A 79 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7205 (mt-10) REVERT: A 102 ASN cc_start: 0.7960 (m110) cc_final: 0.7665 (m-40) REVERT: A 119 GLU cc_start: 0.7501 (mp0) cc_final: 0.7282 (mp0) REVERT: A 133 ASP cc_start: 0.7794 (t0) cc_final: 0.7565 (t0) REVERT: A 144 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7972 (mtp) REVERT: A 152 SER cc_start: 0.8377 (p) cc_final: 0.8121 (t) REVERT: A 162 LYS cc_start: 0.8378 (tttt) cc_final: 0.8103 (ttmm) REVERT: A 187 ASP cc_start: 0.8136 (t70) cc_final: 0.7870 (t0) REVERT: A 209 LYS cc_start: 0.8110 (ttpp) cc_final: 0.7750 (ttmm) REVERT: A 211 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7312 (mt-10) REVERT: A 240 MET cc_start: 0.1976 (tpt) cc_final: 0.1671 (tpt) REVERT: A 286 ASP cc_start: 0.7546 (m-30) cc_final: 0.6791 (m-30) REVERT: A 294 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7238 (mp0) REVERT: A 316 GLU cc_start: 0.7768 (mp0) cc_final: 0.7381 (mp0) REVERT: A 317 MET cc_start: 0.8624 (mtp) cc_final: 0.8369 (mtp) REVERT: A 319 MET cc_start: 0.8543 (tpp) cc_final: 0.8253 (tpt) REVERT: A 321 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7606 (tm-30) REVERT: A 341 LYS cc_start: 0.8444 (mptt) cc_final: 0.8097 (mptt) REVERT: A 344 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7466 (mp0) REVERT: A 352 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7518 (mt-10) REVERT: A 362 ASP cc_start: 0.7816 (m-30) cc_final: 0.6784 (m-30) REVERT: A 386 LEU cc_start: 0.8632 (mt) cc_final: 0.8363 (mt) REVERT: A 406 ASP cc_start: 0.7344 (m-30) cc_final: 0.7091 (t0) REVERT: A 458 MET cc_start: 0.8178 (mmm) cc_final: 0.7862 (mmm) REVERT: A 466 MET cc_start: 0.8184 (ptt) cc_final: 0.7972 (ptp) REVERT: A 530 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.8023 (ptpp) REVERT: A 531 TYR cc_start: 0.8294 (m-80) cc_final: 0.7837 (m-80) REVERT: A 545 ASN cc_start: 0.8267 (m-40) cc_final: 0.8025 (m110) REVERT: A 548 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7716 (tm-30) REVERT: A 567 GLU cc_start: 0.7915 (tp30) cc_final: 0.7495 (tp30) REVERT: A 591 THR cc_start: 0.8610 (m) cc_final: 0.7809 (p) REVERT: A 595 MET cc_start: 0.8415 (mmm) cc_final: 0.7887 (mmm) REVERT: A 599 GLU cc_start: 0.7816 (pt0) cc_final: 0.7598 (pm20) REVERT: A 637 VAL cc_start: 0.7611 (t) cc_final: 0.7349 (p) REVERT: A 655 THR cc_start: 0.8430 (m) cc_final: 0.7954 (t) REVERT: A 667 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7782 (tp) REVERT: A 671 ASP cc_start: 0.7439 (m-30) cc_final: 0.7103 (m-30) REVERT: A 686 ARG cc_start: 0.7252 (mtp85) cc_final: 0.6816 (mtp85) REVERT: B 23 LYS cc_start: 0.7810 (mptm) cc_final: 0.7597 (mmtp) REVERT: B 46 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8482 (m) REVERT: B 47 PHE cc_start: 0.8123 (t80) cc_final: 0.7842 (t80) REVERT: B 65 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7279 (mm-30) REVERT: B 115 LEU cc_start: 0.8782 (mt) cc_final: 0.8568 (mp) REVERT: B 120 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7999 (m-30) REVERT: B 131 ASN cc_start: 0.8592 (t0) cc_final: 0.8288 (t0) REVERT: B 136 LYS cc_start: 0.8218 (mmmm) cc_final: 0.7994 (tppp) REVERT: B 176 ASN cc_start: 0.8153 (t0) cc_final: 0.7935 (t0) REVERT: B 184 ARG cc_start: 0.8299 (tpp-160) cc_final: 0.7962 (tpt90) REVERT: B 217 GLU cc_start: 0.7897 (mp0) cc_final: 0.7453 (mp0) REVERT: B 295 ASP cc_start: 0.8138 (t0) cc_final: 0.7883 (t0) REVERT: B 316 GLU cc_start: 0.6923 (tm-30) cc_final: 0.6481 (tm-30) REVERT: B 318 ASP cc_start: 0.7830 (t0) cc_final: 0.7444 (t0) REVERT: B 319 MET cc_start: 0.8499 (tpp) cc_final: 0.8136 (tpt) REVERT: B 333 LYS cc_start: 0.8332 (ttpp) cc_final: 0.7999 (ttpt) REVERT: B 406 ASP cc_start: 0.7312 (m-30) cc_final: 0.6994 (t0) REVERT: B 420 MET cc_start: 0.8658 (mmm) cc_final: 0.8031 (mmm) REVERT: B 452 ARG cc_start: 0.8336 (mtp85) cc_final: 0.8022 (mtp180) REVERT: B 456 LYS cc_start: 0.8360 (mttm) cc_final: 0.7950 (mmtm) REVERT: B 550 MET cc_start: 0.8417 (mtm) cc_final: 0.8140 (mtp) REVERT: B 556 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7564 (mm-30) REVERT: B 586 TYR cc_start: 0.8369 (m-80) cc_final: 0.7652 (m-80) REVERT: B 598 MET cc_start: 0.7842 (mtp) cc_final: 0.6819 (mtm) REVERT: B 628 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6880 (mm-30) REVERT: B 681 THR cc_start: 0.8746 (m) cc_final: 0.8437 (p) REVERT: B 686 ARG cc_start: 0.7444 (mtp85) cc_final: 0.6873 (mtp85) outliers start: 32 outliers final: 20 residues processed: 338 average time/residue: 1.8564 time to fit residues: 677.4586 Evaluate side-chains 353 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 326 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 224 VAL 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 414 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 661 THR Chi-restraints excluded: chain A residue 667 LEU 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 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 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 684 TYR 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: 1.9990 chunk 105 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 129 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 89 optimal weight: 0.0030 chunk 108 optimal weight: 0.6980 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.126711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.112924 restraints weight = 17058.414| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.69 r_work: 0.3371 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12431 Z= 0.146 Angle : 0.581 10.018 16796 Z= 0.296 Chirality : 0.043 0.186 1794 Planarity : 0.004 0.041 2131 Dihedral : 10.624 165.039 1731 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.37 % Allowed : 25.71 % Favored : 71.92 % 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: 0.63 (0.22), residues: 1466 helix: 1.16 (0.20), residues: 698 sheet: -0.57 (0.40), residues: 173 loop : -0.01 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 9 HIS 0.003 0.001 HIS B 422 PHE 0.026 0.001 PHE A 564 TYR 0.022 0.001 TYR A 140 ARG 0.009 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03175 ( 554) hydrogen bonds : angle 4.97136 ( 1602) SS BOND : bond 0.00198 ( 3) SS BOND : angle 1.99177 ( 6) covalent geometry : bond 0.00337 (12428) covalent geometry : angle 0.57951 (16790) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11776.23 seconds wall clock time: 207 minutes 52.13 seconds (12472.13 seconds total)