Starting phenix.real_space_refine on Thu Jul 2 17:07:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xka_66953/07_2026/9xka_66953.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xka_66953/07_2026/9xka_66953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xka_66953/07_2026/9xka_66953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xka_66953/07_2026/9xka_66953.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xka_66953/07_2026/9xka_66953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xka_66953/07_2026/9xka_66953.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 3 5.49 5 Mg 1 5.21 5 S 40 5.16 5 C 5865 2.51 5 N 1535 2.21 5 O 1665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9109 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4514 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 20, 'TRANS': 551} Chain: "B" Number of atoms: 4563 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 573, 4552 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 13, 'TRANS': 559} Conformer: "B" Number of residues, atoms: 573, 4552 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 13, 'TRANS': 559} bond proxies already assigned to first conformer: 4620 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE B 255 " occ=0.42 ... (20 atoms not shown) pdb=" CZ BPHE B 255 " occ=0.58 Time building chain proxies: 1.91, per 1000 atoms: 0.21 Number of scatterers: 9109 At special positions: 0 Unit cell: (104.58, 102.09, 122.01, 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 40 16.00 P 3 15.00 Mg 1 11.99 O 1665 8.00 N 1535 7.00 C 5865 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 313.3 milliseconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2162 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 5 sheets defined 71.8% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 removed outlier: 3.611A pdb=" N LEU A 5 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 6 " --> pdb=" O ALA A 3 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR A 7 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLY A 10 " --> pdb=" O TYR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 42 Proline residue: A 19 - end of helix Proline residue: A 33 - end of helix Processing helix chain 'A' and resid 42 through 47 Processing helix chain 'A' and resid 48 through 98 Processing helix chain 'A' and resid 100 through 108 Processing helix chain 'A' and resid 108 through 134 removed outlier: 3.690A pdb=" N ASP A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 152 Processing helix chain 'A' and resid 155 through 201 removed outlier: 3.715A pdb=" N PHE A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 201 through 207 Processing helix chain 'A' and resid 210 through 264 removed outlier: 3.546A pdb=" N GLU A 214 " --> pdb=" O GLN A 210 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) Proline residue: A 241 - end of helix Processing helix chain 'A' and resid 268 through 281 Processing helix chain 'A' and resid 281 through 311 removed outlier: 4.369A pdb=" N GLU A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'A' and resid 437 through 448 Processing helix chain 'A' and resid 459 through 462 removed outlier: 3.656A pdb=" N ASP A 462 " --> pdb=" O LEU A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 459 through 462' Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 473 through 487 Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 552 through 558 removed outlier: 4.142A pdb=" N ALA A 558 " --> pdb=" O GLU A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 572 Processing helix chain 'B' and resid 8 through 19 Processing helix chain 'B' and resid 20 through 41 Processing helix chain 'B' and resid 41 through 53 removed outlier: 3.665A pdb=" N LEU B 45 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ASP B 47 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU B 53 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 107 Proline residue: B 83 - end of helix Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 119 through 142 removed outlier: 4.282A pdb=" N ASP B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER B 129 " --> pdb=" O VAL B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 161 Processing helix chain 'B' and resid 161 through 210 Proline residue: B 173 - end of helix Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'B' and resid 219 through 273 removed outlier: 3.687A pdb=" N GLY B 240 " --> pdb=" O ASN B 236 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASN B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Proline residue: B 250 - end of helix Processing helix chain 'B' and resid 278 through 294 removed outlier: 4.378A pdb=" N THR B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN B 291 " --> pdb=" O ASN B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 321 removed outlier: 3.970A pdb=" N ASP B 298 " --> pdb=" O LYS B 294 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER B 304 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 389 Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 410 through 417 Processing helix chain 'B' and resid 431 through 437 Processing helix chain 'B' and resid 444 through 455 Processing helix chain 'B' and resid 457 through 464 Processing helix chain 'B' and resid 480 through 495 removed outlier: 4.443A pdb=" N ASN B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 525 Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 559 through 567 Processing helix chain 'B' and resid 567 through 579 removed outlier: 3.755A pdb=" N TYR B 571 " --> pdb=" O LYS B 567 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG B 572 " --> pdb=" O GLY B 568 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 350 through 357 removed outlier: 4.386A pdb=" N GLN A 351 " --> pdb=" O MET A 338 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N MET A 338 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE A 353 " --> pdb=" O ASP A 336 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP A 336 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N PHE A 355 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLU A 334 " --> pdb=" O PHE A 355 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 357 " --> pdb=" O ALA A 332 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ILE A 335 " --> pdb=" O THR A 392 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N THR A 392 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LYS A 337 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N SER A 390 " --> pdb=" O LYS A 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 410 through 413 removed outlier: 6.557A pdb=" N ALA A 411 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ASP A 496 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 413 " --> pdb=" O ASP A 496 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU A 493 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ILE A 526 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU A 495 " --> pdb=" O ILE A 526 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 363 " --> pdb=" O ILE A 525 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY A 364 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N LEU A 542 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE A 366 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE A 539 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 550 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL A 541 " --> pdb=" O VAL A 548 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 422 through 423 Processing sheet with id=AA4, first strand: chain 'B' and resid 364 through 365 removed outlier: 4.064A pdb=" N VAL B 347 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS B 396 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 500 through 503 removed outlier: 6.676A pdb=" N LEU B 500 " --> pdb=" O PHE B 531 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE B 533 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU B 502 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU B 556 " --> pdb=" O VAL B 548 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN B 550 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ILE B 554 " --> pdb=" O ASN B 550 " (cutoff:3.500A) 624 hydrogen bonds defined for protein. 1834 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: 1.29 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2936 1.34 - 1.46: 1480 1.46 - 1.57: 4773 1.57 - 1.69: 3 1.69 - 1.81: 79 Bond restraints: 9271 Sorted by residual: bond pdb=" CB GLU B 337 " pdb=" CG GLU B 337 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.77e+00 bond pdb=" CA PHE A 453 " pdb=" CB PHE A 453 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 1.04e+00 bond pdb=" CB ASP B 120 " pdb=" CG ASP B 120 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.03e+00 bond pdb=" C SER B 301 " pdb=" O SER B 301 " ideal model delta sigma weight residual 1.237 1.247 -0.010 1.19e-02 7.06e+03 7.24e-01 bond pdb=" CA VAL A 32 " pdb=" C VAL A 32 " ideal model delta sigma weight residual 1.524 1.534 -0.009 1.11e-02 8.12e+03 6.78e-01 ... (remaining 9266 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 12459 1.92 - 3.84: 85 3.84 - 5.76: 17 5.76 - 7.67: 1 7.67 - 9.59: 2 Bond angle restraints: 12564 Sorted by residual: angle pdb=" CB MET A 147 " pdb=" CG MET A 147 " pdb=" SD MET A 147 " ideal model delta sigma weight residual 112.70 122.29 -9.59 3.00e+00 1.11e-01 1.02e+01 angle pdb=" CA GLU B 337 " pdb=" CB GLU B 337 " pdb=" CG GLU B 337 " ideal model delta sigma weight residual 114.10 119.85 -5.75 2.00e+00 2.50e-01 8.27e+00 angle pdb=" CB GLU B 337 " pdb=" CG GLU B 337 " pdb=" CD GLU B 337 " ideal model delta sigma weight residual 112.60 117.45 -4.85 1.70e+00 3.46e-01 8.13e+00 angle pdb=" C ILE B 43 " pdb=" N LEU B 44 " pdb=" CA LEU B 44 " ideal model delta sigma weight residual 121.54 126.87 -5.33 1.91e+00 2.74e-01 7.78e+00 angle pdb=" CB MET A 34 " pdb=" CG MET A 34 " pdb=" SD MET A 34 " ideal model delta sigma weight residual 112.70 105.75 6.95 3.00e+00 1.11e-01 5.37e+00 ... (remaining 12559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 4790 17.87 - 35.74: 576 35.74 - 53.61: 191 53.61 - 71.48: 42 71.48 - 89.35: 16 Dihedral angle restraints: 5615 sinusoidal: 2271 harmonic: 3344 Sorted by residual: dihedral pdb=" CA GLN A 281 " pdb=" C GLN A 281 " pdb=" N ILE A 282 " pdb=" CA ILE A 282 " ideal model delta harmonic sigma weight residual 180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ASN A 402 " pdb=" C ASN A 402 " pdb=" N LEU A 403 " pdb=" CA LEU A 403 " ideal model delta harmonic sigma weight residual 180.00 161.66 18.34 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA PRO B 42 " pdb=" C PRO B 42 " pdb=" N ILE B 43 " pdb=" CA ILE B 43 " ideal model delta harmonic sigma weight residual 180.00 162.65 17.35 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 5612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1002 0.030 - 0.060: 321 0.060 - 0.090: 94 0.090 - 0.120: 59 0.120 - 0.149: 6 Chirality restraints: 1482 Sorted by residual: chirality pdb=" CA PHE A 453 " pdb=" N PHE A 453 " pdb=" C PHE A 453 " pdb=" CB PHE A 453 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA PHE B 41 " pdb=" N PHE B 41 " pdb=" C PHE B 41 " pdb=" CB PHE B 41 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ILE B 501 " pdb=" N ILE B 501 " pdb=" C ILE B 501 " pdb=" CB ILE B 501 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 1479 not shown) Planarity restraints: 1577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 44 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.12e+00 pdb=" C LEU B 44 " 0.052 2.00e-02 2.50e+03 pdb=" O LEU B 44 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU B 45 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 41 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO B 42 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 42 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 42 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 120 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.91e+00 pdb=" CG ASP B 120 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASP B 120 " -0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP B 120 " -0.008 2.00e-02 2.50e+03 ... (remaining 1574 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 72 2.60 - 3.18: 7675 3.18 - 3.75: 14593 3.75 - 4.33: 19909 4.33 - 4.90: 33764 Nonbonded interactions: 76013 Sorted by model distance: nonbonded pdb=" OG SER A 374 " pdb="MG MG A 702 " model vdw 2.027 2.170 nonbonded pdb=" OE1 GLN A 415 " pdb="MG MG A 702 " model vdw 2.037 2.170 nonbonded pdb=" OG1 THR B 31 " pdb=" OH TYR B 86 " model vdw 2.097 3.040 nonbonded pdb=" O1G ANP A 701 " pdb="MG MG A 702 " model vdw 2.124 2.170 nonbonded pdb=" O2B ANP A 701 " pdb="MG MG A 702 " model vdw 2.163 2.170 ... (remaining 76008 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.42 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: 2.370 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.810 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 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 : 0.002 0.040 9271 Z= 0.120 Angle : 0.457 9.593 12564 Z= 0.239 Chirality : 0.037 0.149 1482 Planarity : 0.003 0.036 1577 Dihedral : 17.896 89.352 3453 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.51 % Allowed : 25.38 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.25), residues: 1144 helix: 2.41 (0.18), residues: 783 sheet: 0.08 (0.76), residues: 47 loop : -0.71 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 536 TYR 0.009 0.001 TYR A 7 PHE 0.017 0.001 PHE A 453 TRP 0.010 0.001 TRP B 196 HIS 0.002 0.000 HIS B 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 ( 9271) covalent geometry : angle 0.45663 / 0.24 (12564) hydrogen bonds : bond 0.12818 / 8.74 ( 624) hydrogen bonds : angle 4.60113 / 3.49 ( 1834) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.357 Fit side-chains REVERT: A 224 GLU cc_start: 0.8465 (tt0) cc_final: 0.7970 (tp30) REVERT: A 337 LYS cc_start: 0.8046 (mttt) cc_final: 0.7789 (mppt) REVERT: A 470 ARG cc_start: 0.6894 (mtt-85) cc_final: 0.6456 (mmt-90) REVERT: A 504 TYR cc_start: 0.5383 (OUTLIER) cc_final: 0.4400 (m-80) REVERT: A 507 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7514 (tm-30) REVERT: B 55 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7893 (mpp) REVERT: B 305 GLU cc_start: 0.7704 (mm-30) cc_final: 0.6986 (mp0) REVERT: B 412 GLU cc_start: 0.7863 (tt0) cc_final: 0.7112 (mp0) REVERT: B 416 LYS cc_start: 0.8458 (tttt) cc_final: 0.8006 (ttmm) REVERT: B 542 ASN cc_start: 0.7738 (m-40) cc_final: 0.7448 (m110) outliers start: 25 outliers final: 19 residues processed: 127 average time/residue: 0.4994 time to fit residues: 67.8792 Evaluate side-chains 127 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 548 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 ASN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.125875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.095712 restraints weight = 19128.464| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.15 r_work: 0.2871 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2733 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.0504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9271 Z= 0.142 Angle : 0.478 7.321 12564 Z= 0.254 Chirality : 0.038 0.140 1482 Planarity : 0.003 0.036 1577 Dihedral : 6.616 69.989 1305 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.71 % Allowed : 23.77 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.25), residues: 1144 helix: 2.52 (0.18), residues: 779 sheet: -0.14 (0.73), residues: 47 loop : -0.68 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 536 TYR 0.009 0.001 TYR B 244 PHE 0.020 0.001 PHE A 453 TRP 0.009 0.001 TRP B 196 HIS 0.002 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 9271) covalent geometry : angle 0.47821 / 0.25 (12564) hydrogen bonds : bond 0.05344 / 3.60 ( 624) hydrogen bonds : angle 4.00784 / 3.00 ( 1834) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 0.375 Fit side-chains REVERT: A 47 ARG cc_start: 0.7435 (mmt180) cc_final: 0.7219 (mpt90) REVERT: A 224 GLU cc_start: 0.8362 (tt0) cc_final: 0.7756 (tp30) REVERT: A 337 LYS cc_start: 0.8009 (mttt) cc_final: 0.7684 (mppt) REVERT: A 416 LYS cc_start: 0.8041 (tttm) cc_final: 0.7736 (tttm) REVERT: A 470 ARG cc_start: 0.6587 (mtt-85) cc_final: 0.6086 (mmt-90) REVERT: A 504 TYR cc_start: 0.5398 (OUTLIER) cc_final: 0.4409 (m-80) REVERT: A 556 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.7101 (pt) REVERT: A 570 GLN cc_start: 0.6430 (OUTLIER) cc_final: 0.6050 (tt0) REVERT: B 159 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.5578 (ttt180) REVERT: B 260 TYR cc_start: 0.8261 (OUTLIER) cc_final: 0.8035 (t80) REVERT: B 305 GLU cc_start: 0.7606 (mm-30) cc_final: 0.6820 (mp0) REVERT: B 394 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7829 (pp) REVERT: B 412 GLU cc_start: 0.7748 (tt0) cc_final: 0.6872 (mp0) REVERT: B 416 LYS cc_start: 0.8417 (tttt) cc_final: 0.7942 (ttmm) REVERT: B 506 THR cc_start: 0.5640 (OUTLIER) cc_final: 0.5276 (m) REVERT: B 542 ASN cc_start: 0.7643 (m-40) cc_final: 0.7349 (m110) outliers start: 37 outliers final: 15 residues processed: 145 average time/residue: 0.6103 time to fit residues: 94.3262 Evaluate side-chains 129 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 159 ARG Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 532 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 59 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN A 471 ASN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.126436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.096880 restraints weight = 20655.801| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.21 r_work: 0.2869 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.0638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9271 Z= 0.136 Angle : 0.472 8.285 12564 Z= 0.251 Chirality : 0.038 0.141 1482 Planarity : 0.003 0.036 1577 Dihedral : 5.763 59.387 1285 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.61 % Allowed : 23.57 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.25), residues: 1144 helix: 2.52 (0.18), residues: 779 sheet: -0.29 (0.71), residues: 47 loop : -0.63 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 536 TYR 0.010 0.001 TYR B 244 PHE 0.018 0.001 PHE A 453 TRP 0.009 0.001 TRP B 196 HIS 0.002 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 9271) covalent geometry : angle 0.47222 / 0.25 (12564) hydrogen bonds : bond 0.05125 / 3.44 ( 624) hydrogen bonds : angle 3.92396 / 2.94 ( 1834) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.371 Fit side-chains REVERT: A 47 ARG cc_start: 0.7343 (mmt180) cc_final: 0.7129 (mpt90) REVERT: A 224 GLU cc_start: 0.8326 (tt0) cc_final: 0.7653 (tp30) REVERT: A 313 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7292 (mm-40) REVERT: A 337 LYS cc_start: 0.8037 (mttt) cc_final: 0.7684 (mppt) REVERT: A 416 LYS cc_start: 0.7967 (tttm) cc_final: 0.7658 (tttm) REVERT: A 504 TYR cc_start: 0.5352 (OUTLIER) cc_final: 0.4345 (m-80) REVERT: A 570 GLN cc_start: 0.6277 (OUTLIER) cc_final: 0.5990 (tt0) REVERT: B 159 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.5506 (ttt180) REVERT: B 260 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.7975 (t80) REVERT: B 305 GLU cc_start: 0.7514 (mm-30) cc_final: 0.6688 (mp0) REVERT: B 371 VAL cc_start: 0.8231 (OUTLIER) cc_final: 0.8028 (t) REVERT: B 394 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7748 (pp) REVERT: B 412 GLU cc_start: 0.7686 (tt0) cc_final: 0.6790 (mp0) REVERT: B 416 LYS cc_start: 0.8281 (tttt) cc_final: 0.7791 (ttmm) REVERT: B 506 THR cc_start: 0.5695 (OUTLIER) cc_final: 0.5333 (m) REVERT: B 542 ASN cc_start: 0.7589 (m-40) cc_final: 0.7306 (m110) outliers start: 36 outliers final: 19 residues processed: 140 average time/residue: 0.5758 time to fit residues: 86.3094 Evaluate side-chains 135 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 159 ARG Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 532 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN A 471 ASN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.126932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.097308 restraints weight = 20268.857| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.18 r_work: 0.2889 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.0733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9271 Z= 0.120 Angle : 0.452 7.715 12564 Z= 0.241 Chirality : 0.038 0.139 1482 Planarity : 0.003 0.041 1577 Dihedral : 5.625 59.384 1285 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.71 % Allowed : 23.37 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.25), residues: 1144 helix: 2.62 (0.18), residues: 779 sheet: -0.39 (0.70), residues: 47 loop : -0.59 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 536 TYR 0.008 0.001 TYR A 7 PHE 0.018 0.001 PHE A 453 TRP 0.009 0.001 TRP B 196 HIS 0.002 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 ( 9271) covalent geometry : angle 0.45217 / 0.24 (12564) hydrogen bonds : bond 0.04800 / 3.21 ( 624) hydrogen bonds : angle 3.84129 / 2.88 ( 1834) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 0.408 Fit side-chains REVERT: A 47 ARG cc_start: 0.7405 (mmt180) cc_final: 0.7199 (mpt90) REVERT: A 136 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.5829 (tpt90) REVERT: A 224 GLU cc_start: 0.8350 (tt0) cc_final: 0.7728 (tp30) REVERT: A 313 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7263 (mm-40) REVERT: A 337 LYS cc_start: 0.8043 (mttt) cc_final: 0.7723 (mppt) REVERT: A 416 LYS cc_start: 0.7988 (tttm) cc_final: 0.7699 (tttm) REVERT: A 504 TYR cc_start: 0.5332 (OUTLIER) cc_final: 0.4327 (m-80) REVERT: A 570 GLN cc_start: 0.6475 (OUTLIER) cc_final: 0.6122 (tt0) REVERT: B 260 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.7991 (t80) REVERT: B 305 GLU cc_start: 0.7541 (mm-30) cc_final: 0.6740 (mp0) REVERT: B 394 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7792 (pp) REVERT: B 412 GLU cc_start: 0.7694 (tt0) cc_final: 0.6817 (mp0) REVERT: B 416 LYS cc_start: 0.8313 (tttt) cc_final: 0.7845 (ttmm) REVERT: B 506 THR cc_start: 0.5649 (OUTLIER) cc_final: 0.5299 (m) REVERT: B 542 ASN cc_start: 0.7639 (m-40) cc_final: 0.7390 (m110) outliers start: 37 outliers final: 16 residues processed: 138 average time/residue: 0.6175 time to fit residues: 90.7721 Evaluate side-chains 129 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 260 TYR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 532 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 61 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN A 471 ASN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.124125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.095361 restraints weight = 24608.024| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.61 r_work: 0.2818 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9271 Z= 0.170 Angle : 0.511 8.451 12564 Z= 0.268 Chirality : 0.040 0.143 1482 Planarity : 0.004 0.048 1577 Dihedral : 5.657 60.616 1282 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.21 % Allowed : 22.37 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.25), residues: 1144 helix: 2.41 (0.18), residues: 779 sheet: -0.65 (0.68), residues: 47 loop : -0.70 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 536 TYR 0.012 0.001 TYR B 244 PHE 0.024 0.001 PHE A 208 TRP 0.008 0.001 TRP A 228 HIS 0.002 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 9271) covalent geometry : angle 0.51137 / 0.27 (12564) hydrogen bonds : bond 0.05489 / 3.69 ( 624) hydrogen bonds : angle 3.96136 / 2.96 ( 1834) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 110 time to evaluate : 0.383 Fit side-chains REVERT: A 136 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.5916 (tpt90) REVERT: A 224 GLU cc_start: 0.8328 (tt0) cc_final: 0.7671 (tp30) REVERT: A 313 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7283 (mm-40) REVERT: A 337 LYS cc_start: 0.8037 (mttt) cc_final: 0.7680 (mppt) REVERT: A 416 LYS cc_start: 0.8016 (tttm) cc_final: 0.7676 (tttm) REVERT: A 504 TYR cc_start: 0.5354 (OUTLIER) cc_final: 0.4363 (m-80) REVERT: A 507 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7448 (tm-30) REVERT: A 570 GLN cc_start: 0.6419 (OUTLIER) cc_final: 0.6037 (tt0) REVERT: B 159 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.5464 (ttt180) REVERT: B 180 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7370 (ttp-170) REVERT: B 305 GLU cc_start: 0.7560 (mm-30) cc_final: 0.6770 (mp0) REVERT: B 394 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7804 (pp) REVERT: B 412 GLU cc_start: 0.7775 (tt0) cc_final: 0.6808 (mp0) REVERT: B 416 LYS cc_start: 0.8355 (tttt) cc_final: 0.7883 (ttmm) REVERT: B 506 THR cc_start: 0.5649 (OUTLIER) cc_final: 0.5284 (m) REVERT: B 542 ASN cc_start: 0.7606 (m-40) cc_final: 0.7328 (m110) outliers start: 42 outliers final: 18 residues processed: 144 average time/residue: 0.6121 time to fit residues: 94.0194 Evaluate side-chains 135 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 159 ARG Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 180 ARG Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 506 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 11 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN A 277 ASN A 471 ASN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 423 GLN B 562 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.127700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.098955 restraints weight = 22835.817| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.50 r_work: 0.2866 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9271 Z= 0.123 Angle : 0.463 8.257 12564 Z= 0.246 Chirality : 0.038 0.141 1482 Planarity : 0.003 0.050 1577 Dihedral : 5.441 59.946 1280 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.51 % Allowed : 23.77 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.25), residues: 1144 helix: 2.55 (0.18), residues: 779 sheet: -0.73 (0.67), residues: 47 loop : -0.64 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 536 TYR 0.009 0.001 TYR A 7 PHE 0.018 0.001 PHE A 453 TRP 0.010 0.001 TRP B 196 HIS 0.001 0.000 HIS B 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 9271) covalent geometry : angle 0.46343 / 0.25 (12564) hydrogen bonds : bond 0.04895 / 3.28 ( 624) hydrogen bonds : angle 3.86290 / 2.89 ( 1834) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.392 Fit side-chains REVERT: A 136 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.5785 (tpt90) REVERT: A 224 GLU cc_start: 0.8331 (tt0) cc_final: 0.7675 (tp30) REVERT: A 313 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7185 (mm-40) REVERT: A 337 LYS cc_start: 0.8034 (mttt) cc_final: 0.7693 (mppt) REVERT: A 416 LYS cc_start: 0.7947 (tttm) cc_final: 0.7618 (tttm) REVERT: A 504 TYR cc_start: 0.5365 (OUTLIER) cc_final: 0.4361 (m-80) REVERT: A 570 GLN cc_start: 0.6360 (OUTLIER) cc_final: 0.5975 (tt0) REVERT: B 305 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6698 (mp0) REVERT: B 394 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7679 (pp) REVERT: B 412 GLU cc_start: 0.7683 (tt0) cc_final: 0.6746 (mp0) REVERT: B 416 LYS cc_start: 0.8290 (tttt) cc_final: 0.7803 (ttmm) REVERT: B 506 THR cc_start: 0.5685 (OUTLIER) cc_final: 0.5305 (m) REVERT: B 542 ASN cc_start: 0.7599 (m-40) cc_final: 0.7345 (m110) outliers start: 35 outliers final: 17 residues processed: 137 average time/residue: 0.6029 time to fit residues: 88.2151 Evaluate side-chains 129 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 506 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 34 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 4 optimal weight: 0.0970 chunk 106 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN A 471 ASN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN B 562 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.124563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.094315 restraints weight = 17873.294| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.08 r_work: 0.2852 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9271 Z= 0.161 Angle : 0.506 8.698 12564 Z= 0.265 Chirality : 0.039 0.144 1482 Planarity : 0.004 0.052 1577 Dihedral : 5.639 59.826 1280 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.61 % Allowed : 23.77 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.25), residues: 1144 helix: 2.40 (0.18), residues: 779 sheet: -0.86 (0.67), residues: 47 loop : -0.72 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 536 TYR 0.012 0.001 TYR B 244 PHE 0.022 0.001 PHE A 208 TRP 0.008 0.001 TRP A 228 HIS 0.002 0.001 HIS A 553 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 9271) covalent geometry : angle 0.50643 / 0.27 (12564) hydrogen bonds : bond 0.05382 / 3.62 ( 624) hydrogen bonds : angle 3.94329 / 2.95 ( 1834) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.410 Fit side-chains REVERT: A 136 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.5920 (tpt90) REVERT: A 224 GLU cc_start: 0.8307 (tt0) cc_final: 0.7739 (tp30) REVERT: A 313 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7295 (mm-40) REVERT: A 337 LYS cc_start: 0.8074 (mttt) cc_final: 0.7753 (mppt) REVERT: A 416 LYS cc_start: 0.8037 (tttm) cc_final: 0.7712 (tttm) REVERT: A 504 TYR cc_start: 0.5528 (OUTLIER) cc_final: 0.4456 (m-80) REVERT: A 570 GLN cc_start: 0.6530 (OUTLIER) cc_final: 0.6152 (tt0) REVERT: B 159 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.5456 (ttt180) REVERT: B 180 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7438 (ttp-170) REVERT: B 305 GLU cc_start: 0.7611 (mm-30) cc_final: 0.6869 (mp0) REVERT: B 394 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7858 (pp) REVERT: B 412 GLU cc_start: 0.7718 (tt0) cc_final: 0.6841 (mp0) REVERT: B 416 LYS cc_start: 0.8396 (tttt) cc_final: 0.7911 (ttmm) REVERT: B 506 THR cc_start: 0.5635 (OUTLIER) cc_final: 0.5278 (m) REVERT: B 542 ASN cc_start: 0.7638 (m-40) cc_final: 0.7382 (m110) outliers start: 36 outliers final: 17 residues processed: 134 average time/residue: 0.6228 time to fit residues: 88.9866 Evaluate side-chains 127 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 159 ARG Chi-restraints excluded: chain B residue 180 ARG Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 506 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 42 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 30 optimal weight: 0.0970 chunk 84 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN A 277 ASN A 471 ASN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN B 423 GLN B 562 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.126207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.096561 restraints weight = 16077.882| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.91 r_work: 0.2897 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9271 Z= 0.127 Angle : 0.479 9.443 12564 Z= 0.252 Chirality : 0.038 0.142 1482 Planarity : 0.004 0.053 1577 Dihedral : 5.477 59.723 1280 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.01 % Allowed : 24.47 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.25), residues: 1144 helix: 2.51 (0.18), residues: 779 sheet: -0.85 (0.67), residues: 47 loop : -0.66 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 536 TYR 0.009 0.001 TYR A 7 PHE 0.018 0.001 PHE A 453 TRP 0.010 0.001 TRP B 196 HIS 0.002 0.000 HIS B 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 ( 9271) covalent geometry : angle 0.47880 / 0.25 (12564) hydrogen bonds : bond 0.04928 / 3.30 ( 624) hydrogen bonds : angle 3.87316 / 2.90 ( 1834) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.379 Fit side-chains REVERT: A 136 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.5832 (tpt90) REVERT: A 224 GLU cc_start: 0.8280 (tt0) cc_final: 0.7711 (tp30) REVERT: A 313 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7228 (mm-40) REVERT: A 337 LYS cc_start: 0.8077 (mttt) cc_final: 0.7751 (mppt) REVERT: A 416 LYS cc_start: 0.8014 (tttm) cc_final: 0.7721 (tttm) REVERT: A 504 TYR cc_start: 0.5513 (OUTLIER) cc_final: 0.4479 (m-80) REVERT: A 507 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7480 (tm-30) REVERT: A 570 GLN cc_start: 0.6456 (OUTLIER) cc_final: 0.6054 (tt0) REVERT: B 305 GLU cc_start: 0.7556 (mm-30) cc_final: 0.6810 (mp0) REVERT: B 394 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7744 (pp) REVERT: B 412 GLU cc_start: 0.7657 (tt0) cc_final: 0.6789 (mp0) REVERT: B 416 LYS cc_start: 0.8399 (tttt) cc_final: 0.7921 (ttmm) REVERT: B 506 THR cc_start: 0.5619 (OUTLIER) cc_final: 0.5250 (m) REVERT: B 542 ASN cc_start: 0.7628 (m-40) cc_final: 0.7349 (m110) outliers start: 30 outliers final: 20 residues processed: 129 average time/residue: 0.5929 time to fit residues: 81.7996 Evaluate side-chains 130 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 543 ASP Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 532 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN A 277 ASN A 471 ASN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN B 562 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.127066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.098203 restraints weight = 21537.353| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.35 r_work: 0.2885 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9271 Z= 0.120 Angle : 0.473 9.132 12564 Z= 0.248 Chirality : 0.038 0.139 1482 Planarity : 0.003 0.055 1577 Dihedral : 5.375 59.898 1280 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.11 % Allowed : 24.37 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.25), residues: 1144 helix: 2.57 (0.18), residues: 779 sheet: -0.88 (0.67), residues: 47 loop : -0.63 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 536 TYR 0.009 0.001 TYR A 7 PHE 0.018 0.001 PHE A 453 TRP 0.010 0.001 TRP B 66 HIS 0.002 0.000 HIS B 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 ( 9271) covalent geometry : angle 0.47254 / 0.25 (12564) hydrogen bonds : bond 0.04764 / 3.18 ( 624) hydrogen bonds : angle 3.83363 / 2.86 ( 1834) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.302 Fit side-chains REVERT: A 136 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.5831 (tpt90) REVERT: A 224 GLU cc_start: 0.8329 (tt0) cc_final: 0.7761 (tp30) REVERT: A 313 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7226 (mm-40) REVERT: A 337 LYS cc_start: 0.8125 (mttt) cc_final: 0.7772 (mppt) REVERT: A 416 LYS cc_start: 0.7966 (tttm) cc_final: 0.7691 (tttp) REVERT: A 504 TYR cc_start: 0.5479 (OUTLIER) cc_final: 0.4421 (m-80) REVERT: A 507 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7510 (tm-30) REVERT: A 570 GLN cc_start: 0.6496 (OUTLIER) cc_final: 0.6095 (tt0) REVERT: B 180 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7424 (ttp-170) REVERT: B 305 GLU cc_start: 0.7551 (mm-30) cc_final: 0.6783 (mp0) REVERT: B 394 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7779 (pp) REVERT: B 412 GLU cc_start: 0.7747 (tt0) cc_final: 0.6874 (mp0) REVERT: B 416 LYS cc_start: 0.8380 (tttt) cc_final: 0.7907 (ttmm) REVERT: B 459 PHE cc_start: 0.6951 (t80) cc_final: 0.6586 (t80) REVERT: B 463 GLN cc_start: 0.6232 (mt0) cc_final: 0.5995 (mm-40) REVERT: B 506 THR cc_start: 0.5638 (OUTLIER) cc_final: 0.5269 (m) REVERT: B 542 ASN cc_start: 0.7631 (m-40) cc_final: 0.7353 (m110) outliers start: 31 outliers final: 16 residues processed: 132 average time/residue: 0.6246 time to fit residues: 87.6519 Evaluate side-chains 130 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 180 ARG Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 506 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.2980 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 113 optimal weight: 0.4980 chunk 100 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN A 471 ASN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN B 562 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.127872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.098398 restraints weight = 14980.534| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.85 r_work: 0.2930 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9271 Z= 0.115 Angle : 0.464 9.468 12564 Z= 0.244 Chirality : 0.038 0.138 1482 Planarity : 0.003 0.057 1577 Dihedral : 5.086 59.959 1279 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.61 % Allowed : 24.87 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.25), residues: 1144 helix: 2.65 (0.18), residues: 779 sheet: -0.85 (0.66), residues: 47 loop : -0.61 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 536 TYR 0.008 0.001 TYR A 7 PHE 0.018 0.001 PHE A 453 TRP 0.011 0.001 TRP B 66 HIS 0.002 0.000 HIS B 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 9271) covalent geometry : angle 0.46407 / 0.24 (12564) hydrogen bonds : bond 0.04628 / 3.09 ( 624) hydrogen bonds : angle 3.80247 / 2.84 ( 1834) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.251 Fit side-chains REVERT: A 136 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.5718 (tpt90) REVERT: A 224 GLU cc_start: 0.8268 (tt0) cc_final: 0.7682 (tp30) REVERT: A 313 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7177 (mm-40) REVERT: A 337 LYS cc_start: 0.8052 (mttt) cc_final: 0.7712 (mppt) REVERT: A 416 LYS cc_start: 0.7916 (tttm) cc_final: 0.7653 (tttp) REVERT: A 504 TYR cc_start: 0.5397 (OUTLIER) cc_final: 0.4336 (m-80) REVERT: A 507 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7464 (tm-30) REVERT: A 570 GLN cc_start: 0.6515 (OUTLIER) cc_final: 0.6112 (tt0) REVERT: B 180 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7272 (ttp-170) REVERT: B 305 GLU cc_start: 0.7498 (mm-30) cc_final: 0.6731 (mp0) REVERT: B 394 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7757 (pp) REVERT: B 412 GLU cc_start: 0.7665 (tt0) cc_final: 0.6806 (mp0) REVERT: B 416 LYS cc_start: 0.8333 (tttt) cc_final: 0.7837 (ttmm) REVERT: B 459 PHE cc_start: 0.6959 (t80) cc_final: 0.6622 (t80) REVERT: B 463 GLN cc_start: 0.6192 (mt0) cc_final: 0.5972 (mm-40) REVERT: B 542 ASN cc_start: 0.7599 (m-40) cc_final: 0.7326 (m110) outliers start: 26 outliers final: 14 residues processed: 130 average time/residue: 0.5542 time to fit residues: 76.9590 Evaluate side-chains 128 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 180 ARG Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 496 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 84 optimal weight: 0.0980 chunk 26 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN A 471 ASN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN B 562 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.127256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.097941 restraints weight = 21620.078| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.30 r_work: 0.2886 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9271 Z= 0.126 Angle : 0.488 10.193 12564 Z= 0.254 Chirality : 0.038 0.139 1482 Planarity : 0.004 0.058 1577 Dihedral : 4.971 59.986 1277 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.81 % Allowed : 24.77 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.25), residues: 1144 helix: 2.61 (0.18), residues: 779 sheet: -0.88 (0.66), residues: 47 loop : -0.64 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 536 TYR 0.009 0.001 TYR A 7 PHE 0.018 0.001 PHE A 453 TRP 0.010 0.001 TRP B 66 HIS 0.001 0.000 HIS B 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 9271) covalent geometry : angle 0.48772 / 0.25 (12564) hydrogen bonds : bond 0.04774 / 3.19 ( 624) hydrogen bonds : angle 3.81794 / 2.85 ( 1834) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3999.90 seconds wall clock time: 68 minutes 52.05 seconds (4132.05 seconds total)