Starting phenix.real_space_refine on Sat Aug 23 11:52:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jfy_36219/08_2025/8jfy_36219.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jfy_36219/08_2025/8jfy_36219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jfy_36219/08_2025/8jfy_36219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jfy_36219/08_2025/8jfy_36219.map" model { file = "/net/cci-nas-00/data/ceres_data/8jfy_36219/08_2025/8jfy_36219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jfy_36219/08_2025/8jfy_36219.cif" } resolution = 2.79 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= 0.031 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: 8 Type Number sf(0) Gaussians Ca 12 9.91 5 Fe 2 7.16 5 Zn 2 6.06 5 P 2 5.49 5 S 66 5.16 5 C 7456 2.51 5 N 2058 2.21 5 O 2272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11870 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1172 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 146} Chain: "D" Number of atoms: 4750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4750 Classifications: {'peptide': 587} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 564} Chain breaks: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 9 Unusual residues: {' CA': 2, ' FE': 1, ' ZN': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Restraints were copied for chains: B, C Time building chain proxies: 4.01, per 1000 atoms: 0.34 Number of scatterers: 11870 At special positions: 0 Unit cell: (84.645, 170.145, 106.875, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 Fe 2 26.01 Ca 12 19.99 S 66 16.00 P 2 15.00 O 2272 8.00 N 2058 7.00 C 7456 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: 1.03 Conformation dependent library (CDL) restraints added in 351.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 701 " pdb="ZN ZN C 701 " - pdb=" NE2 HIS C 360 " pdb="ZN ZN C 701 " - pdb=" NE2 HIS C 271 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" NE2 HIS D 360 " pdb="ZN ZN D 701 " - pdb=" NE2 HIS D 271 " 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2776 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 10 sheets defined 57.9% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 1 through 5 removed outlier: 4.046A pdb=" N GLN A 4 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 21 removed outlier: 4.081A pdb=" N GLU A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 40 Processing helix chain 'A' and resid 45 through 56 removed outlier: 4.820A pdb=" N ASP A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN A 54 " --> pdb=" O GLN A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 79 removed outlier: 3.557A pdb=" N ASP A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 removed outlier: 4.083A pdb=" N GLU A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 114 Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 138 through 148 Processing helix chain 'D' and resid 2 through 29 removed outlier: 3.754A pdb=" N ILE D 6 " --> pdb=" O ASP D 2 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET D 25 " --> pdb=" O ALA D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 44 removed outlier: 3.865A pdb=" N ASN D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 52 removed outlier: 3.979A pdb=" N LYS D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE D 51 " --> pdb=" O GLU D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 114 removed outlier: 3.745A pdb=" N LYS D 114 " --> pdb=" O ASP D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 139 removed outlier: 3.897A pdb=" N GLN D 138 " --> pdb=" O LYS D 134 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU D 139 " --> pdb=" O SER D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 174 Processing helix chain 'D' and resid 194 through 209 Processing helix chain 'D' and resid 222 through 230 Processing helix chain 'D' and resid 230 through 239 Processing helix chain 'D' and resid 242 through 257 removed outlier: 3.577A pdb=" N GLU D 252 " --> pdb=" O ALA D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 284 Processing helix chain 'D' and resid 306 through 319 removed outlier: 3.655A pdb=" N GLN D 312 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 352 Processing helix chain 'D' and resid 413 through 418 removed outlier: 3.863A pdb=" N LYS D 416 " --> pdb=" O SER D 413 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU D 418 " --> pdb=" O THR D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 439 removed outlier: 3.531A pdb=" N ALA D 431 " --> pdb=" O VAL D 427 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS D 433 " --> pdb=" O SER D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 454 Processing helix chain 'D' and resid 463 through 474 Processing helix chain 'D' and resid 479 through 488 removed outlier: 4.623A pdb=" N ASP D 485 " --> pdb=" O ARG D 481 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS D 486 " --> pdb=" O LEU D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 507 removed outlier: 3.511A pdb=" N LEU D 505 " --> pdb=" O THR D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 513 removed outlier: 4.011A pdb=" N LEU D 511 " --> pdb=" O THR D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 526 removed outlier: 3.610A pdb=" N ALA D 523 " --> pdb=" O SER D 519 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA D 526 " --> pdb=" O ASP D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 539 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.633A pdb=" N LEU D 557 " --> pdb=" O THR D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 579 removed outlier: 4.001A pdb=" N ASP D 579 " --> pdb=" O CYS D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 605 Processing helix chain 'B' and resid 1 through 5 removed outlier: 4.045A pdb=" N GLN B 4 " --> pdb=" O MET B 1 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 21 removed outlier: 4.081A pdb=" N GLU B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 40 Processing helix chain 'B' and resid 45 through 56 removed outlier: 4.820A pdb=" N ASP B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN B 54 " --> pdb=" O GLN B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 79 removed outlier: 3.557A pdb=" N ASP B 79 " --> pdb=" O ARG B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 94 removed outlier: 4.084A pdb=" N GLU B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 114 Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 138 through 148 Processing helix chain 'C' and resid 2 through 29 removed outlier: 3.754A pdb=" N ILE C 6 " --> pdb=" O ASP C 2 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 removed outlier: 3.865A pdb=" N ASN C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 52 removed outlier: 3.978A pdb=" N LYS C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 114 removed outlier: 3.745A pdb=" N LYS C 114 " --> pdb=" O ASP C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 139 removed outlier: 3.897A pdb=" N GLN C 138 " --> pdb=" O LYS C 134 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU C 139 " --> pdb=" O SER C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 174 Processing helix chain 'C' and resid 194 through 209 Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 230 through 239 Processing helix chain 'C' and resid 242 through 257 removed outlier: 3.577A pdb=" N GLU C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 306 through 319 removed outlier: 3.655A pdb=" N GLN C 312 " --> pdb=" O THR C 308 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 352 Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.863A pdb=" N LYS C 416 " --> pdb=" O SER C 413 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C 418 " --> pdb=" O THR C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 439 removed outlier: 3.531A pdb=" N ALA C 431 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS C 433 " --> pdb=" O SER C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 454 Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 479 through 488 removed outlier: 4.623A pdb=" N ASP C 485 " --> pdb=" O ARG C 481 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LYS C 486 " --> pdb=" O LEU C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 507 removed outlier: 3.512A pdb=" N LEU C 505 " --> pdb=" O THR C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 513 removed outlier: 4.011A pdb=" N LEU C 511 " --> pdb=" O THR C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 526 removed outlier: 3.610A pdb=" N ALA C 523 " --> pdb=" O SER C 519 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA C 526 " --> pdb=" O ASP C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 539 Processing helix chain 'C' and resid 547 through 559 removed outlier: 3.634A pdb=" N LEU C 557 " --> pdb=" O THR C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 579 removed outlier: 4.001A pdb=" N ASP C 579 " --> pdb=" O CYS C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 605 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'D' and resid 142 through 145 removed outlier: 6.497A pdb=" N LEU D 268 " --> pdb=" O ILE D 357 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 213 through 215 Processing sheet with id=AA4, first strand: chain 'D' and resid 320 through 321 Processing sheet with id=AA5, first strand: chain 'D' and resid 460 through 462 Processing sheet with id=AA6, first strand: chain 'B' and resid 27 through 28 Processing sheet with id=AA7, first strand: chain 'C' and resid 142 through 145 removed outlier: 6.496A pdb=" N LEU C 268 " --> pdb=" O ILE C 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 213 through 215 Processing sheet with id=AA9, first strand: chain 'C' and resid 320 through 321 Processing sheet with id=AB1, first strand: chain 'C' and resid 460 through 462 592 hydrogen bonds defined for protein. 1734 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2271 1.33 - 1.45: 2941 1.45 - 1.57: 6742 1.57 - 1.69: 0 1.69 - 1.82: 120 Bond restraints: 12074 Sorted by residual: bond pdb=" CA HIS C 360 " pdb=" C HIS C 360 " ideal model delta sigma weight residual 1.523 1.473 0.051 1.34e-02 5.57e+03 1.43e+01 bond pdb=" CA SER D 359 " pdb=" C SER D 359 " ideal model delta sigma weight residual 1.521 1.474 0.047 1.26e-02 6.30e+03 1.40e+01 bond pdb=" CA SER C 359 " pdb=" C SER C 359 " ideal model delta sigma weight residual 1.521 1.474 0.047 1.26e-02 6.30e+03 1.40e+01 bond pdb=" CA HIS D 360 " pdb=" C HIS D 360 " ideal model delta sigma weight residual 1.523 1.473 0.050 1.34e-02 5.57e+03 1.39e+01 bond pdb=" C VAL C 356 " pdb=" O VAL C 356 " ideal model delta sigma weight residual 1.236 1.204 0.032 1.00e-02 1.00e+04 1.01e+01 ... (remaining 12069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 15899 1.62 - 3.25: 310 3.25 - 4.87: 52 4.87 - 6.49: 11 6.49 - 8.11: 14 Bond angle restraints: 16286 Sorted by residual: angle pdb=" C GLU D 361 " pdb=" N CYS D 362 " pdb=" CA CYS D 362 " ideal model delta sigma weight residual 120.87 128.98 -8.11 1.42e+00 4.96e-01 3.27e+01 angle pdb=" C GLU C 361 " pdb=" N CYS C 362 " pdb=" CA CYS C 362 " ideal model delta sigma weight residual 120.87 128.95 -8.08 1.42e+00 4.96e-01 3.24e+01 angle pdb=" N VAL B 56 " pdb=" CA VAL B 56 " pdb=" C VAL B 56 " ideal model delta sigma weight residual 112.29 109.10 3.19 9.40e-01 1.13e+00 1.15e+01 angle pdb=" N VAL A 56 " pdb=" CA VAL A 56 " pdb=" C VAL A 56 " ideal model delta sigma weight residual 112.29 109.13 3.16 9.40e-01 1.13e+00 1.13e+01 angle pdb=" N ASN B 43 " pdb=" CA ASN B 43 " pdb=" C ASN B 43 " ideal model delta sigma weight residual 109.81 116.44 -6.63 2.21e+00 2.05e-01 9.00e+00 ... (remaining 16281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 6448 17.15 - 34.29: 644 34.29 - 51.44: 206 51.44 - 68.59: 36 68.59 - 85.73: 16 Dihedral angle restraints: 7350 sinusoidal: 3066 harmonic: 4284 Sorted by residual: dihedral pdb=" CA ASN C 30 " pdb=" C ASN C 30 " pdb=" N TRP C 31 " pdb=" CA TRP C 31 " ideal model delta harmonic sigma weight residual -180.00 -157.48 -22.52 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA ASN D 30 " pdb=" C ASN D 30 " pdb=" N TRP D 31 " pdb=" CA TRP D 31 " ideal model delta harmonic sigma weight residual -180.00 -157.49 -22.51 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA ASP B 3 " pdb=" CB ASP B 3 " pdb=" CG ASP B 3 " pdb=" OD1 ASP B 3 " ideal model delta sinusoidal sigma weight residual -30.00 -89.47 59.47 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 7347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1174 0.032 - 0.065: 418 0.065 - 0.097: 130 0.097 - 0.130: 48 0.130 - 0.162: 2 Chirality restraints: 1772 Sorted by residual: chirality pdb=" CA ASP D 372 " pdb=" N ASP D 372 " pdb=" C ASP D 372 " pdb=" CB ASP D 372 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CA ASP C 372 " pdb=" N ASP C 372 " pdb=" C ASP C 372 " pdb=" CB ASP C 372 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.40e-01 chirality pdb=" CA SER D 359 " pdb=" N SER D 359 " pdb=" C SER D 359 " pdb=" CB SER D 359 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 1769 not shown) Planarity restraints: 2140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 360 " 0.053 2.00e-02 2.50e+03 5.76e-02 4.97e+01 pdb=" CG HIS C 360 " -0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS C 360 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS C 360 " -0.078 2.00e-02 2.50e+03 pdb=" CE1 HIS C 360 " -0.023 2.00e-02 2.50e+03 pdb=" NE2 HIS C 360 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 360 " -0.053 2.00e-02 2.50e+03 5.76e-02 4.97e+01 pdb=" CG HIS D 360 " 0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS D 360 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS D 360 " 0.078 2.00e-02 2.50e+03 pdb=" CE1 HIS D 360 " 0.023 2.00e-02 2.50e+03 pdb=" NE2 HIS D 360 " -0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 355 " 0.013 2.00e-02 2.50e+03 9.22e-03 1.70e+00 pdb=" CG TYR C 355 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR C 355 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 355 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR C 355 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 355 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 355 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 355 " 0.002 2.00e-02 2.50e+03 ... (remaining 2137 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 284 2.68 - 3.24: 11768 3.24 - 3.79: 18796 3.79 - 4.35: 25270 4.35 - 4.90: 41836 Nonbonded interactions: 97954 Sorted by model distance: nonbonded pdb=" OD1 ASN C 219 " pdb="ZN ZN C 701 " model vdw 2.127 2.230 nonbonded pdb=" OD1 ASN D 219 " pdb="ZN ZN D 701 " model vdw 2.127 2.230 nonbonded pdb=" NH2 ARG D 191 " pdb=" O THR C 331 " model vdw 2.168 3.120 nonbonded pdb=" O THR D 331 " pdb=" NH2 ARG C 191 " model vdw 2.174 3.120 nonbonded pdb=" OG1 THR A 27 " pdb=" OG1 THR A 63 " model vdw 2.176 3.040 ... (remaining 97949 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' } ncs_group { reference = chain 'D' selection = chain 'C' } 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: 3.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.430 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 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 : 0.005 0.207 12078 Z= 0.233 Angle : 0.609 8.115 16286 Z= 0.353 Chirality : 0.039 0.162 1772 Planarity : 0.003 0.058 2140 Dihedral : 15.450 85.735 4574 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.27 % Allowed : 1.92 % Favored : 97.81 % Rotamer: Outliers : 0.39 % Allowed : 16.85 % Favored : 82.77 % 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 aren not related in a simple way. whole: 1.14 (0.23), residues: 1460 helix: 1.33 (0.19), residues: 784 sheet: 1.48 (0.54), residues: 108 loop : -0.11 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 101 TYR 0.022 0.001 TYR C 355 PHE 0.015 0.001 PHE B 69 TRP 0.009 0.001 TRP C 480 HIS 0.065 0.003 HIS D 360 Details of bonding type rmsd covalent geometry : bond 0.00324 (12074) covalent geometry : angle 0.60912 (16286) hydrogen bonds : bond 0.15653 ( 592) hydrogen bonds : angle 5.01665 ( 1734) metal coordination : bond 0.18509 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 0.460 Fit side-chains REVERT: A 72 MET cc_start: 0.3886 (pp-130) cc_final: 0.3120 (mpm) REVERT: A 95 LYS cc_start: 0.6430 (mptt) cc_final: 0.5967 (tppt) REVERT: B 72 MET cc_start: 0.3888 (pp-130) cc_final: 0.3119 (mpm) REVERT: B 95 LYS cc_start: 0.6427 (mptt) cc_final: 0.5969 (tppt) outliers start: 5 outliers final: 2 residues processed: 136 average time/residue: 0.6076 time to fit residues: 89.0758 Evaluate side-chains 123 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 121 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain C residue 359 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.0570 chunk 55 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 HIS D 398 ASN C 121 HIS C 398 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.227499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.141867 restraints weight = 13475.699| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.58 r_work: 0.3473 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12078 Z= 0.118 Angle : 0.527 10.427 16286 Z= 0.280 Chirality : 0.042 0.173 1772 Planarity : 0.004 0.032 2140 Dihedral : 4.024 28.030 1606 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.01 % Favored : 96.85 % Rotamer: Outliers : 1.55 % Allowed : 16.15 % Favored : 82.30 % 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 aren not related in a simple way. whole: 1.22 (0.23), residues: 1460 helix: 1.54 (0.19), residues: 770 sheet: 0.92 (0.54), residues: 108 loop : -0.12 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 101 TYR 0.020 0.002 TYR C 49 PHE 0.014 0.001 PHE C 591 TRP 0.008 0.001 TRP D 318 HIS 0.007 0.001 HIS C 561 Details of bonding type rmsd covalent geometry : bond 0.00243 (12074) covalent geometry : angle 0.52699 (16286) hydrogen bonds : bond 0.04303 ( 592) hydrogen bonds : angle 4.20945 ( 1734) metal coordination : bond 0.00268 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.4815 (ppp) cc_final: 0.3478 (ttt) REVERT: A 95 LYS cc_start: 0.6790 (mptt) cc_final: 0.6178 (tppt) REVERT: D 193 LYS cc_start: 0.8387 (mppt) cc_final: 0.8150 (mtmm) REVERT: D 282 LEU cc_start: 0.7719 (mp) cc_final: 0.7444 (tt) REVERT: B 73 MET cc_start: 0.4820 (ppp) cc_final: 0.3480 (ttt) REVERT: B 95 LYS cc_start: 0.6786 (mptt) cc_final: 0.6176 (tppt) REVERT: C 193 LYS cc_start: 0.8386 (mppt) cc_final: 0.8139 (mtmm) REVERT: C 270 VAL cc_start: 0.8753 (m) cc_final: 0.8362 (p) REVERT: C 282 LEU cc_start: 0.7755 (mp) cc_final: 0.7503 (tt) outliers start: 20 outliers final: 8 residues processed: 142 average time/residue: 0.6142 time to fit residues: 93.7030 Evaluate side-chains 135 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 432 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 9 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 0.0770 chunk 1 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 14 optimal weight: 0.0870 overall best weight: 1.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.223608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.130723 restraints weight = 13328.729| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.00 r_work: 0.3410 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12078 Z= 0.147 Angle : 0.546 7.921 16286 Z= 0.292 Chirality : 0.043 0.178 1772 Planarity : 0.004 0.039 2140 Dihedral : 4.161 17.243 1604 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.29 % Favored : 96.58 % Rotamer: Outliers : 1.85 % Allowed : 16.15 % Favored : 81.99 % 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 aren not related in a simple way. whole: 0.89 (0.22), residues: 1460 helix: 1.29 (0.19), residues: 790 sheet: 0.52 (0.53), residues: 104 loop : -0.29 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 91 TYR 0.022 0.002 TYR C 16 PHE 0.017 0.002 PHE D 591 TRP 0.009 0.001 TRP D 338 HIS 0.008 0.001 HIS D 561 Details of bonding type rmsd covalent geometry : bond 0.00330 (12074) covalent geometry : angle 0.54638 (16286) hydrogen bonds : bond 0.04696 ( 592) hydrogen bonds : angle 4.15935 ( 1734) metal coordination : bond 0.00491 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.376 Fit side-chains REVERT: A 3 ASP cc_start: 0.3230 (OUTLIER) cc_final: 0.2758 (t70) REVERT: A 95 LYS cc_start: 0.6801 (mptt) cc_final: 0.6327 (tppt) REVERT: D 193 LYS cc_start: 0.8418 (mppt) cc_final: 0.8177 (mtmm) REVERT: B 3 ASP cc_start: 0.3188 (OUTLIER) cc_final: 0.2712 (t70) REVERT: B 95 LYS cc_start: 0.6825 (mptt) cc_final: 0.6342 (tppt) REVERT: C 193 LYS cc_start: 0.8412 (mppt) cc_final: 0.8164 (mtmm) REVERT: C 225 MET cc_start: 0.9080 (mmm) cc_final: 0.8043 (mmt) outliers start: 24 outliers final: 11 residues processed: 131 average time/residue: 0.6243 time to fit residues: 87.6328 Evaluate side-chains 131 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 439 MET Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 439 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 133 optimal weight: 20.0000 chunk 25 optimal weight: 0.9980 chunk 54 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 404 HIS C 404 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.223282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.139632 restraints weight = 13120.173| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.33 r_work: 0.3374 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12078 Z= 0.114 Angle : 0.516 8.585 16286 Z= 0.271 Chirality : 0.041 0.170 1772 Planarity : 0.004 0.036 2140 Dihedral : 4.027 17.636 1604 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.01 % Favored : 96.85 % Rotamer: Outliers : 2.09 % Allowed : 16.92 % Favored : 80.99 % 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 aren not related in a simple way. whole: 1.01 (0.23), residues: 1460 helix: 1.42 (0.19), residues: 778 sheet: 0.39 (0.53), residues: 104 loop : -0.23 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 18 TYR 0.029 0.002 TYR C 16 PHE 0.013 0.001 PHE C 591 TRP 0.007 0.001 TRP D 338 HIS 0.006 0.001 HIS C 561 Details of bonding type rmsd covalent geometry : bond 0.00242 (12074) covalent geometry : angle 0.51616 (16286) hydrogen bonds : bond 0.03910 ( 592) hydrogen bonds : angle 4.06340 ( 1734) metal coordination : bond 0.00328 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.3293 (OUTLIER) cc_final: 0.2790 (t70) REVERT: A 73 MET cc_start: 0.5591 (ppp) cc_final: 0.3599 (ttt) REVERT: A 95 LYS cc_start: 0.6916 (mptt) cc_final: 0.6380 (tppt) REVERT: D 24 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7152 (mm-30) REVERT: D 193 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8224 (mtmm) REVERT: D 470 MET cc_start: 0.1976 (OUTLIER) cc_final: 0.1529 (ppp) REVERT: B 3 ASP cc_start: 0.3296 (OUTLIER) cc_final: 0.2793 (t70) REVERT: B 73 MET cc_start: 0.5582 (ppp) cc_final: 0.3591 (ttt) REVERT: B 95 LYS cc_start: 0.6931 (mptt) cc_final: 0.6404 (tppt) REVERT: C 24 GLU cc_start: 0.7310 (mm-30) cc_final: 0.7006 (mm-30) REVERT: C 193 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8227 (mtmm) REVERT: C 470 MET cc_start: 0.1996 (OUTLIER) cc_final: 0.1518 (ppp) outliers start: 27 outliers final: 14 residues processed: 140 average time/residue: 0.5522 time to fit residues: 83.3332 Evaluate side-chains 139 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 193 LYS Chi-restraints excluded: chain D residue 244 LYS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 439 MET Chi-restraints excluded: chain D residue 470 MET Chi-restraints excluded: chain D residue 521 MET Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 439 MET Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 521 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 44 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 103 optimal weight: 0.0970 chunk 50 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN B 112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.222632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.131925 restraints weight = 13232.297| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.35 r_work: 0.3355 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12078 Z= 0.140 Angle : 0.540 10.258 16286 Z= 0.285 Chirality : 0.042 0.173 1772 Planarity : 0.004 0.038 2140 Dihedral : 4.155 19.026 1604 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.15 % Favored : 96.71 % Rotamer: Outliers : 2.40 % Allowed : 17.31 % Favored : 80.29 % 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 aren not related in a simple way. whole: 0.78 (0.23), residues: 1460 helix: 1.25 (0.19), residues: 790 sheet: 0.04 (0.53), residues: 104 loop : -0.33 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 352 TYR 0.019 0.002 TYR C 49 PHE 0.015 0.001 PHE C 591 TRP 0.007 0.001 TRP C 338 HIS 0.008 0.001 HIS C 561 Details of bonding type rmsd covalent geometry : bond 0.00314 (12074) covalent geometry : angle 0.54044 (16286) hydrogen bonds : bond 0.04286 ( 592) hydrogen bonds : angle 4.13218 ( 1734) metal coordination : bond 0.00428 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.370 Fit side-chains REVERT: A 3 ASP cc_start: 0.3186 (OUTLIER) cc_final: 0.2703 (t70) REVERT: A 95 LYS cc_start: 0.6992 (mptt) cc_final: 0.6442 (tptm) REVERT: D 193 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8256 (mtmm) REVERT: D 194 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7506 (mpp80) REVERT: D 470 MET cc_start: 0.1958 (OUTLIER) cc_final: 0.1536 (ppp) REVERT: B 3 ASP cc_start: 0.3182 (OUTLIER) cc_final: 0.2698 (t70) REVERT: B 95 LYS cc_start: 0.6972 (mptt) cc_final: 0.6416 (tptm) REVERT: C 193 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8254 (mtmm) REVERT: C 194 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7502 (mpp80) REVERT: C 470 MET cc_start: 0.1954 (OUTLIER) cc_final: 0.1532 (ppp) outliers start: 31 outliers final: 17 residues processed: 142 average time/residue: 0.5674 time to fit residues: 86.6096 Evaluate side-chains 141 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 193 LYS Chi-restraints excluded: chain D residue 194 ARG Chi-restraints excluded: chain D residue 244 LYS Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 439 MET Chi-restraints excluded: chain D residue 470 MET Chi-restraints excluded: chain D residue 521 MET Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 439 MET Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 521 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 13 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 88 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 130 optimal weight: 10.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN D 542 ASN B 112 ASN C 542 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.220888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.130491 restraints weight = 13202.135| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.44 r_work: 0.3322 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12078 Z= 0.177 Angle : 0.583 9.088 16286 Z= 0.311 Chirality : 0.044 0.182 1772 Planarity : 0.004 0.041 2140 Dihedral : 4.373 19.482 1604 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.42 % Favored : 96.44 % Rotamer: Outliers : 2.63 % Allowed : 17.93 % Favored : 79.44 % 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 aren not related in a simple way. whole: 0.53 (0.22), residues: 1460 helix: 0.96 (0.19), residues: 812 sheet: -0.37 (0.54), residues: 94 loop : -0.29 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 127 TYR 0.020 0.002 TYR D 49 PHE 0.018 0.002 PHE C 591 TRP 0.007 0.001 TRP D 256 HIS 0.008 0.001 HIS D 561 Details of bonding type rmsd covalent geometry : bond 0.00408 (12074) covalent geometry : angle 0.58330 (16286) hydrogen bonds : bond 0.04858 ( 592) hydrogen bonds : angle 4.32499 ( 1734) metal coordination : bond 0.00591 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 0.290 Fit side-chains REVERT: A 1 MET cc_start: 0.1875 (tmm) cc_final: 0.0422 (ptp) REVERT: A 73 MET cc_start: 0.5525 (ppp) cc_final: 0.3806 (ttt) REVERT: A 95 LYS cc_start: 0.6854 (mptt) cc_final: 0.6288 (tptm) REVERT: D 24 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7028 (mm-30) REVERT: D 193 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8300 (mtmm) REVERT: D 194 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7620 (mpp80) REVERT: D 470 MET cc_start: 0.2214 (OUTLIER) cc_final: 0.1854 (ppp) REVERT: B 1 MET cc_start: 0.1870 (tmm) cc_final: 0.0422 (ptp) REVERT: B 73 MET cc_start: 0.5525 (ppp) cc_final: 0.3806 (ttt) REVERT: B 95 LYS cc_start: 0.6892 (mptt) cc_final: 0.6311 (tptm) REVERT: C 24 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7059 (mm-30) REVERT: C 193 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8209 (mtmm) REVERT: C 194 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7614 (mpp80) REVERT: C 470 MET cc_start: 0.2246 (OUTLIER) cc_final: 0.1906 (ppp) outliers start: 34 outliers final: 21 residues processed: 141 average time/residue: 0.6436 time to fit residues: 97.1757 Evaluate side-chains 148 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 193 LYS Chi-restraints excluded: chain D residue 194 ARG Chi-restraints excluded: chain D residue 244 LYS Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 439 MET Chi-restraints excluded: chain D residue 470 MET Chi-restraints excluded: chain D residue 521 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 439 MET Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 521 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 93 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN B 112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.219770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.128176 restraints weight = 13237.126| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.95 r_work: 0.3378 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12078 Z= 0.187 Angle : 0.608 10.951 16286 Z= 0.322 Chirality : 0.044 0.189 1772 Planarity : 0.004 0.042 2140 Dihedral : 4.454 23.071 1604 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.42 % Favored : 96.44 % Rotamer: Outliers : 2.63 % Allowed : 17.85 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.22), residues: 1460 helix: 0.83 (0.18), residues: 812 sheet: -0.45 (0.54), residues: 94 loop : -0.37 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 127 TYR 0.023 0.002 TYR C 16 PHE 0.020 0.002 PHE C 591 TRP 0.008 0.002 TRP C 256 HIS 0.007 0.002 HIS C 561 Details of bonding type rmsd covalent geometry : bond 0.00433 (12074) covalent geometry : angle 0.60813 (16286) hydrogen bonds : bond 0.04944 ( 592) hydrogen bonds : angle 4.43447 ( 1734) metal coordination : bond 0.00633 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 0.355 Fit side-chains REVERT: A 1 MET cc_start: 0.1920 (tmm) cc_final: -0.0054 (ptp) REVERT: A 73 MET cc_start: 0.5300 (ppp) cc_final: 0.3113 (ttt) REVERT: A 95 LYS cc_start: 0.6794 (mptt) cc_final: 0.6286 (tptm) REVERT: D 193 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8282 (mtmm) REVERT: D 194 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7522 (mpp80) REVERT: D 424 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.5870 (tmt) REVERT: D 470 MET cc_start: 0.2336 (OUTLIER) cc_final: 0.2004 (ppp) REVERT: B 1 MET cc_start: 0.1918 (tmm) cc_final: -0.0068 (ptp) REVERT: B 73 MET cc_start: 0.5278 (ppp) cc_final: 0.3127 (ttt) REVERT: B 95 LYS cc_start: 0.6801 (mptt) cc_final: 0.6289 (tptm) REVERT: C 193 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8272 (mtmm) REVERT: C 194 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7512 (mpp80) REVERT: C 424 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.5856 (tmt) REVERT: C 470 MET cc_start: 0.2291 (OUTLIER) cc_final: 0.1979 (ppp) outliers start: 34 outliers final: 16 residues processed: 137 average time/residue: 0.6217 time to fit residues: 91.3909 Evaluate side-chains 144 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 193 LYS Chi-restraints excluded: chain D residue 194 ARG Chi-restraints excluded: chain D residue 244 LYS Chi-restraints excluded: chain D residue 424 MET Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 439 MET Chi-restraints excluded: chain D residue 470 MET Chi-restraints excluded: chain D residue 521 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 439 MET Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 521 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 7 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 126 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN B 112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.219919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.137141 restraints weight = 13049.547| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.74 r_work: 0.3332 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12078 Z= 0.139 Angle : 0.572 11.773 16286 Z= 0.302 Chirality : 0.043 0.205 1772 Planarity : 0.004 0.037 2140 Dihedral : 4.297 21.320 1604 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.36 % Favored : 96.51 % Rotamer: Outliers : 2.63 % Allowed : 17.85 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.22), residues: 1460 helix: 0.95 (0.19), residues: 810 sheet: -0.24 (0.52), residues: 104 loop : -0.42 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 352 TYR 0.025 0.002 TYR D 16 PHE 0.014 0.001 PHE D 591 TRP 0.009 0.001 TRP D 338 HIS 0.006 0.001 HIS D 561 Details of bonding type rmsd covalent geometry : bond 0.00311 (12074) covalent geometry : angle 0.57244 (16286) hydrogen bonds : bond 0.04233 ( 592) hydrogen bonds : angle 4.36206 ( 1734) metal coordination : bond 0.00438 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.328 Fit side-chains REVERT: A 1 MET cc_start: 0.2100 (tmm) cc_final: 0.0338 (ptp) REVERT: A 73 MET cc_start: 0.5191 (ppp) cc_final: 0.3139 (ttt) REVERT: A 95 LYS cc_start: 0.6688 (mptt) cc_final: 0.6132 (tptm) REVERT: D 194 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7291 (mpp80) REVERT: D 225 MET cc_start: 0.8913 (mmm) cc_final: 0.8087 (mmm) REVERT: D 424 MET cc_start: 0.6955 (OUTLIER) cc_final: 0.5765 (tmt) REVERT: D 470 MET cc_start: 0.2394 (OUTLIER) cc_final: 0.2087 (ppp) REVERT: B 1 MET cc_start: 0.2107 (tmm) cc_final: 0.0362 (ptp) REVERT: B 73 MET cc_start: 0.5194 (ppp) cc_final: 0.3117 (ttt) REVERT: B 95 LYS cc_start: 0.6683 (mptt) cc_final: 0.6135 (tptm) REVERT: C 194 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7287 (mpp80) REVERT: C 424 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.5755 (tmt) REVERT: C 470 MET cc_start: 0.2397 (OUTLIER) cc_final: 0.2091 (ppp) outliers start: 34 outliers final: 18 residues processed: 135 average time/residue: 0.6073 time to fit residues: 87.9203 Evaluate side-chains 143 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 194 ARG Chi-restraints excluded: chain D residue 244 LYS Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 424 MET Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 439 MET Chi-restraints excluded: chain D residue 470 MET Chi-restraints excluded: chain D residue 521 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 439 MET Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 521 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 91 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN B 112 ASN C 601 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.219935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.143940 restraints weight = 13030.456| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 3.60 r_work: 0.3373 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12078 Z= 0.121 Angle : 0.566 11.446 16286 Z= 0.291 Chirality : 0.042 0.200 1772 Planarity : 0.004 0.034 2140 Dihedral : 4.203 22.186 1604 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.15 % Favored : 96.71 % Rotamer: Outliers : 2.24 % Allowed : 18.16 % Favored : 79.60 % 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 aren not related in a simple way. whole: 0.64 (0.23), residues: 1460 helix: 1.10 (0.19), residues: 800 sheet: -0.38 (0.53), residues: 108 loop : -0.28 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 352 TYR 0.042 0.002 TYR C 49 PHE 0.011 0.001 PHE C 591 TRP 0.009 0.001 TRP D 338 HIS 0.008 0.001 HIS D 561 Details of bonding type rmsd covalent geometry : bond 0.00265 (12074) covalent geometry : angle 0.56645 (16286) hydrogen bonds : bond 0.03896 ( 592) hydrogen bonds : angle 4.18317 ( 1734) metal coordination : bond 0.00329 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.409 Fit side-chains REVERT: A 1 MET cc_start: 0.1948 (tmm) cc_final: 0.0289 (ptp) REVERT: A 73 MET cc_start: 0.5409 (ppp) cc_final: 0.4272 (ttt) REVERT: A 95 LYS cc_start: 0.6946 (mptt) cc_final: 0.6380 (tptm) REVERT: D 194 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7517 (mpp80) REVERT: D 424 MET cc_start: 0.7030 (OUTLIER) cc_final: 0.5874 (tmt) REVERT: D 470 MET cc_start: 0.2452 (OUTLIER) cc_final: 0.2094 (ppp) REVERT: B 1 MET cc_start: 0.2036 (tmm) cc_final: 0.0351 (ptp) REVERT: B 73 MET cc_start: 0.5402 (ppp) cc_final: 0.4266 (ttt) REVERT: B 95 LYS cc_start: 0.6953 (mptt) cc_final: 0.6392 (tptm) REVERT: C 194 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7521 (mpp80) REVERT: C 225 MET cc_start: 0.8883 (mmm) cc_final: 0.8184 (mmm) REVERT: C 424 MET cc_start: 0.7018 (OUTLIER) cc_final: 0.5830 (tmt) REVERT: C 470 MET cc_start: 0.2409 (OUTLIER) cc_final: 0.2076 (ppp) outliers start: 29 outliers final: 18 residues processed: 140 average time/residue: 0.5787 time to fit residues: 87.1311 Evaluate side-chains 144 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 194 ARG Chi-restraints excluded: chain D residue 244 LYS Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 424 MET Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 439 MET Chi-restraints excluded: chain D residue 470 MET Chi-restraints excluded: chain D residue 521 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 439 MET Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 521 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 143 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 107 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN B 112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.220118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.136525 restraints weight = 13026.869| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.57 r_work: 0.3349 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12078 Z= 0.144 Angle : 0.603 11.694 16286 Z= 0.309 Chirality : 0.043 0.205 1772 Planarity : 0.004 0.035 2140 Dihedral : 4.263 20.973 1604 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.08 % Favored : 96.78 % Rotamer: Outliers : 2.16 % Allowed : 18.47 % Favored : 79.37 % 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 aren not related in a simple way. whole: 0.55 (0.22), residues: 1460 helix: 1.02 (0.19), residues: 798 sheet: -0.23 (0.53), residues: 104 loop : -0.35 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 352 TYR 0.042 0.002 TYR D 49 PHE 0.011 0.001 PHE D 339 TRP 0.008 0.001 TRP D 338 HIS 0.007 0.001 HIS C 561 Details of bonding type rmsd covalent geometry : bond 0.00327 (12074) covalent geometry : angle 0.60262 (16286) hydrogen bonds : bond 0.04253 ( 592) hydrogen bonds : angle 4.30553 ( 1734) metal coordination : bond 0.00416 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.356 Fit side-chains REVERT: A 1 MET cc_start: 0.2059 (tmm) cc_final: 0.0569 (ptp) REVERT: A 73 MET cc_start: 0.4899 (ppp) cc_final: 0.3270 (ttt) REVERT: A 95 LYS cc_start: 0.6884 (mptt) cc_final: 0.6291 (tptm) REVERT: D 97 GLU cc_start: 0.8077 (tp30) cc_final: 0.7509 (mp0) REVERT: D 194 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7472 (mpp80) REVERT: D 424 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.5843 (tmt) REVERT: D 470 MET cc_start: 0.2507 (OUTLIER) cc_final: 0.2189 (ppp) REVERT: D 518 MET cc_start: 0.3788 (ppp) cc_final: 0.3436 (pmm) REVERT: B 1 MET cc_start: 0.2077 (tmm) cc_final: 0.0586 (ptp) REVERT: B 73 MET cc_start: 0.4901 (ppp) cc_final: 0.3267 (ttt) REVERT: B 95 LYS cc_start: 0.6885 (mptt) cc_final: 0.6296 (tptm) REVERT: C 194 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7472 (mpp80) REVERT: C 225 MET cc_start: 0.8945 (mmm) cc_final: 0.8194 (mmm) REVERT: C 424 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.5823 (tmt) REVERT: C 470 MET cc_start: 0.2381 (OUTLIER) cc_final: 0.2090 (ppp) REVERT: C 518 MET cc_start: 0.3769 (ppp) cc_final: 0.3557 (pmm) outliers start: 28 outliers final: 18 residues processed: 138 average time/residue: 0.6434 time to fit residues: 94.8205 Evaluate side-chains 146 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 194 ARG Chi-restraints excluded: chain D residue 244 LYS Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 424 MET Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 439 MET Chi-restraints excluded: chain D residue 470 MET Chi-restraints excluded: chain D residue 521 MET Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 439 MET Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 521 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 57 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 135 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 126 optimal weight: 0.2980 chunk 9 optimal weight: 0.0170 chunk 46 optimal weight: 1.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN D 601 HIS B 112 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.222110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.134935 restraints weight = 13106.907| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.84 r_work: 0.3440 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12078 Z= 0.108 Angle : 0.563 12.414 16286 Z= 0.285 Chirality : 0.041 0.189 1772 Planarity : 0.003 0.031 2140 Dihedral : 4.078 21.776 1604 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.81 % Favored : 97.05 % Rotamer: Outliers : 1.78 % Allowed : 18.86 % Favored : 79.37 % 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 aren not related in a simple way. whole: 0.70 (0.23), residues: 1460 helix: 1.15 (0.19), residues: 804 sheet: -0.25 (0.53), residues: 108 loop : -0.29 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 352 TYR 0.040 0.001 TYR D 49 PHE 0.008 0.001 PHE D 339 TRP 0.009 0.001 TRP D 338 HIS 0.007 0.001 HIS C 561 Details of bonding type rmsd covalent geometry : bond 0.00230 (12074) covalent geometry : angle 0.56311 (16286) hydrogen bonds : bond 0.03488 ( 592) hydrogen bonds : angle 4.11772 ( 1734) metal coordination : bond 0.00245 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4922.74 seconds wall clock time: 84 minutes 7.00 seconds (5047.00 seconds total)