Starting phenix.real_space_refine on Wed Aug 5 18:42:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xih_38373/08_2026/8xih_38373.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xih_38373/08_2026/8xih_38373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xih_38373/08_2026/8xih_38373.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xih_38373/08_2026/8xih_38373.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xih_38373/08_2026/8xih_38373.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xih_38373/08_2026/8xih_38373.map" } resolution = 3.2 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 31 5.49 5 Mg 2 5.21 5 S 27 5.16 5 C 7326 2.51 5 N 1941 2.21 5 O 2091 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 11418 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4744 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 25, 'TRANS': 553} Chain breaks: 4 Chain: "B" Number of atoms: 6020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 6020 Classifications: {'peptide': 735} Link IDs: {'PTRANS': 33, 'TRANS': 701} Chain breaks: 4 Chain: "G" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 169 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "H" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 337 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "E" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 146 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.67, per 1000 atoms: 0.23 Number of scatterers: 11418 At special positions: 0 Unit cell: (102, 94.35, 130.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 27 16.00 P 31 15.00 Mg 2 11.99 O 2091 8.00 N 1941 7.00 C 7326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 551.9 milliseconds 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2498 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 20 sheets defined 33.6% alpha, 18.5% beta 0 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 112 through 125 Processing helix chain 'A' and resid 292 through 298 removed outlier: 4.615A pdb=" N VAL A 296 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 292 through 298' Processing helix chain 'A' and resid 300 through 304 Processing helix chain 'A' and resid 306 through 321 removed outlier: 3.694A pdb=" N ASN A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.546A pdb=" N ARG A 369 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 370 through 383 Processing helix chain 'A' and resid 406 through 423 Processing helix chain 'A' and resid 442 through 451 removed outlier: 4.162A pdb=" N ILE A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE A 449 " --> pdb=" O GLN A 445 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 removed outlier: 3.733A pdb=" N ARG A 455 " --> pdb=" O LYS A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 488 Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 528 through 546 Processing helix chain 'A' and resid 603 through 624 Proline residue: A 621 - end of helix Processing helix chain 'A' and resid 640 through 656 Processing helix chain 'A' and resid 735 through 748 Processing helix chain 'A' and resid 761 through 771 Processing helix chain 'B' and resid 13 through 17 removed outlier: 3.579A pdb=" N LEU B 17 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 54 Processing helix chain 'B' and resid 105 through 108 Processing helix chain 'B' and resid 109 through 126 removed outlier: 3.969A pdb=" N TYR B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N PHE B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 194 removed outlier: 4.168A pdb=" N VAL B 194 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 201 Processing helix chain 'B' and resid 243 through 250 removed outlier: 3.670A pdb=" N HIS B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 322 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.582A pdb=" N ARG B 369 " --> pdb=" O ASN B 365 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 370 through 383 Processing helix chain 'B' and resid 405 through 423 Processing helix chain 'B' and resid 442 through 450 removed outlier: 3.645A pdb=" N ILE B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 456 Processing helix chain 'B' and resid 477 through 486 Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 528 through 546 Processing helix chain 'B' and resid 579 through 582 removed outlier: 4.052A pdb=" N GLU B 582 " --> pdb=" O LYS B 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 579 through 582' Processing helix chain 'B' and resid 602 through 624 Proline residue: B 621 - end of helix Processing helix chain 'B' and resid 640 through 657 Processing helix chain 'B' and resid 735 through 748 Processing helix chain 'B' and resid 761 through 770 Processing sheet with id=AA1, first strand: chain 'A' and resid 340 through 341 Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 10 removed outlier: 6.557A pdb=" N GLN A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 217 removed outlier: 4.284A pdb=" N ARG A 286 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 326 through 327 Processing sheet with id=AA5, first strand: chain 'A' and resid 356 through 359 removed outlier: 5.091A pdb=" N ARG A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE A 353 " --> pdb=" O ARG A 357 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 395 through 398 Processing sheet with id=AA7, first strand: chain 'A' and resid 464 through 467 Processing sheet with id=AA8, first strand: chain 'A' and resid 507 through 509 Processing sheet with id=AA9, first strand: chain 'A' and resid 584 through 590 removed outlier: 6.722A pdb=" N ILE A 561 " --> pdb=" O VAL A 631 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL A 633 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE A 563 " --> pdb=" O VAL A 633 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ASP A 635 " --> pdb=" O ILE A 563 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE A 565 " --> pdb=" O ASP A 635 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 731 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASP A 670 " --> pdb=" O MET A 729 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N MET A 729 " --> pdb=" O ASP A 670 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N HIS A 672 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LEU A 727 " --> pdb=" O HIS A 672 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU A 706 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A 698 " --> pdb=" O PHE A 710 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 340 through 341 Processing sheet with id=AB2, first strand: chain 'B' and resid 8 through 10 removed outlier: 6.650A pdb=" N GLN B 137 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 60 through 62 Processing sheet with id=AB4, first strand: chain 'B' and resid 79 through 82 Processing sheet with id=AB5, first strand: chain 'B' and resid 278 through 281 removed outlier: 6.691A pdb=" N SER B 267 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 325 through 326 removed outlier: 4.020A pdb=" N LEU B 325 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 356 through 359 removed outlier: 4.885A pdb=" N ARG B 357 " --> pdb=" O PHE B 353 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE B 353 " --> pdb=" O ARG B 357 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 395 through 398 removed outlier: 3.941A pdb=" N ILE B 432 " --> pdb=" O LEU B 395 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 465 through 467 Processing sheet with id=AC1, first strand: chain 'B' and resid 507 through 509 removed outlier: 3.850A pdb=" N ARG B 522 " --> pdb=" O LYS B 508 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 584 through 590 removed outlier: 3.505A pdb=" N ILE B 561 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP B 635 " --> pdb=" O ILE B 565 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL B 567 " --> pdb=" O ASP B 635 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE B 630 " --> pdb=" O GLY B 667 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL B 669 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILE B 632 " --> pdb=" O VAL B 669 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU B 671 " --> pdb=" O ILE B 632 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ARG B 634 " --> pdb=" O LEU B 671 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN B 726 " --> pdb=" O HIS B 672 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU B 706 " --> pdb=" O VAL B 702 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1197 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 2.12 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3217 1.34 - 1.46: 2408 1.46 - 1.58: 6027 1.58 - 1.70: 59 1.70 - 1.82: 46 Bond restraints: 11757 Sorted by residual: bond pdb=" C3' DG H 12 " pdb=" O3' DG H 12 " ideal model delta sigma weight residual 1.435 1.486 -0.051 1.30e-02 5.92e+03 1.52e+01 bond pdb=" C1' DT E 4 " pdb=" N1 DT E 4 " ideal model delta sigma weight residual 1.468 1.522 -0.054 1.40e-02 5.10e+03 1.49e+01 bond pdb=" C3' DA E 6 " pdb=" C2' DA E 6 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C5' DT E 4 " pdb=" C4' DT E 4 " ideal model delta sigma weight residual 1.512 1.536 -0.024 7.00e-03 2.04e+04 1.16e+01 bond pdb=" C3' DT G 0 " pdb=" C2' DT G 0 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.96e+00 ... (remaining 11752 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 15697 2.21 - 4.41: 269 4.41 - 6.62: 34 6.62 - 8.82: 7 8.82 - 11.03: 1 Bond angle restraints: 16008 Sorted by residual: angle pdb=" C3' DG H 12 " pdb=" O3' DG H 12 " pdb=" P DT H 13 " ideal model delta sigma weight residual 119.70 125.08 -5.38 1.20e+00 6.94e-01 2.01e+01 angle pdb=" O4' DG G 3 " pdb=" C4' DG G 3 " pdb=" C3' DG G 3 " ideal model delta sigma weight residual 106.00 103.41 2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" O4' DA E 7 " pdb=" C4' DA E 7 " pdb=" C3' DA E 7 " ideal model delta sigma weight residual 106.00 103.46 2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" O5' DT E 4 " pdb=" C5' DT E 4 " pdb=" C4' DT E 4 " ideal model delta sigma weight residual 109.40 112.75 -3.35 8.00e-01 1.56e+00 1.75e+01 angle pdb=" N3 DT H 1 " pdb=" C4 DT H 1 " pdb=" O4 DT H 1 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 ... (remaining 16003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 6590 35.97 - 71.94: 357 71.94 - 107.90: 11 107.90 - 143.87: 3 143.87 - 179.84: 4 Dihedral angle restraints: 6965 sinusoidal: 3093 harmonic: 3872 Sorted by residual: dihedral pdb=" C4' DG H 12 " pdb=" C3' DG H 12 " pdb=" O3' DG H 12 " pdb=" P DT H 13 " ideal model delta sinusoidal sigma weight residual -140.00 39.84 -179.84 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG H 15 " pdb=" C3' DG H 15 " pdb=" O3' DG H 15 " pdb=" P DT H 16 " ideal model delta sinusoidal sigma weight residual 220.00 54.66 165.34 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DG H 4 " pdb=" C3' DG H 4 " pdb=" O3' DG H 4 " pdb=" P DG H 5 " ideal model delta sinusoidal sigma weight residual 220.00 72.02 147.98 1 3.50e+01 8.16e-04 1.45e+01 ... (remaining 6962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1424 0.055 - 0.110: 254 0.110 - 0.166: 55 0.166 - 0.221: 8 0.221 - 0.276: 2 Chirality restraints: 1743 Sorted by residual: chirality pdb=" CB ILE B 84 " pdb=" CA ILE B 84 " pdb=" CG1 ILE B 84 " pdb=" CG2 ILE B 84 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CG LEU A 8 " pdb=" CB LEU A 8 " pdb=" CD1 LEU A 8 " pdb=" CD2 LEU A 8 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C3' DG G 1 " pdb=" C4' DG G 1 " pdb=" O3' DG G 1 " pdb=" C2' DG G 1 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.62e-01 ... (remaining 1740 not shown) Planarity restraints: 1922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 70 " -0.058 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO B 71 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO B 71 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 71 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 490 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.36e+00 pdb=" N PRO A 491 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 491 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 491 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 337 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO B 338 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 338 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 338 " -0.030 5.00e-02 4.00e+02 ... (remaining 1919 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 112 2.62 - 3.19: 9208 3.19 - 3.76: 17252 3.76 - 4.33: 23344 4.33 - 4.90: 39542 Nonbonded interactions: 89458 Sorted by model distance: nonbonded pdb=" OP1 DA H 3 " pdb="MG MG H 101 " model vdw 2.044 2.170 nonbonded pdb=" OP2 DT G 0 " pdb="MG MG G 101 " model vdw 2.085 2.170 nonbonded pdb=" OP2 DT H 1 " pdb="MG MG H 101 " model vdw 2.259 2.170 nonbonded pdb=" OG SER B 50 " pdb=" O GLY B 55 " model vdw 2.263 3.040 nonbonded pdb=" O ASN B 290 " pdb=" NH2 ARG B 295 " model vdw 2.268 3.120 ... (remaining 89453 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.750 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.040 Find NCS groups from input model: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 : 0.004 0.054 11757 Z= 0.235 Angle : 0.680 11.026 16008 Z= 0.412 Chirality : 0.047 0.276 1743 Planarity : 0.005 0.085 1922 Dihedral : 20.099 179.842 4467 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 0.93 % Allowed : 31.18 % Favored : 67.88 % 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: -1.04 (0.23), residues: 1294 helix: 1.23 (0.27), residues: 372 sheet: -0.66 (0.31), residues: 295 loop : -1.95 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 128 TYR 0.012 0.001 TYR A 490 PHE 0.020 0.001 PHE A 481 TRP 0.017 0.001 TRP A 214 HIS 0.004 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.24 (11757) covalent geometry : angle 0.67965 / 0.41 (16008) hydrogen bonds : bond 0.14494 / 9.84 ( 429) hydrogen bonds : angle 6.62370 / 4.47 ( 1197) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: B 195 ARG cc_start: 0.8329 (mmm160) cc_final: 0.8126 (mmm160) REVERT: B 266 MET cc_start: 0.7430 (ptm) cc_final: 0.7182 (ppp) outliers start: 11 outliers final: 3 residues processed: 116 average time/residue: 0.1296 time to fit residues: 20.8993 Evaluate side-chains 109 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 106 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 445 GLN Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 580 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 0.0970 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN A 568 HIS ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 HIS B 580 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.153333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.112999 restraints weight = 17408.104| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.87 r_work: 0.3182 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.0608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11757 Z= 0.120 Angle : 0.570 6.897 16008 Z= 0.304 Chirality : 0.045 0.310 1743 Planarity : 0.005 0.061 1922 Dihedral : 17.362 175.724 1792 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 2.46 % Allowed : 29.57 % Favored : 67.97 % 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: -0.76 (0.24), residues: 1294 helix: 1.71 (0.28), residues: 375 sheet: -0.77 (0.30), residues: 303 loop : -1.82 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 128 TYR 0.014 0.001 TYR A 490 PHE 0.011 0.001 PHE B 577 TRP 0.007 0.001 TRP A 131 HIS 0.008 0.001 HIS B 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (11757) covalent geometry : angle 0.57034 / 0.30 (16008) hydrogen bonds : bond 0.04183 / 2.79 ( 429) hydrogen bonds : angle 5.45964 / 3.68 ( 1197) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.443 Fit side-chains REVERT: B 160 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7839 (ttmt) REVERT: B 266 MET cc_start: 0.7690 (ptm) cc_final: 0.6470 (ppp) REVERT: B 608 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7693 (tt) outliers start: 29 outliers final: 12 residues processed: 135 average time/residue: 0.1283 time to fit residues: 23.9856 Evaluate side-chains 115 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 608 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 58 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN B 445 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.150688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.109948 restraints weight = 17651.927| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.47 r_work: 0.3156 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.0780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11757 Z= 0.154 Angle : 0.573 7.037 16008 Z= 0.305 Chirality : 0.046 0.330 1743 Planarity : 0.004 0.058 1922 Dihedral : 17.285 173.744 1787 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 3.23 % Allowed : 29.40 % Favored : 67.37 % 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: -0.73 (0.24), residues: 1294 helix: 1.79 (0.28), residues: 375 sheet: -0.87 (0.31), residues: 299 loop : -1.76 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 456 TYR 0.013 0.001 TYR A 490 PHE 0.013 0.001 PHE B 462 TRP 0.007 0.001 TRP A 214 HIS 0.004 0.001 HIS B 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (11757) covalent geometry : angle 0.57344 / 0.31 (16008) hydrogen bonds : bond 0.04209 / 2.80 ( 429) hydrogen bonds : angle 5.28381 / 3.56 ( 1197) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 0.408 Fit side-chains REVERT: A 520 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.5440 (pm20) REVERT: B 160 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7899 (ttmt) REVERT: B 266 MET cc_start: 0.7724 (ptm) cc_final: 0.6410 (ppp) REVERT: B 429 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8103 (t80) REVERT: B 482 HIS cc_start: 0.7453 (OUTLIER) cc_final: 0.6574 (t70) REVERT: B 486 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8069 (mmmt) REVERT: B 608 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7707 (tt) outliers start: 38 outliers final: 22 residues processed: 139 average time/residue: 0.1215 time to fit residues: 23.4218 Evaluate side-chains 135 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 486 LYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 671 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 9 optimal weight: 20.0000 chunk 123 optimal weight: 0.0570 chunk 12 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 4 optimal weight: 0.0370 chunk 109 optimal weight: 0.9980 overall best weight: 1.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN A 571 HIS B 445 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.151217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.109699 restraints weight = 17671.917| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.60 r_work: 0.3136 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11757 Z= 0.135 Angle : 0.559 7.161 16008 Z= 0.297 Chirality : 0.045 0.333 1743 Planarity : 0.004 0.058 1922 Dihedral : 17.236 173.052 1787 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 4.16 % Allowed : 28.80 % Favored : 67.03 % 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: -0.66 (0.24), residues: 1294 helix: 1.83 (0.27), residues: 375 sheet: -0.79 (0.31), residues: 298 loop : -1.73 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 570 TYR 0.014 0.001 TYR A 490 PHE 0.014 0.001 PHE B 489 TRP 0.007 0.001 TRP A 214 HIS 0.003 0.000 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (11757) covalent geometry : angle 0.55918 / 0.30 (16008) hydrogen bonds : bond 0.03822 / 2.53 ( 429) hydrogen bonds : angle 5.19951 / 3.52 ( 1197) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 111 time to evaluate : 0.488 Fit side-chains REVERT: A 455 ARG cc_start: 0.8154 (ttp-170) cc_final: 0.7884 (tmm160) REVERT: A 520 GLU cc_start: 0.6255 (OUTLIER) cc_final: 0.5419 (pm20) REVERT: B 21 TYR cc_start: 0.7532 (OUTLIER) cc_final: 0.6973 (m-80) REVERT: B 160 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7867 (ttmt) REVERT: B 266 MET cc_start: 0.7718 (ptm) cc_final: 0.6397 (ppp) REVERT: B 429 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8129 (t80) REVERT: B 608 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7714 (tt) outliers start: 49 outliers final: 32 residues processed: 152 average time/residue: 0.1140 time to fit residues: 24.2655 Evaluate side-chains 144 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 107 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 571 HIS Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 45 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN A 382 ASN A 414 ASN ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.148683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.107689 restraints weight = 17634.487| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.50 r_work: 0.3121 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 11757 Z= 0.204 Angle : 0.613 7.433 16008 Z= 0.325 Chirality : 0.047 0.334 1743 Planarity : 0.005 0.062 1922 Dihedral : 17.313 174.327 1787 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 4.93 % Allowed : 27.70 % Favored : 67.37 % 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: -0.75 (0.24), residues: 1294 helix: 1.78 (0.27), residues: 375 sheet: -0.84 (0.30), residues: 308 loop : -1.83 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 128 TYR 0.013 0.001 TYR A 490 PHE 0.015 0.001 PHE B 577 TRP 0.008 0.001 TRP A 131 HIS 0.009 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 (11757) covalent geometry : angle 0.61323 / 0.33 (16008) hydrogen bonds : bond 0.04424 / 2.93 ( 429) hydrogen bonds : angle 5.24861 / 3.55 ( 1197) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 109 time to evaluate : 0.432 Fit side-chains REVERT: A 2 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7693 (ptpp) REVERT: A 520 GLU cc_start: 0.6249 (OUTLIER) cc_final: 0.5483 (pm20) REVERT: B 21 TYR cc_start: 0.7569 (OUTLIER) cc_final: 0.7060 (m-80) REVERT: B 160 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7964 (ttmt) REVERT: B 266 MET cc_start: 0.7734 (ptm) cc_final: 0.6397 (ppp) REVERT: B 429 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8178 (t80) REVERT: B 482 HIS cc_start: 0.7645 (OUTLIER) cc_final: 0.6965 (t70) REVERT: B 608 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7763 (tt) outliers start: 58 outliers final: 38 residues processed: 156 average time/residue: 0.1132 time to fit residues: 25.4629 Evaluate side-chains 150 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 105 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 571 HIS Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 113 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 10 optimal weight: 0.4980 chunk 117 optimal weight: 9.9990 chunk 64 optimal weight: 0.0980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.151446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.110002 restraints weight = 17749.064| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.63 r_work: 0.3165 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11757 Z= 0.120 Angle : 0.560 7.275 16008 Z= 0.296 Chirality : 0.045 0.336 1743 Planarity : 0.004 0.059 1922 Dihedral : 17.251 171.953 1787 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.65 % Allowed : 29.65 % Favored : 66.69 % 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: -0.59 (0.24), residues: 1294 helix: 1.89 (0.27), residues: 376 sheet: -0.73 (0.30), residues: 308 loop : -1.72 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 128 TYR 0.015 0.001 TYR A 490 PHE 0.014 0.001 PHE B 489 TRP 0.016 0.001 TRP A 214 HIS 0.003 0.000 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (11757) covalent geometry : angle 0.56017 / 0.30 (16008) hydrogen bonds : bond 0.03563 / 2.36 ( 429) hydrogen bonds : angle 5.12433 / 3.47 ( 1197) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 109 time to evaluate : 0.333 Fit side-chains REVERT: A 520 GLU cc_start: 0.6266 (OUTLIER) cc_final: 0.5505 (pm20) REVERT: B 21 TYR cc_start: 0.7542 (OUTLIER) cc_final: 0.6981 (m-80) REVERT: B 160 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7852 (ttmt) REVERT: B 266 MET cc_start: 0.7673 (ptm) cc_final: 0.6329 (ppp) REVERT: B 275 MET cc_start: 0.5627 (pmm) cc_final: 0.4856 (pmm) REVERT: B 429 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8055 (t80) REVERT: B 608 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7703 (tt) outliers start: 43 outliers final: 30 residues processed: 144 average time/residue: 0.1036 time to fit residues: 21.0300 Evaluate side-chains 137 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 102 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 671 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 0.0170 chunk 46 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 chunk 96 optimal weight: 0.5980 chunk 123 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.152247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.110876 restraints weight = 17580.563| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.62 r_work: 0.3156 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11757 Z= 0.112 Angle : 0.557 7.796 16008 Z= 0.292 Chirality : 0.044 0.341 1743 Planarity : 0.004 0.057 1922 Dihedral : 17.193 171.816 1787 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.74 % Allowed : 28.97 % Favored : 67.29 % 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: -0.51 (0.24), residues: 1294 helix: 1.97 (0.27), residues: 375 sheet: -0.67 (0.30), residues: 318 loop : -1.69 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 128 TYR 0.022 0.001 TYR B 289 PHE 0.012 0.001 PHE B 489 TRP 0.014 0.001 TRP A 214 HIS 0.002 0.000 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (11757) covalent geometry : angle 0.55697 / 0.29 (16008) hydrogen bonds : bond 0.03356 / 2.22 ( 429) hydrogen bonds : angle 5.03553 / 3.41 ( 1197) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 106 time to evaluate : 0.398 Fit side-chains REVERT: A 520 GLU cc_start: 0.6271 (OUTLIER) cc_final: 0.5499 (pm20) REVERT: B 21 TYR cc_start: 0.7506 (OUTLIER) cc_final: 0.6921 (m-80) REVERT: B 160 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7830 (ttmt) REVERT: B 266 MET cc_start: 0.7633 (ptm) cc_final: 0.6315 (ppp) REVERT: B 429 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.7960 (t80) REVERT: B 547 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.7622 (mpt180) REVERT: B 608 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7682 (tt) outliers start: 44 outliers final: 35 residues processed: 144 average time/residue: 0.0975 time to fit residues: 19.5299 Evaluate side-chains 140 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 99 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 127 HIS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 101 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 125 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN A 365 ASN ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 HIS B 290 ASN B 445 GLN B 571 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.147275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.105618 restraints weight = 17731.701| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.61 r_work: 0.3104 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 11757 Z= 0.238 Angle : 0.655 8.200 16008 Z= 0.344 Chirality : 0.049 0.345 1743 Planarity : 0.005 0.064 1922 Dihedral : 17.282 170.728 1787 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 4.84 % Allowed : 28.46 % Favored : 66.69 % 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: -0.76 (0.24), residues: 1294 helix: 1.80 (0.27), residues: 374 sheet: -0.88 (0.30), residues: 318 loop : -1.82 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 128 TYR 0.016 0.002 TYR B 289 PHE 0.016 0.002 PHE B 578 TRP 0.009 0.002 TRP B 214 HIS 0.010 0.001 HIS B 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.24 (11757) covalent geometry : angle 0.65490 / 0.34 (16008) hydrogen bonds : bond 0.04907 / 3.25 ( 429) hydrogen bonds : angle 5.25246 / 3.56 ( 1197) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 104 time to evaluate : 0.423 Fit side-chains REVERT: A 2 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7707 (ptpp) REVERT: A 520 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.5473 (pm20) REVERT: B 21 TYR cc_start: 0.7612 (OUTLIER) cc_final: 0.7109 (m-80) REVERT: B 160 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7962 (ttmt) REVERT: B 266 MET cc_start: 0.7681 (ptm) cc_final: 0.6304 (ppp) REVERT: B 429 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8301 (t80) REVERT: B 547 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.7638 (mpt180) REVERT: B 608 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7731 (tt) outliers start: 57 outliers final: 38 residues processed: 152 average time/residue: 0.1024 time to fit residues: 21.7665 Evaluate side-chains 146 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 101 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 571 HIS Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 757 SER Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 47 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 98 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 64 optimal weight: 40.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.149154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.107627 restraints weight = 17523.305| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.61 r_work: 0.3134 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11757 Z= 0.146 Angle : 0.597 8.521 16008 Z= 0.315 Chirality : 0.046 0.327 1743 Planarity : 0.004 0.063 1922 Dihedral : 17.260 169.419 1787 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 4.16 % Allowed : 29.14 % Favored : 66.69 % 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: -0.66 (0.24), residues: 1294 helix: 1.88 (0.27), residues: 374 sheet: -0.78 (0.30), residues: 308 loop : -1.78 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 570 TYR 0.015 0.001 TYR B 289 PHE 0.014 0.001 PHE B 577 TRP 0.018 0.001 TRP A 214 HIS 0.003 0.001 HIS B 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (11757) covalent geometry : angle 0.59747 / 0.31 (16008) hydrogen bonds : bond 0.04093 / 2.72 ( 429) hydrogen bonds : angle 5.16934 / 3.52 ( 1197) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 105 time to evaluate : 0.431 Fit side-chains REVERT: A 137 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7776 (mm-40) REVERT: A 520 GLU cc_start: 0.6226 (OUTLIER) cc_final: 0.5470 (pm20) REVERT: B 21 TYR cc_start: 0.7584 (OUTLIER) cc_final: 0.7058 (m-80) REVERT: B 76 MET cc_start: 0.5217 (tpt) cc_final: 0.3727 (ttt) REVERT: B 160 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7910 (ttmt) REVERT: B 266 MET cc_start: 0.7664 (ptm) cc_final: 0.6294 (ppp) REVERT: B 275 MET cc_start: 0.5659 (pmm) cc_final: 0.4897 (pmm) REVERT: B 287 MET cc_start: 0.6651 (OUTLIER) cc_final: 0.6298 (tmm) REVERT: B 429 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8129 (t80) REVERT: B 547 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.7665 (mpt180) REVERT: B 608 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7718 (tt) outliers start: 49 outliers final: 36 residues processed: 147 average time/residue: 0.1087 time to fit residues: 23.0800 Evaluate side-chains 143 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 99 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 3 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN B 571 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.148542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.106986 restraints weight = 17718.423| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.63 r_work: 0.3125 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 11757 Z= 0.175 Angle : 0.610 9.404 16008 Z= 0.320 Chirality : 0.047 0.333 1743 Planarity : 0.005 0.063 1922 Dihedral : 17.273 169.072 1787 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 4.16 % Allowed : 29.48 % Favored : 66.36 % 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: -0.70 (0.24), residues: 1294 helix: 1.84 (0.27), residues: 375 sheet: -0.86 (0.30), residues: 318 loop : -1.78 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 128 TYR 0.018 0.001 TYR B 289 PHE 0.015 0.001 PHE B 577 TRP 0.024 0.002 TRP A 214 HIS 0.006 0.001 HIS B 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (11757) covalent geometry : angle 0.60970 / 0.32 (16008) hydrogen bonds : bond 0.04194 / 2.79 ( 429) hydrogen bonds : angle 5.18128 / 3.53 ( 1197) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 103 time to evaluate : 0.295 Fit side-chains REVERT: A 137 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7803 (mm-40) REVERT: A 520 GLU cc_start: 0.6220 (OUTLIER) cc_final: 0.5462 (pm20) REVERT: B 21 TYR cc_start: 0.7614 (OUTLIER) cc_final: 0.7074 (m-80) REVERT: B 76 MET cc_start: 0.5213 (tpt) cc_final: 0.3753 (ttt) REVERT: B 160 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7933 (ttmt) REVERT: B 266 MET cc_start: 0.7667 (ptm) cc_final: 0.6287 (ppp) REVERT: B 287 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.6292 (tmm) REVERT: B 429 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8180 (t80) REVERT: B 547 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.7689 (mpt180) REVERT: B 608 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7699 (tt) outliers start: 49 outliers final: 38 residues processed: 145 average time/residue: 0.1082 time to fit residues: 22.2091 Evaluate side-chains 147 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 101 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 159 TYR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 477 PHE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 721 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 99 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 112 optimal weight: 0.0030 chunk 56 optimal weight: 0.0970 chunk 59 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN ** B 123 GLN ** 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 = 0.3906 r_free = 0.3906 target = 0.151652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.110326 restraints weight = 17622.172| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.60 r_work: 0.3150 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11757 Z= 0.113 Angle : 0.574 9.828 16008 Z= 0.300 Chirality : 0.045 0.339 1743 Planarity : 0.004 0.058 1922 Dihedral : 17.233 169.878 1787 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.65 % Allowed : 29.82 % Favored : 66.53 % 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: -0.50 (0.24), residues: 1294 helix: 1.99 (0.27), residues: 375 sheet: -0.68 (0.30), residues: 308 loop : -1.68 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 128 TYR 0.017 0.001 TYR B 289 PHE 0.014 0.001 PHE A 481 TRP 0.021 0.001 TRP A 214 HIS 0.002 0.000 HIS B 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (11757) covalent geometry : angle 0.57374 / 0.30 (16008) hydrogen bonds : bond 0.03380 / 2.24 ( 429) hydrogen bonds : angle 5.06601 / 3.44 ( 1197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2414.83 seconds wall clock time: 42 minutes 7.16 seconds (2527.16 seconds total)