Starting phenix.real_space_refine on Thu Aug 6 15:48:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zm2_74419/08_2026/9zm2_74419.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zm2_74419/08_2026/9zm2_74419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zm2_74419/08_2026/9zm2_74419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zm2_74419/08_2026/9zm2_74419.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zm2_74419/08_2026/9zm2_74419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zm2_74419/08_2026/9zm2_74419.map" } resolution = 3.29 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= 0.007 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: 5 Type Number sf(0) Gaussians Zn 8 6.06 5 S 128 5.16 5 C 9824 2.51 5 N 2704 2.21 5 O 2756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15420 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3853 Classifications: {'peptide': 474} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 451} Chain breaks: 3 Chain: "B" Number of atoms: 3853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3853 Classifications: {'peptide': 474} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 451} Chain breaks: 3 Chain: "C" Number of atoms: 3853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3853 Classifications: {'peptide': 474} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 451} Chain breaks: 3 Chain: "D" Number of atoms: 3853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3853 Classifications: {'peptide': 474} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 451} Chain breaks: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 434 SG CYS A 200 36.703 60.780 32.087 1.00200.69 S ATOM 456 SG CYS A 203 34.060 61.057 29.379 1.00212.68 S ATOM 1116 SG CYS A 282 33.243 59.241 32.635 1.00214.79 S ATOM 2291 SG CYS A 459 31.410 34.728 42.759 1.00241.82 S ATOM 2313 SG CYS A 462 29.404 37.614 41.145 1.00262.17 S ATOM 3070 SG CYS A 574 29.312 37.175 44.917 1.00268.70 S ATOM 4287 SG CYS B 200 36.883 99.160 67.284 1.00153.06 S ATOM 4309 SG CYS B 203 33.853 101.279 66.507 1.00176.98 S ATOM 4969 SG CYS B 282 33.964 97.638 65.338 1.00167.64 S ATOM 6144 SG CYS B 459 39.126 82.125 44.420 1.00157.73 S ATOM 6166 SG CYS B 462 36.358 83.901 46.436 1.00151.36 S ATOM 6923 SG CYS B 574 36.986 80.169 46.966 1.00178.96 S ATOM 8140 SG CYS C 200 32.882 74.106 112.881 1.00167.77 S ATOM 8162 SG CYS C 203 29.367 74.640 114.143 1.00172.26 S ATOM 8822 SG CYS C 282 30.153 74.940 110.397 1.00171.12 S ATOM 9997 SG CYS C 459 36.080 92.484 91.246 1.00143.82 S ATOM 10019 SG CYS C 462 33.289 90.472 92.955 1.00147.82 S ATOM 10776 SG CYS C 574 34.726 89.235 89.654 1.00165.34 S ATOM 11993 SG CYS D 200 41.328 24.525 100.297 1.00279.33 S ATOM 12015 SG CYS D 203 38.109 22.660 100.778 1.00289.54 S ATOM 12675 SG CYS D 282 37.956 26.359 100.244 1.00286.07 S ATOM 13850 SG CYS D 459 36.854 49.529 112.663 1.00188.21 S ATOM 13872 SG CYS D 462 34.963 46.890 110.590 1.00214.00 S ATOM 14629 SG CYS D 574 36.197 50.082 108.923 1.00222.72 S Time building chain proxies: 3.15, per 1000 atoms: 0.20 Number of scatterers: 15420 At special positions: 0 Unit cell: (75.97, 128.4, 146.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 8 29.99 S 128 16.00 O 2756 8.00 N 2704 7.00 C 9824 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: 1.18 Conformation dependent library (CDL) restraints added in 696.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 276 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 203 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 200 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 282 " pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" ND1 HIS A 567 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 462 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 574 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 459 " pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 276 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 203 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 200 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 282 " pdb=" ZN B 702 " pdb="ZN ZN B 702 " - pdb=" ND1 HIS B 567 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 462 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 574 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 459 " pdb=" ZN C 701 " pdb="ZN ZN C 701 " - pdb=" NE2 HIS C 276 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 200 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 203 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 282 " pdb=" ZN C 702 " pdb="ZN ZN C 702 " - pdb=" ND1 HIS C 567 " pdb="ZN ZN C 702 " - pdb=" SG CYS C 462 " pdb="ZN ZN C 702 " - pdb=" SG CYS C 574 " pdb="ZN ZN C 702 " - pdb=" SG CYS C 459 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" NE2 HIS D 276 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 200 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 203 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 282 " pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" ND1 HIS D 567 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 574 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 462 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 459 " Number of angles added : 24 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3688 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 9 sheets defined 64.2% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 183 through 192 Processing helix chain 'A' and resid 200 through 213 removed outlier: 3.566A pdb=" N ALA A 204 " --> pdb=" O CYS A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 230 removed outlier: 3.670A pdb=" N GLU A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 254 Processing helix chain 'A' and resid 258 through 265 Processing helix chain 'A' and resid 269 through 278 removed outlier: 3.586A pdb=" N PHE A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 310 Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 375 through 400 Processing helix chain 'A' and resid 440 through 444 Processing helix chain 'A' and resid 459 through 465 Processing helix chain 'A' and resid 468 through 484 Processing helix chain 'A' and resid 491 through 506 Processing helix chain 'A' and resid 513 through 520 Processing helix chain 'A' and resid 549 through 569 removed outlier: 5.906A pdb=" N VAL A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N THR A 562 " --> pdb=" O GLN A 558 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY A 563 " --> pdb=" O ALA A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 582 through 587 Processing helix chain 'A' and resid 594 through 605 Processing helix chain 'A' and resid 613 through 629 Processing helix chain 'A' and resid 632 through 653 removed outlier: 3.895A pdb=" N ASP A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 666 Processing helix chain 'B' and resid 64 through 75 Processing helix chain 'B' and resid 183 through 192 Processing helix chain 'B' and resid 200 through 213 removed outlier: 3.599A pdb=" N ALA B 204 " --> pdb=" O CYS B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 230 removed outlier: 3.654A pdb=" N GLU B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 254 Processing helix chain 'B' and resid 258 through 265 Processing helix chain 'B' and resid 269 through 278 removed outlier: 3.618A pdb=" N PHE B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 310 Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 375 through 400 Processing helix chain 'B' and resid 440 through 444 Processing helix chain 'B' and resid 459 through 466 removed outlier: 4.020A pdb=" N ALA B 466 " --> pdb=" O CYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 484 Processing helix chain 'B' and resid 491 through 506 Processing helix chain 'B' and resid 513 through 520 removed outlier: 3.568A pdb=" N ARG B 520 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 569 removed outlier: 5.790A pdb=" N VAL B 561 " --> pdb=" O ARG B 557 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N THR B 562 " --> pdb=" O GLN B 558 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY B 563 " --> pdb=" O ALA B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 579 Processing helix chain 'B' and resid 582 through 587 Processing helix chain 'B' and resid 594 through 605 Processing helix chain 'B' and resid 613 through 629 Processing helix chain 'B' and resid 632 through 653 removed outlier: 3.905A pdb=" N ASP B 641 " --> pdb=" O VAL B 637 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG B 644 " --> pdb=" O ALA B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 665 Processing helix chain 'C' and resid 64 through 75 Processing helix chain 'C' and resid 183 through 192 Processing helix chain 'C' and resid 200 through 213 removed outlier: 3.592A pdb=" N ALA C 204 " --> pdb=" O CYS C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 230 removed outlier: 3.690A pdb=" N GLU C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 254 Processing helix chain 'C' and resid 258 through 265 Processing helix chain 'C' and resid 269 through 278 removed outlier: 3.603A pdb=" N PHE C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 310 Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 375 through 400 Processing helix chain 'C' and resid 440 through 444 Processing helix chain 'C' and resid 459 through 466 removed outlier: 4.000A pdb=" N ALA C 466 " --> pdb=" O CYS C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 484 Processing helix chain 'C' and resid 491 through 506 Processing helix chain 'C' and resid 513 through 520 removed outlier: 3.595A pdb=" N ARG C 520 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 569 removed outlier: 5.874A pdb=" N VAL C 561 " --> pdb=" O ARG C 557 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N THR C 562 " --> pdb=" O GLN C 558 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY C 563 " --> pdb=" O ALA C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 579 Processing helix chain 'C' and resid 582 through 587 Processing helix chain 'C' and resid 594 through 605 Processing helix chain 'C' and resid 613 through 629 Processing helix chain 'C' and resid 632 through 653 removed outlier: 3.880A pdb=" N ASP C 641 " --> pdb=" O VAL C 637 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG C 644 " --> pdb=" O ALA C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 659 through 666 Processing helix chain 'D' and resid 64 through 75 Processing helix chain 'D' and resid 183 through 191 Processing helix chain 'D' and resid 200 through 213 removed outlier: 3.762A pdb=" N ALA D 204 " --> pdb=" O CYS D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 230 removed outlier: 3.779A pdb=" N GLU D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 254 Processing helix chain 'D' and resid 258 through 266 Processing helix chain 'D' and resid 269 through 278 Processing helix chain 'D' and resid 289 through 310 Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 375 through 400 Processing helix chain 'D' and resid 440 through 444 Processing helix chain 'D' and resid 459 through 465 Processing helix chain 'D' and resid 468 through 484 Processing helix chain 'D' and resid 491 through 506 Processing helix chain 'D' and resid 513 through 520 Processing helix chain 'D' and resid 549 through 569 removed outlier: 5.856A pdb=" N VAL D 561 " --> pdb=" O ARG D 557 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N THR D 562 " --> pdb=" O GLN D 558 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY D 563 " --> pdb=" O ALA D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 581 Processing helix chain 'D' and resid 582 through 587 Processing helix chain 'D' and resid 594 through 605 Processing helix chain 'D' and resid 613 through 629 Processing helix chain 'D' and resid 632 through 653 removed outlier: 3.928A pdb=" N ASP D 641 " --> pdb=" O VAL D 637 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG D 644 " --> pdb=" O ALA D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 659 through 666 Processing sheet with id=AA1, first strand: chain 'A' and resid 348 through 350 Processing sheet with id=AA2, first strand: chain 'A' and resid 451 through 452 Processing sheet with id=AA3, first strand: chain 'B' and resid 348 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 451 through 452 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.959A pdb=" N THR C 433 " --> pdb=" O GLN C 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 348 through 350 removed outlier: 3.525A pdb=" N SER C 349 " --> pdb=" O ARG C 589 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 451 through 452 Processing sheet with id=AA8, first strand: chain 'D' and resid 348 through 350 Processing sheet with id=AA9, first strand: chain 'D' and resid 451 through 452 834 hydrogen bonds defined for protein. 2466 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: 2.22 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5044 1.35 - 1.47: 3761 1.47 - 1.59: 6811 1.59 - 1.71: 0 1.71 - 1.83: 172 Bond restraints: 15788 Sorted by residual: bond pdb=" C ASN B 330 " pdb=" O ASN B 330 " ideal model delta sigma weight residual 1.235 1.229 0.006 4.70e-03 4.53e+04 1.77e+00 bond pdb=" CA HIS A 333 " pdb=" C HIS A 333 " ideal model delta sigma weight residual 1.532 1.522 0.011 9.60e-03 1.09e+04 1.20e+00 bond pdb=" N PRO B 319 " pdb=" CA PRO B 319 " ideal model delta sigma weight residual 1.469 1.483 -0.014 1.28e-02 6.10e+03 1.19e+00 bond pdb=" C ASN D 489 " pdb=" N VAL D 490 " ideal model delta sigma weight residual 1.334 1.321 0.013 1.29e-02 6.01e+03 9.68e-01 bond pdb=" CA GLN D 78 " pdb=" CB GLN D 78 " ideal model delta sigma weight residual 1.523 1.535 -0.012 1.21e-02 6.83e+03 9.57e-01 ... (remaining 15783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 21223 2.24 - 4.47: 201 4.47 - 6.71: 10 6.71 - 8.94: 1 8.94 - 11.18: 1 Bond angle restraints: 21436 Sorted by residual: angle pdb=" CB MET D 643 " pdb=" CG MET D 643 " pdb=" SD MET D 643 " ideal model delta sigma weight residual 112.70 123.88 -11.18 3.00e+00 1.11e-01 1.39e+01 angle pdb=" CB MET D 492 " pdb=" CG MET D 492 " pdb=" SD MET D 492 " ideal model delta sigma weight residual 112.70 120.14 -7.44 3.00e+00 1.11e-01 6.15e+00 angle pdb=" N VAL D 267 " pdb=" CA VAL D 267 " pdb=" C VAL D 267 " ideal model delta sigma weight residual 110.42 108.27 2.15 9.60e-01 1.09e+00 5.03e+00 angle pdb=" CB MET C 309 " pdb=" CG MET C 309 " pdb=" SD MET C 309 " ideal model delta sigma weight residual 112.70 119.35 -6.65 3.00e+00 1.11e-01 4.91e+00 angle pdb=" CA TRP A 363 " pdb=" CB TRP A 363 " pdb=" CG TRP A 363 " ideal model delta sigma weight residual 113.60 117.75 -4.15 1.90e+00 2.77e-01 4.78e+00 ... (remaining 21431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 8124 17.31 - 34.63: 945 34.63 - 51.94: 302 51.94 - 69.25: 86 69.25 - 86.57: 23 Dihedral angle restraints: 9480 sinusoidal: 3840 harmonic: 5640 Sorted by residual: dihedral pdb=" CA ASP A 605 " pdb=" CB ASP A 605 " pdb=" CG ASP A 605 " pdb=" OD1 ASP A 605 " ideal model delta sinusoidal sigma weight residual -30.00 -89.57 59.57 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP C 654 " pdb=" CB ASP C 654 " pdb=" CG ASP C 654 " pdb=" OD1 ASP C 654 " ideal model delta sinusoidal sigma weight residual -30.00 -89.42 59.42 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP D 654 " pdb=" CB ASP D 654 " pdb=" CG ASP D 654 " pdb=" OD1 ASP D 654 " ideal model delta sinusoidal sigma weight residual -30.00 -89.11 59.11 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 9477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1591 0.026 - 0.052: 565 0.052 - 0.078: 195 0.078 - 0.104: 43 0.104 - 0.129: 26 Chirality restraints: 2420 Sorted by residual: chirality pdb=" CA VAL D 446 " pdb=" N VAL D 446 " pdb=" C VAL D 446 " pdb=" CB VAL D 446 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE C 655 " pdb=" N ILE C 655 " pdb=" C ILE C 655 " pdb=" CB ILE C 655 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.01e-01 chirality pdb=" CA VAL B 446 " pdb=" N VAL B 446 " pdb=" C VAL B 446 " pdb=" CB VAL B 446 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 2417 not shown) Planarity restraints: 2732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 322 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.91e+00 pdb=" N PRO A 323 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 323 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 323 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 571 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO B 572 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 572 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 572 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 446 " -0.021 5.00e-02 4.00e+02 3.13e-02 1.56e+00 pdb=" N PRO D 447 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO D 447 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 447 " -0.017 5.00e-02 4.00e+02 ... (remaining 2729 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 6409 2.91 - 3.40: 17140 3.40 - 3.90: 25529 3.90 - 4.40: 29081 4.40 - 4.90: 46558 Nonbonded interactions: 124717 Sorted by model distance: nonbonded pdb=" OD1 ASP D 65 " pdb=" N LEU D 66 " model vdw 2.407 3.120 nonbonded pdb=" O VAL B 663 " pdb=" O LYS B 666 " model vdw 2.427 3.040 nonbonded pdb=" O VAL C 663 " pdb=" O LYS C 666 " model vdw 2.432 3.040 nonbonded pdb=" OG1 THR C 60 " pdb=" OG SER C 244 " model vdw 2.435 3.040 nonbonded pdb=" O HIS A 333 " pdb=" OE2 GLU A 335 " model vdw 2.437 3.040 ... (remaining 124712 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.190 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 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 : 0.003 0.036 15820 Z= 0.145 Angle : 0.538 11.176 21460 Z= 0.287 Chirality : 0.032 0.129 2420 Planarity : 0.003 0.035 2732 Dihedral : 17.413 86.565 5792 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.02 % Favored : 95.92 % Rotamer: Outliers : 0.75 % Allowed : 20.43 % Favored : 78.82 % 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: 1.84 (0.21), residues: 1864 helix: 2.52 (0.15), residues: 1192 sheet: None (None), residues: 0 loop : -1.30 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 77 TYR 0.008 0.001 TYR B 59 PHE 0.011 0.001 PHE D 271 TRP 0.009 0.001 TRP A 363 HIS 0.009 0.001 HIS B 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (15788) covalent geometry : angle 0.53522 / 0.29 (21436) hydrogen bonds : bond 0.12729 / 8.61 ( 834) hydrogen bonds : angle 4.80478 / 3.41 ( 2466) metal coordination : bond 0.01279 / 0.80 ( 32) metal coordination : angle 1.72273 / 1.14 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 GLN cc_start: 0.4359 (OUTLIER) cc_final: 0.4143 (mm-40) REVERT: A 400 MET cc_start: 0.8417 (ttm) cc_final: 0.8192 (tmm) REVERT: A 463 GLU cc_start: 0.8282 (pt0) cc_final: 0.7856 (pt0) REVERT: A 492 MET cc_start: 0.8226 (mmt) cc_final: 0.7844 (mmm) REVERT: B 199 ARG cc_start: 0.8471 (ptt-90) cc_final: 0.8250 (ptm160) REVERT: B 399 MET cc_start: 0.7778 (mmm) cc_final: 0.7008 (mmm) REVERT: C 313 THR cc_start: 0.8945 (m) cc_final: 0.8527 (t) REVERT: C 400 MET cc_start: 0.8297 (mmp) cc_final: 0.7916 (ttp) REVERT: C 607 TYR cc_start: 0.8826 (m-80) cc_final: 0.8382 (m-10) REVERT: C 659 ASP cc_start: 0.8471 (t70) cc_final: 0.7993 (t0) REVERT: D 243 MET cc_start: 0.8711 (ttm) cc_final: 0.8160 (mtt) REVERT: D 369 MET cc_start: 0.8391 (mtp) cc_final: 0.7940 (ptp) REVERT: D 374 LEU cc_start: 0.7900 (mt) cc_final: 0.7669 (pt) REVERT: D 619 CYS cc_start: 0.9415 (m) cc_final: 0.9181 (m) outliers start: 13 outliers final: 2 residues processed: 121 average time/residue: 0.1112 time to fit residues: 20.6139 Evaluate side-chains 75 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain D residue 509 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.085935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.058721 restraints weight = 51391.587| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.63 r_work: 0.2978 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15820 Z= 0.157 Angle : 0.541 11.185 21460 Z= 0.277 Chirality : 0.036 0.162 2420 Planarity : 0.003 0.030 2732 Dihedral : 4.495 85.749 2092 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.59 % Favored : 96.35 % Rotamer: Outliers : 1.68 % Allowed : 18.98 % Favored : 79.34 % 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: 1.91 (0.21), residues: 1864 helix: 2.55 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : -1.30 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 305 TYR 0.009 0.001 TYR C 332 PHE 0.015 0.001 PHE B 271 TRP 0.013 0.001 TRP A 363 HIS 0.006 0.001 HIS B 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (15788) covalent geometry : angle 0.53778 / 0.28 (21436) hydrogen bonds : bond 0.04116 / 2.81 ( 834) hydrogen bonds : angle 3.86936 / 2.80 ( 2466) metal coordination : bond 0.01250 / 0.80 ( 32) metal coordination : angle 1.77056 / 1.00 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ASP cc_start: 0.8800 (m-30) cc_final: 0.8462 (m-30) REVERT: A 400 MET cc_start: 0.8320 (ttm) cc_final: 0.7899 (ppp) REVERT: A 463 GLU cc_start: 0.8365 (pt0) cc_final: 0.7918 (pt0) REVERT: A 492 MET cc_start: 0.8230 (mmt) cc_final: 0.7962 (mmm) REVERT: B 462 CYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8632 (m) REVERT: C 313 THR cc_start: 0.8851 (m) cc_final: 0.8531 (t) REVERT: C 462 CYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8385 (m) REVERT: C 607 TYR cc_start: 0.8787 (m-80) cc_final: 0.8493 (m-10) REVERT: C 659 ASP cc_start: 0.7990 (t70) cc_final: 0.7713 (t0) REVERT: D 369 MET cc_start: 0.8522 (mtp) cc_final: 0.8112 (ptp) REVERT: D 374 LEU cc_start: 0.7950 (mt) cc_final: 0.7594 (pt) REVERT: D 492 MET cc_start: 0.8785 (mmp) cc_final: 0.8494 (mmp) REVERT: D 619 CYS cc_start: 0.9495 (m) cc_final: 0.9220 (m) outliers start: 29 outliers final: 8 residues processed: 102 average time/residue: 0.0932 time to fit residues: 15.0563 Evaluate side-chains 80 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 462 CYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 176 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 chunk 167 optimal weight: 7.9990 chunk 173 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 293 ASN ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.085931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.058320 restraints weight = 52285.693| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.82 r_work: 0.2973 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15820 Z= 0.129 Angle : 0.504 8.112 21460 Z= 0.260 Chirality : 0.035 0.127 2420 Planarity : 0.003 0.031 2732 Dihedral : 4.147 86.899 2087 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.27 % Favored : 96.67 % Rotamer: Outliers : 1.45 % Allowed : 19.21 % Favored : 79.34 % 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: 1.73 (0.20), residues: 1864 helix: 2.51 (0.15), residues: 1176 sheet: None (None), residues: 0 loop : -1.40 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 199 TYR 0.007 0.001 TYR D 470 PHE 0.012 0.001 PHE B 271 TRP 0.011 0.001 TRP A 363 HIS 0.004 0.001 HIS C 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (15788) covalent geometry : angle 0.50050 / 0.26 (21436) hydrogen bonds : bond 0.03696 / 2.53 ( 834) hydrogen bonds : angle 3.66048 / 2.65 ( 2466) metal coordination : bond 0.01342 / 0.83 ( 32) metal coordination : angle 1.85381 / 1.09 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: A 292 ASP cc_start: 0.8883 (m-30) cc_final: 0.8466 (m-30) REVERT: A 400 MET cc_start: 0.8373 (ttm) cc_final: 0.7869 (ppp) REVERT: A 463 GLU cc_start: 0.8359 (pt0) cc_final: 0.8013 (pt0) REVERT: A 492 MET cc_start: 0.8304 (mmt) cc_final: 0.8040 (mmm) REVERT: B 292 ASP cc_start: 0.8818 (m-30) cc_final: 0.8511 (m-30) REVERT: B 462 CYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8685 (m) REVERT: C 313 THR cc_start: 0.8956 (m) cc_final: 0.8626 (t) REVERT: C 462 CYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8381 (m) REVERT: C 607 TYR cc_start: 0.8888 (m-80) cc_final: 0.8569 (m-10) REVERT: C 659 ASP cc_start: 0.8165 (t70) cc_final: 0.7829 (t0) REVERT: D 400 MET cc_start: 0.7300 (ptt) cc_final: 0.7010 (ptm) REVERT: D 492 MET cc_start: 0.8920 (mmp) cc_final: 0.8575 (mmp) REVERT: D 506 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8608 (pt0) REVERT: D 619 CYS cc_start: 0.9505 (OUTLIER) cc_final: 0.9214 (m) REVERT: D 643 MET cc_start: 0.9319 (mmm) cc_final: 0.9088 (mmm) outliers start: 25 outliers final: 11 residues processed: 95 average time/residue: 0.0773 time to fit residues: 12.7793 Evaluate side-chains 83 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 462 CYS Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 463 GLU Chi-restraints excluded: chain D residue 619 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 180 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 HIS B 338 GLN ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN C 274 HIS ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.084706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.056959 restraints weight = 52709.324| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.72 r_work: 0.2933 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15820 Z= 0.201 Angle : 0.551 6.589 21460 Z= 0.282 Chirality : 0.037 0.190 2420 Planarity : 0.004 0.032 2732 Dihedral : 4.256 86.448 2087 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.70 % Favored : 96.24 % Rotamer: Outliers : 2.14 % Allowed : 18.98 % Favored : 78.88 % 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: 1.55 (0.20), residues: 1864 helix: 2.38 (0.15), residues: 1176 sheet: None (None), residues: 0 loop : -1.51 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 234 TYR 0.009 0.001 TYR C 470 PHE 0.019 0.001 PHE B 271 TRP 0.012 0.001 TRP A 363 HIS 0.006 0.001 HIS B 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (15788) covalent geometry : angle 0.54627 / 0.28 (21436) hydrogen bonds : bond 0.03816 / 2.62 ( 834) hydrogen bonds : angle 3.76051 / 2.72 ( 2466) metal coordination : bond 0.01793 / 1.12 ( 32) metal coordination : angle 2.14648 / 1.25 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 69 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 HIS cc_start: 0.9242 (OUTLIER) cc_final: 0.8813 (m170) REVERT: A 400 MET cc_start: 0.8356 (ttm) cc_final: 0.7877 (ppp) REVERT: A 463 GLU cc_start: 0.8408 (pt0) cc_final: 0.8098 (pt0) REVERT: A 492 MET cc_start: 0.8337 (mmt) cc_final: 0.7981 (mmm) REVERT: B 292 ASP cc_start: 0.8759 (m-30) cc_final: 0.8411 (m-30) REVERT: B 462 CYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8663 (m) REVERT: C 313 THR cc_start: 0.9037 (m) cc_final: 0.8722 (t) REVERT: C 607 TYR cc_start: 0.8781 (m-80) cc_final: 0.8504 (m-10) REVERT: C 657 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8418 (mp) REVERT: C 659 ASP cc_start: 0.8113 (t70) cc_final: 0.7827 (t0) REVERT: D 400 MET cc_start: 0.7246 (ptt) cc_final: 0.6967 (ptm) REVERT: D 492 MET cc_start: 0.8941 (mmp) cc_final: 0.8672 (mmp) REVERT: D 612 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8821 (tt) REVERT: D 619 CYS cc_start: 0.9499 (OUTLIER) cc_final: 0.9202 (m) REVERT: D 643 MET cc_start: 0.9338 (mmm) cc_final: 0.9130 (mmm) outliers start: 37 outliers final: 19 residues processed: 102 average time/residue: 0.0854 time to fit residues: 14.7981 Evaluate side-chains 92 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 463 GLU Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 619 CYS Chi-restraints excluded: chain D residue 657 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 157 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 86 optimal weight: 0.1980 chunk 13 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 73 optimal weight: 0.0980 chunk 175 optimal weight: 0.1980 chunk 182 optimal weight: 20.0000 chunk 119 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.085902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.057852 restraints weight = 52636.391| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.87 r_work: 0.2970 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15820 Z= 0.100 Angle : 0.497 8.310 21460 Z= 0.254 Chirality : 0.035 0.153 2420 Planarity : 0.003 0.030 2732 Dihedral : 4.170 86.323 2087 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.95 % Favored : 97.00 % Rotamer: Outliers : 1.62 % Allowed : 18.92 % Favored : 79.46 % 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: 1.65 (0.20), residues: 1864 helix: 2.44 (0.16), residues: 1180 sheet: None (None), residues: 0 loop : -1.45 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 557 TYR 0.007 0.001 TYR D 470 PHE 0.008 0.001 PHE B 642 TRP 0.011 0.001 TRP A 363 HIS 0.015 0.001 HIS C 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (15788) covalent geometry : angle 0.49452 / 0.25 (21436) hydrogen bonds : bond 0.03271 / 2.23 ( 834) hydrogen bonds : angle 3.51714 / 2.55 ( 2466) metal coordination : bond 0.01105 / 0.73 ( 32) metal coordination : angle 1.57537 / 0.93 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 HIS cc_start: 0.9181 (OUTLIER) cc_final: 0.8874 (m-70) REVERT: A 335 GLU cc_start: 0.7672 (mp0) cc_final: 0.7239 (mp0) REVERT: A 400 MET cc_start: 0.8363 (ttm) cc_final: 0.7865 (ppp) REVERT: A 463 GLU cc_start: 0.8268 (pt0) cc_final: 0.7989 (pt0) REVERT: A 492 MET cc_start: 0.8317 (mmt) cc_final: 0.7957 (mmm) REVERT: B 292 ASP cc_start: 0.8849 (m-30) cc_final: 0.8437 (m-30) REVERT: B 462 CYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8704 (m) REVERT: B 600 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8936 (mm) REVERT: C 313 THR cc_start: 0.9037 (m) cc_final: 0.8710 (t) REVERT: C 607 TYR cc_start: 0.8802 (m-80) cc_final: 0.8515 (m-10) REVERT: C 659 ASP cc_start: 0.8206 (t70) cc_final: 0.7862 (t0) REVERT: D 305 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8723 (ttm110) REVERT: D 309 MET cc_start: 0.9203 (mpp) cc_final: 0.8836 (mpp) REVERT: D 400 MET cc_start: 0.7273 (ptt) cc_final: 0.6980 (ptm) REVERT: D 492 MET cc_start: 0.8966 (mmp) cc_final: 0.8664 (mmp) REVERT: D 612 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8814 (tt) REVERT: D 619 CYS cc_start: 0.9500 (OUTLIER) cc_final: 0.9197 (m) outliers start: 28 outliers final: 16 residues processed: 102 average time/residue: 0.0838 time to fit residues: 14.4726 Evaluate side-chains 92 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 305 ARG Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 619 CYS Chi-restraints excluded: chain D residue 657 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 17 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 163 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 627 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.081775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.052970 restraints weight = 50604.706| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 4.03 r_work: 0.2758 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15820 Z= 0.212 Angle : 0.564 9.162 21460 Z= 0.287 Chirality : 0.037 0.129 2420 Planarity : 0.004 0.033 2732 Dihedral : 4.259 84.101 2087 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.76 % Favored : 96.19 % Rotamer: Outliers : 2.20 % Allowed : 19.16 % Favored : 78.65 % 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: 1.51 (0.20), residues: 1864 helix: 2.39 (0.16), residues: 1172 sheet: None (None), residues: 0 loop : -1.57 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 234 TYR 0.010 0.001 TYR D 667 PHE 0.020 0.001 PHE B 271 TRP 0.008 0.001 TRP A 363 HIS 0.005 0.001 HIS B 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (15788) covalent geometry : angle 0.55937 / 0.29 (21436) hydrogen bonds : bond 0.03791 / 2.60 ( 834) hydrogen bonds : angle 3.71706 / 2.69 ( 2466) metal coordination : bond 0.01781 / 1.17 ( 32) metal coordination : angle 2.30777 / 1.35 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 71 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 HIS cc_start: 0.8825 (OUTLIER) cc_final: 0.8334 (m170) REVERT: A 335 GLU cc_start: 0.7970 (mp0) cc_final: 0.7558 (mp0) REVERT: A 400 MET cc_start: 0.8438 (ttm) cc_final: 0.7919 (tmm) REVERT: A 463 GLU cc_start: 0.8462 (pt0) cc_final: 0.8120 (pt0) REVERT: A 492 MET cc_start: 0.8269 (mmt) cc_final: 0.7873 (mmm) REVERT: B 292 ASP cc_start: 0.8925 (m-30) cc_final: 0.8518 (m-30) REVERT: B 462 CYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8668 (m) REVERT: C 313 THR cc_start: 0.9204 (m) cc_final: 0.8808 (t) REVERT: C 607 TYR cc_start: 0.8908 (m-80) cc_final: 0.8512 (m-10) REVERT: C 659 ASP cc_start: 0.8614 (t70) cc_final: 0.8111 (t0) REVERT: D 309 MET cc_start: 0.9127 (mpp) cc_final: 0.8810 (mpp) REVERT: D 400 MET cc_start: 0.7386 (ptt) cc_final: 0.7112 (ptm) REVERT: D 492 MET cc_start: 0.8826 (mmp) cc_final: 0.8548 (mmp) REVERT: D 612 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8828 (tp) REVERT: D 619 CYS cc_start: 0.9491 (OUTLIER) cc_final: 0.9216 (m) outliers start: 38 outliers final: 24 residues processed: 105 average time/residue: 0.0772 time to fit residues: 13.9986 Evaluate side-chains 97 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 463 GLU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 619 CYS Chi-restraints excluded: chain D residue 657 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 83 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.082551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.053841 restraints weight = 50451.329| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 4.04 r_work: 0.2782 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15820 Z= 0.146 Angle : 0.516 8.257 21460 Z= 0.262 Chirality : 0.035 0.131 2420 Planarity : 0.003 0.032 2732 Dihedral : 4.219 84.543 2087 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.06 % Favored : 96.89 % Rotamer: Outliers : 1.85 % Allowed : 19.62 % Favored : 78.53 % 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: 1.55 (0.20), residues: 1864 helix: 2.43 (0.16), residues: 1172 sheet: None (None), residues: 0 loop : -1.58 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 589 TYR 0.008 0.001 TYR D 470 PHE 0.013 0.001 PHE B 271 TRP 0.011 0.001 TRP A 363 HIS 0.003 0.001 HIS C 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (15788) covalent geometry : angle 0.51278 / 0.26 (21436) hydrogen bonds : bond 0.03337 / 2.29 ( 834) hydrogen bonds : angle 3.54005 / 2.57 ( 2466) metal coordination : bond 0.01387 / 0.89 ( 32) metal coordination : angle 1.70152 / 0.98 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 71 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 HIS cc_start: 0.8862 (OUTLIER) cc_final: 0.8386 (m-70) REVERT: A 335 GLU cc_start: 0.7961 (mp0) cc_final: 0.7577 (mp0) REVERT: A 400 MET cc_start: 0.8438 (ttm) cc_final: 0.7911 (tmm) REVERT: A 463 GLU cc_start: 0.8335 (pt0) cc_final: 0.8015 (pt0) REVERT: A 492 MET cc_start: 0.8256 (mmt) cc_final: 0.7966 (mmm) REVERT: B 292 ASP cc_start: 0.8903 (m-30) cc_final: 0.8499 (m-30) REVERT: B 462 CYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8666 (m) REVERT: C 313 THR cc_start: 0.9183 (m) cc_final: 0.8823 (t) REVERT: C 607 TYR cc_start: 0.8903 (m-80) cc_final: 0.8502 (m-10) REVERT: C 659 ASP cc_start: 0.8562 (t70) cc_final: 0.8082 (t0) REVERT: D 400 MET cc_start: 0.7489 (ptt) cc_final: 0.7216 (ptm) REVERT: D 492 MET cc_start: 0.8825 (mmp) cc_final: 0.8530 (mmp) REVERT: D 612 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8810 (tp) REVERT: D 619 CYS cc_start: 0.9491 (OUTLIER) cc_final: 0.9205 (m) outliers start: 32 outliers final: 25 residues processed: 100 average time/residue: 0.0813 time to fit residues: 13.9606 Evaluate side-chains 97 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 619 CYS Chi-restraints excluded: chain D residue 657 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 172 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 139 optimal weight: 0.8980 chunk 158 optimal weight: 8.9990 chunk 186 optimal weight: 5.9990 chunk 69 optimal weight: 0.2980 chunk 34 optimal weight: 3.9990 chunk 176 optimal weight: 0.7980 chunk 145 optimal weight: 10.0000 chunk 140 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.083486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.055147 restraints weight = 50869.139| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 4.05 r_work: 0.2821 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15820 Z= 0.100 Angle : 0.509 14.630 21460 Z= 0.255 Chirality : 0.035 0.169 2420 Planarity : 0.003 0.032 2732 Dihedral : 4.157 85.140 2087 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.11 % Favored : 96.83 % Rotamer: Outliers : 1.50 % Allowed : 20.37 % Favored : 78.12 % 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: 1.60 (0.21), residues: 1864 helix: 2.44 (0.16), residues: 1176 sheet: None (None), residues: 0 loop : -1.52 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 305 TYR 0.007 0.001 TYR B 469 PHE 0.008 0.001 PHE A 271 TRP 0.012 0.001 TRP D 363 HIS 0.003 0.000 HIS A 567 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (15788) covalent geometry : angle 0.50719 / 0.26 (21436) hydrogen bonds : bond 0.02981 / 2.02 ( 834) hydrogen bonds : angle 3.42303 / 2.48 ( 2466) metal coordination : bond 0.00932 / 0.60 ( 32) metal coordination : angle 1.34517 / 0.80 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 HIS cc_start: 0.8803 (OUTLIER) cc_final: 0.8459 (m-70) REVERT: A 292 ASP cc_start: 0.9142 (t0) cc_final: 0.8754 (m-30) REVERT: A 335 GLU cc_start: 0.8010 (mp0) cc_final: 0.7601 (mp0) REVERT: A 400 MET cc_start: 0.8463 (ttm) cc_final: 0.7966 (tmm) REVERT: A 492 MET cc_start: 0.8180 (mmt) cc_final: 0.7913 (mmm) REVERT: B 292 ASP cc_start: 0.8900 (m-30) cc_final: 0.8490 (m-30) REVERT: B 462 CYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8640 (m) REVERT: C 203 CYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8105 (m) REVERT: C 313 THR cc_start: 0.9151 (m) cc_final: 0.8788 (t) REVERT: C 607 TYR cc_start: 0.8852 (m-80) cc_final: 0.8596 (m-10) REVERT: C 659 ASP cc_start: 0.8511 (t70) cc_final: 0.8023 (t0) REVERT: D 309 MET cc_start: 0.9231 (mpp) cc_final: 0.9026 (mpp) REVERT: D 400 MET cc_start: 0.7454 (ptt) cc_final: 0.7164 (ptm) REVERT: D 492 MET cc_start: 0.8832 (mmp) cc_final: 0.8517 (mmp) REVERT: D 612 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8718 (tt) REVERT: D 619 CYS cc_start: 0.9485 (m) cc_final: 0.9203 (m) outliers start: 26 outliers final: 16 residues processed: 96 average time/residue: 0.0957 time to fit residues: 15.3674 Evaluate side-chains 89 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 612 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 57 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 174 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 357 GLN ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.082312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.053515 restraints weight = 50906.131| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 4.06 r_work: 0.2783 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15820 Z= 0.160 Angle : 0.538 9.781 21460 Z= 0.270 Chirality : 0.036 0.167 2420 Planarity : 0.003 0.033 2732 Dihedral : 4.182 84.136 2087 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.27 % Favored : 96.67 % Rotamer: Outliers : 1.45 % Allowed : 20.54 % Favored : 78.01 % 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: 1.60 (0.21), residues: 1864 helix: 2.43 (0.16), residues: 1176 sheet: None (None), residues: 0 loop : -1.52 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 398 TYR 0.008 0.001 TYR C 470 PHE 0.015 0.001 PHE B 271 TRP 0.007 0.001 TRP A 363 HIS 0.004 0.001 HIS B 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (15788) covalent geometry : angle 0.53536 / 0.27 (21436) hydrogen bonds : bond 0.03339 / 2.29 ( 834) hydrogen bonds : angle 3.52972 / 2.56 ( 2466) metal coordination : bond 0.01314 / 0.87 ( 32) metal coordination : angle 1.70563 / 1.00 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 HIS cc_start: 0.8139 (t-170) cc_final: 0.7776 (t70) REVERT: A 335 GLU cc_start: 0.8129 (mp0) cc_final: 0.7829 (mp0) REVERT: A 400 MET cc_start: 0.8409 (ttm) cc_final: 0.7906 (tmm) REVERT: A 492 MET cc_start: 0.8242 (mmt) cc_final: 0.7944 (mmm) REVERT: B 209 CYS cc_start: 0.9288 (m) cc_final: 0.8756 (m) REVERT: B 292 ASP cc_start: 0.8913 (m-30) cc_final: 0.8548 (m-30) REVERT: B 462 CYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8628 (m) REVERT: C 203 CYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8135 (m) REVERT: C 313 THR cc_start: 0.9185 (m) cc_final: 0.8797 (t) REVERT: C 607 TYR cc_start: 0.8856 (m-80) cc_final: 0.8461 (m-10) REVERT: C 659 ASP cc_start: 0.8571 (t70) cc_final: 0.8070 (t0) REVERT: D 309 MET cc_start: 0.9118 (mpp) cc_final: 0.8806 (mpp) REVERT: D 400 MET cc_start: 0.7598 (ptt) cc_final: 0.7288 (ptm) REVERT: D 492 MET cc_start: 0.8813 (mmp) cc_final: 0.8514 (mmp) REVERT: D 612 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8750 (tt) REVERT: D 619 CYS cc_start: 0.9485 (m) cc_final: 0.9201 (m) outliers start: 25 outliers final: 19 residues processed: 95 average time/residue: 0.0815 time to fit residues: 13.3769 Evaluate side-chains 92 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 657 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 163 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 ASN ** C 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.082137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.053462 restraints weight = 50997.485| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 4.07 r_work: 0.2778 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15820 Z= 0.162 Angle : 0.539 9.305 21460 Z= 0.271 Chirality : 0.036 0.155 2420 Planarity : 0.003 0.033 2732 Dihedral : 4.206 84.630 2087 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.33 % Favored : 96.62 % Rotamer: Outliers : 1.45 % Allowed : 20.49 % Favored : 78.07 % 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: 1.55 (0.20), residues: 1864 helix: 2.40 (0.16), residues: 1176 sheet: None (None), residues: 0 loop : -1.55 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 234 TYR 0.008 0.001 TYR A 470 PHE 0.015 0.001 PHE B 271 TRP 0.009 0.001 TRP A 363 HIS 0.004 0.001 HIS B 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (15788) covalent geometry : angle 0.53657 / 0.27 (21436) hydrogen bonds : bond 0.03349 / 2.28 ( 834) hydrogen bonds : angle 3.54719 / 2.57 ( 2466) metal coordination : bond 0.01439 / 0.93 ( 32) metal coordination : angle 1.68800 / 0.96 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 MET cc_start: 0.8415 (ttm) cc_final: 0.7912 (tmm) REVERT: A 492 MET cc_start: 0.8257 (mmt) cc_final: 0.7964 (mmm) REVERT: B 209 CYS cc_start: 0.9261 (m) cc_final: 0.8735 (m) REVERT: B 292 ASP cc_start: 0.8936 (m-30) cc_final: 0.8556 (m-30) REVERT: B 462 CYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8652 (m) REVERT: C 203 CYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8143 (m) REVERT: C 313 THR cc_start: 0.9203 (m) cc_final: 0.8814 (t) REVERT: C 400 MET cc_start: 0.8356 (ttp) cc_final: 0.8111 (ttp) REVERT: C 607 TYR cc_start: 0.8871 (m-80) cc_final: 0.8452 (m-10) REVERT: C 659 ASP cc_start: 0.8587 (t70) cc_final: 0.8078 (t0) REVERT: D 309 MET cc_start: 0.9120 (mpp) cc_final: 0.8837 (mpp) REVERT: D 400 MET cc_start: 0.7624 (ptt) cc_final: 0.7280 (ptm) REVERT: D 492 MET cc_start: 0.8797 (mmp) cc_final: 0.8493 (mmp) REVERT: D 612 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8749 (tt) REVERT: D 619 CYS cc_start: 0.9484 (OUTLIER) cc_final: 0.9204 (m) outliers start: 25 outliers final: 21 residues processed: 92 average time/residue: 0.0850 time to fit residues: 13.4998 Evaluate side-chains 92 residues out of total 1728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 463 GLU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain C residue 203 CYS Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 619 CYS Chi-restraints excluded: chain D residue 657 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 161 optimal weight: 4.9990 chunk 129 optimal weight: 0.0000 chunk 103 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 39 optimal weight: 0.4980 chunk 97 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 ASN ** D 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.083237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.054590 restraints weight = 50566.438| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 4.04 r_work: 0.2815 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15820 Z= 0.103 Angle : 0.516 8.962 21460 Z= 0.257 Chirality : 0.035 0.150 2420 Planarity : 0.003 0.031 2732 Dihedral : 4.158 84.633 2087 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.45 % Allowed : 20.60 % Favored : 77.95 % 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: 1.59 (0.21), residues: 1864 helix: 2.43 (0.16), residues: 1176 sheet: None (None), residues: 0 loop : -1.53 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 281 TYR 0.007 0.001 TYR D 470 PHE 0.013 0.001 PHE C 184 TRP 0.010 0.001 TRP A 363 HIS 0.003 0.000 HIS A 567 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.10 (15788) covalent geometry : angle 0.51385 / 0.26 (21436) hydrogen bonds : bond 0.02959 / 2.02 ( 834) hydrogen bonds : angle 3.42053 / 2.48 ( 2466) metal coordination : bond 0.00961 / 0.61 ( 32) metal coordination : angle 1.34358 / 0.79 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3349.92 seconds wall clock time: 58 minutes 9.47 seconds (3489.47 seconds total)