Starting phenix.real_space_refine on Wed May 14 14:27:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jfy_36219/05_2025/8jfy_36219.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jfy_36219/05_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_36219/05_2025/8jfy_36219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jfy_36219/05_2025/8jfy_36219.map" model { file = "/net/cci-nas-00/data/ceres_data/8jfy_36219/05_2025/8jfy_36219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jfy_36219/05_2025/8jfy_36219.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: "C" 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: "C" 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, D Time building chain proxies: 10.60, per 1000 atoms: 0.89 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: 2.95 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.30 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: 4.09 Time building geometry restraints manager: 3.43 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.660 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: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 34.450 Find NCS groups from input model: 0.250 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:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.180 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.009 0.001 TRP C 480 HIS 0.065 0.003 HIS D 360 PHE 0.015 0.001 PHE B 69 TYR 0.022 0.001 TYR C 355 ARG 0.005 0.000 ARG D 101 Details of bonding type rmsd hydrogen bonds : bond 0.15653 ( 592) hydrogen bonds : angle 5.01665 ( 1734) metal coordination : bond 0.18509 ( 4) covalent geometry : bond 0.00324 (12074) covalent geometry : angle 0.60912 (16286) *********************** 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 : 1.281 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: 1.3352 time to fit residues: 196.2517 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 : 1.358 ------------------------------------------------------------------------------- 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 121 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 30.0000 chunk 84 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.4498 r_free = 0.4498 target = 0.224512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.138614 restraints weight = 13092.967| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.65 r_work: 0.3399 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12078 Z= 0.174 Angle : 0.603 11.856 16286 Z= 0.323 Chirality : 0.045 0.186 1772 Planarity : 0.004 0.042 2140 Dihedral : 4.419 28.788 1606 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.88 % Favored : 96.99 % Rotamer: Outliers : 2.47 % Allowed : 16.00 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.22), residues: 1460 helix: 1.25 (0.19), residues: 786 sheet: 0.60 (0.62), residues: 82 loop : -0.23 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 338 HIS 0.007 0.002 HIS D 561 PHE 0.020 0.002 PHE C 591 TYR 0.022 0.002 TYR C 49 ARG 0.004 0.000 ARG D 101 Details of bonding type rmsd hydrogen bonds : bond 0.05254 ( 592) hydrogen bonds : angle 4.34078 ( 1734) metal coordination : bond 0.00966 ( 4) covalent geometry : bond 0.00396 (12074) covalent geometry : angle 0.60303 (16286) *********************** 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 160 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.3097 (OUTLIER) cc_final: 0.2599 (t0) REVERT: A 73 MET cc_start: 0.4885 (ppp) cc_final: 0.3679 (ttt) REVERT: A 95 LYS cc_start: 0.6784 (mptt) cc_final: 0.6220 (tppt) REVERT: D 119 ARG cc_start: 0.8139 (mmt90) cc_final: 0.7752 (tpp-160) REVERT: D 225 MET cc_start: 0.9033 (mmm) cc_final: 0.8162 (mmm) REVERT: D 470 MET cc_start: 0.2271 (OUTLIER) cc_final: 0.1696 (ppp) REVERT: B 3 ASP cc_start: 0.3109 (OUTLIER) cc_final: 0.2611 (t0) REVERT: B 73 MET cc_start: 0.4886 (ppp) cc_final: 0.3677 (ttt) REVERT: B 95 LYS cc_start: 0.6800 (mptt) cc_final: 0.6240 (tppt) REVERT: C 119 ARG cc_start: 0.8136 (mmt90) cc_final: 0.7738 (tpp-160) REVERT: C 225 MET cc_start: 0.9040 (mmm) cc_final: 0.8386 (mmt) REVERT: C 470 MET cc_start: 0.2296 (OUTLIER) cc_final: 0.1720 (ppp) outliers start: 32 outliers final: 12 residues processed: 146 average time/residue: 1.4887 time to fit residues: 233.2965 Evaluate side-chains 140 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 276 ASP Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 470 MET Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 276 ASP Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 470 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 62 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 51 optimal weight: 0.3980 chunk 131 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 = 0.4442 r_free = 0.4442 target = 0.217942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.129080 restraints weight = 13060.744| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.82 r_work: 0.3363 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12078 Z= 0.224 Angle : 0.630 9.136 16286 Z= 0.339 Chirality : 0.046 0.191 1772 Planarity : 0.005 0.043 2140 Dihedral : 4.638 22.416 1604 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.97 % Favored : 95.89 % Rotamer: Outliers : 3.25 % Allowed : 15.53 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.22), residues: 1460 helix: 0.66 (0.18), residues: 816 sheet: -0.01 (0.61), residues: 82 loop : -0.41 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 338 HIS 0.008 0.002 HIS D 561 PHE 0.020 0.002 PHE C 591 TYR 0.023 0.003 TYR D 49 ARG 0.004 0.000 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.05785 ( 592) hydrogen bonds : angle 4.49946 ( 1734) metal coordination : bond 0.00917 ( 4) covalent geometry : bond 0.00525 (12074) covalent geometry : angle 0.62955 (16286) *********************** 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 162 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 120 time to evaluate : 1.284 Fit side-chains REVERT: A 3 ASP cc_start: 0.3117 (OUTLIER) cc_final: 0.2719 (t70) REVERT: A 95 LYS cc_start: 0.6689 (mptt) cc_final: 0.6221 (tptm) REVERT: D 119 ARG cc_start: 0.8142 (mmt90) cc_final: 0.7737 (tpp-160) REVERT: D 194 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7589 (mpp80) REVERT: D 225 MET cc_start: 0.9053 (mmm) cc_final: 0.8109 (mmm) REVERT: D 470 MET cc_start: 0.2166 (OUTLIER) cc_final: 0.1688 (ppp) REVERT: B 3 ASP cc_start: 0.3137 (OUTLIER) cc_final: 0.2684 (t0) REVERT: B 95 LYS cc_start: 0.6688 (mptt) cc_final: 0.6218 (tptm) REVERT: C 119 ARG cc_start: 0.8160 (mmt90) cc_final: 0.7754 (tpp-160) REVERT: C 194 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7606 (mpp80) REVERT: C 225 MET cc_start: 0.9056 (mmm) cc_final: 0.8115 (mmm) REVERT: C 470 MET cc_start: 0.2193 (OUTLIER) cc_final: 0.1656 (ppp) outliers start: 42 outliers final: 20 residues processed: 146 average time/residue: 1.5128 time to fit residues: 236.4619 Evaluate side-chains 144 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 105 GLU 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 263 LEU Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 432 LEU 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 30 THR Chi-restraints excluded: chain B residue 105 GLU 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 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 470 MET Chi-restraints excluded: chain C residue 521 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 110 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 118 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.221010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.129420 restraints weight = 13140.467| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.32 r_work: 0.3364 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12078 Z= 0.152 Angle : 0.562 9.376 16286 Z= 0.299 Chirality : 0.043 0.193 1772 Planarity : 0.004 0.039 2140 Dihedral : 4.392 20.624 1604 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.15 % Favored : 96.71 % Rotamer: Outliers : 2.78 % Allowed : 17.47 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.22), residues: 1460 helix: 0.79 (0.18), residues: 816 sheet: -0.35 (0.54), residues: 94 loop : -0.43 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 338 HIS 0.006 0.001 HIS C 561 PHE 0.015 0.002 PHE D 591 TYR 0.020 0.002 TYR C 49 ARG 0.002 0.000 ARG D 288 Details of bonding type rmsd hydrogen bonds : bond 0.04601 ( 592) hydrogen bonds : angle 4.32792 ( 1734) metal coordination : bond 0.00527 ( 4) covalent geometry : bond 0.00343 (12074) covalent geometry : angle 0.56228 (16286) *********************** 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 162 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.3314 (OUTLIER) cc_final: 0.2944 (t70) REVERT: A 73 MET cc_start: 0.4975 (ppp) cc_final: 0.3667 (ttt) REVERT: A 95 LYS cc_start: 0.6829 (mptt) cc_final: 0.6275 (tptm) REVERT: D 119 ARG cc_start: 0.8158 (mmt90) cc_final: 0.7752 (tpp-160) REVERT: D 193 LYS cc_start: 0.8502 (mppt) cc_final: 0.8292 (mtmm) REVERT: D 194 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7543 (mpp80) REVERT: D 225 MET cc_start: 0.9001 (mmm) cc_final: 0.8258 (mmm) REVERT: D 470 MET cc_start: 0.2169 (OUTLIER) cc_final: 0.1752 (ppp) REVERT: B 3 ASP cc_start: 0.3262 (OUTLIER) cc_final: 0.2881 (t70) REVERT: B 73 MET cc_start: 0.5063 (ppp) cc_final: 0.3656 (ttt) REVERT: B 95 LYS cc_start: 0.6829 (mptt) cc_final: 0.6275 (tptm) REVERT: C 119 ARG cc_start: 0.8151 (mmt90) cc_final: 0.7737 (tpp-160) REVERT: C 193 LYS cc_start: 0.8498 (mppt) cc_final: 0.8286 (mtmm) REVERT: C 194 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7560 (mpp80) REVERT: C 225 MET cc_start: 0.9002 (mmm) cc_final: 0.8257 (mmm) REVERT: C 470 MET cc_start: 0.2164 (OUTLIER) cc_final: 0.1752 (ppp) outliers start: 36 outliers final: 14 residues processed: 142 average time/residue: 1.6108 time to fit residues: 244.4159 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 : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 145 MET 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 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 B residue 3 ASP Chi-restraints excluded: chain B residue 145 MET 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 263 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 128 optimal weight: 20.0000 chunk 82 optimal weight: 0.5980 chunk 93 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 542 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.217071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.144744 restraints weight = 12981.196| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.32 r_work: 0.3334 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 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 : 0.005 0.039 12078 Z= 0.213 Angle : 0.617 9.525 16286 Z= 0.330 Chirality : 0.046 0.186 1772 Planarity : 0.004 0.042 2140 Dihedral : 4.643 22.794 1604 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.84 % Favored : 96.03 % Rotamer: Outliers : 3.32 % Allowed : 17.00 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.22), residues: 1460 helix: 0.63 (0.18), residues: 814 sheet: -0.23 (0.60), residues: 82 loop : -0.47 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 338 HIS 0.008 0.002 HIS C 561 PHE 0.019 0.002 PHE D 591 TYR 0.021 0.002 TYR C 49 ARG 0.003 0.000 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.05441 ( 592) hydrogen bonds : angle 4.52551 ( 1734) metal coordination : bond 0.00690 ( 4) covalent geometry : bond 0.00498 (12074) covalent geometry : angle 0.61652 (16286) *********************** 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 162 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 119 time to evaluate : 1.308 Fit side-chains REVERT: A 3 ASP cc_start: 0.3218 (OUTLIER) cc_final: 0.2840 (t70) REVERT: A 95 LYS cc_start: 0.6832 (mptt) cc_final: 0.6319 (tptm) REVERT: D 119 ARG cc_start: 0.8201 (mmt90) cc_final: 0.7740 (tpp-160) REVERT: D 193 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8333 (mtmm) REVERT: D 194 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7605 (mpp80) REVERT: D 225 MET cc_start: 0.9071 (mmm) cc_final: 0.8247 (mmm) REVERT: B 3 ASP cc_start: 0.3183 (OUTLIER) cc_final: 0.2813 (t70) REVERT: B 95 LYS cc_start: 0.6845 (mptt) cc_final: 0.6323 (tptm) REVERT: C 119 ARG cc_start: 0.8197 (mmt90) cc_final: 0.7735 (tpp-160) REVERT: C 193 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8318 (mtmm) REVERT: C 194 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7620 (mpp80) REVERT: C 225 MET cc_start: 0.9072 (mmm) cc_final: 0.8253 (mmm) outliers start: 43 outliers final: 24 residues processed: 146 average time/residue: 1.4639 time to fit residues: 229.3674 Evaluate side-chains 149 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain D residue 30 ASN 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 270 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 521 MET Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain C residue 30 ASN 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 270 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 432 LEU 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 139 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 0.0470 chunk 25 optimal weight: 0.9980 overall best weight: 0.7480 ------------------------------------------------------------------------------- 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 = 0.4472 r_free = 0.4472 target = 0.221448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.131923 restraints weight = 13278.282| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.39 r_work: 0.3345 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12078 Z= 0.117 Angle : 0.531 9.623 16286 Z= 0.282 Chirality : 0.042 0.167 1772 Planarity : 0.004 0.036 2140 Dihedral : 4.291 22.321 1604 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.01 % Favored : 96.85 % Rotamer: Outliers : 3.40 % Allowed : 16.62 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.23), residues: 1460 helix: 0.86 (0.19), residues: 816 sheet: -0.30 (0.55), residues: 94 loop : -0.43 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 338 HIS 0.006 0.001 HIS C 561 PHE 0.016 0.001 PHE D 11 TYR 0.040 0.002 TYR C 49 ARG 0.002 0.000 ARG D 288 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 592) hydrogen bonds : angle 4.29137 ( 1734) metal coordination : bond 0.00310 ( 4) covalent geometry : bond 0.00247 (12074) covalent geometry : angle 0.53082 (16286) *********************** 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 168 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 124 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.5287 (ppp) cc_final: 0.3813 (ttt) REVERT: A 95 LYS cc_start: 0.6886 (mptt) cc_final: 0.6300 (tptm) REVERT: D 24 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6922 (mm-30) REVERT: D 119 ARG cc_start: 0.8156 (mmt90) cc_final: 0.7736 (tpp-160) REVERT: D 194 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7511 (mpp80) REVERT: D 225 MET cc_start: 0.8963 (mmm) cc_final: 0.8190 (mmm) REVERT: B 73 MET cc_start: 0.5287 (ppp) cc_final: 0.3813 (ttt) REVERT: B 95 LYS cc_start: 0.6896 (mptt) cc_final: 0.6309 (tptm) REVERT: B 120 GLU cc_start: 0.7101 (tp30) cc_final: 0.6886 (mp0) REVERT: C 119 ARG cc_start: 0.8158 (mmt90) cc_final: 0.7735 (tpp-160) REVERT: C 194 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7513 (mpp80) REVERT: C 225 MET cc_start: 0.8969 (mmm) cc_final: 0.8201 (mmm) outliers start: 44 outliers final: 22 residues processed: 150 average time/residue: 1.4814 time to fit residues: 238.1239 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 : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 105 GLU 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 194 ARG Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 521 MET Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 105 GLU 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 194 ARG Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 551 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 119 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 124 optimal weight: 0.9990 chunk 129 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 0.0980 chunk 134 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- 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 = 0.4430 r_free = 0.4430 target = 0.216942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.145727 restraints weight = 13018.004| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.06 r_work: 0.3329 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12078 Z= 0.207 Angle : 0.629 11.495 16286 Z= 0.334 Chirality : 0.045 0.190 1772 Planarity : 0.004 0.041 2140 Dihedral : 4.609 22.334 1604 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.97 % Favored : 95.89 % Rotamer: Outliers : 3.55 % Allowed : 17.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.22), residues: 1460 helix: 0.68 (0.18), residues: 808 sheet: -0.60 (0.54), residues: 94 loop : -0.43 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 338 HIS 0.008 0.002 HIS D 561 PHE 0.019 0.002 PHE B 13 TYR 0.038 0.003 TYR D 49 ARG 0.003 0.000 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.05349 ( 592) hydrogen bonds : angle 4.59921 ( 1734) metal coordination : bond 0.00705 ( 4) covalent geometry : bond 0.00484 (12074) covalent geometry : angle 0.62920 (16286) *********************** 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 175 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 129 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.5319 (ppp) cc_final: 0.2993 (ttt) REVERT: A 95 LYS cc_start: 0.6879 (mptt) cc_final: 0.6369 (tptm) REVERT: D 24 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7030 (mm-30) REVERT: D 97 GLU cc_start: 0.8117 (tp30) cc_final: 0.7370 (mp0) REVERT: D 119 ARG cc_start: 0.8172 (mmt90) cc_final: 0.7695 (tpp-160) REVERT: D 194 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7674 (mpp80) REVERT: D 225 MET cc_start: 0.9070 (mmm) cc_final: 0.8216 (mmm) REVERT: B 73 MET cc_start: 0.5412 (ppp) cc_final: 0.3156 (ttt) REVERT: B 77 MET cc_start: 0.4987 (OUTLIER) cc_final: 0.4733 (tpt) REVERT: B 95 LYS cc_start: 0.6885 (mptt) cc_final: 0.6374 (tptm) REVERT: C 24 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7034 (mm-30) REVERT: C 97 GLU cc_start: 0.8121 (tp30) cc_final: 0.7369 (mp0) REVERT: C 119 ARG cc_start: 0.8169 (mmt90) cc_final: 0.7693 (tpp-160) REVERT: C 194 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7681 (mpp80) REVERT: C 225 MET cc_start: 0.9074 (mmm) cc_final: 0.8223 (mmm) outliers start: 46 outliers final: 28 residues processed: 157 average time/residue: 1.4764 time to fit residues: 248.2888 Evaluate side-chains 158 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 105 GLU 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 194 ARG Chi-restraints excluded: chain D residue 244 LYS Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 521 MET Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 77 MET Chi-restraints excluded: chain B residue 105 GLU 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 194 ARG Chi-restraints excluded: chain C residue 244 LYS Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 551 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 47 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 109 optimal weight: 0.1980 chunk 43 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 131 optimal weight: 9.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4467 r_free = 0.4467 target = 0.220748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.147503 restraints weight = 13149.322| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.22 r_work: 0.3411 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12078 Z= 0.109 Angle : 0.544 11.984 16286 Z= 0.286 Chirality : 0.041 0.165 1772 Planarity : 0.004 0.033 2140 Dihedral : 4.212 23.057 1604 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.08 % Favored : 96.78 % Rotamer: Outliers : 2.47 % Allowed : 18.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.23), residues: 1460 helix: 1.00 (0.19), residues: 802 sheet: -0.53 (0.55), residues: 98 loop : -0.33 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 338 HIS 0.006 0.001 HIS D 561 PHE 0.017 0.001 PHE C 11 TYR 0.035 0.002 TYR D 49 ARG 0.002 0.000 ARG C 288 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 592) hydrogen bonds : angle 4.28534 ( 1734) metal coordination : bond 0.00255 ( 4) covalent geometry : bond 0.00226 (12074) covalent geometry : angle 0.54403 (16286) *********************** 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 165 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.4881 (ppp) cc_final: 0.2911 (ttt) REVERT: A 95 LYS cc_start: 0.6807 (mptt) cc_final: 0.6189 (tptm) REVERT: D 97 GLU cc_start: 0.8021 (tp30) cc_final: 0.7486 (mp0) REVERT: D 119 ARG cc_start: 0.8071 (mmt90) cc_final: 0.7678 (tpp-160) REVERT: D 225 MET cc_start: 0.8915 (mmm) cc_final: 0.8179 (mmm) REVERT: D 470 MET cc_start: 0.2445 (OUTLIER) cc_final: 0.1926 (ppp) REVERT: B 73 MET cc_start: 0.4883 (ppp) cc_final: 0.3005 (ttt) REVERT: B 95 LYS cc_start: 0.6841 (mptt) cc_final: 0.6225 (tptm) REVERT: C 24 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7080 (mm-30) REVERT: C 97 GLU cc_start: 0.8016 (tp30) cc_final: 0.7479 (mp0) REVERT: C 119 ARG cc_start: 0.8087 (mmt90) cc_final: 0.7670 (tpp-160) REVERT: C 225 MET cc_start: 0.8920 (mmm) cc_final: 0.8189 (mmm) REVERT: C 470 MET cc_start: 0.2434 (OUTLIER) cc_final: 0.1911 (ppp) outliers start: 32 outliers final: 16 residues processed: 145 average time/residue: 1.4457 time to fit residues: 225.4874 Evaluate side-chains 142 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 470 MET Chi-restraints excluded: chain D residue 521 MET Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 551 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 124 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4472 r_free = 0.4472 target = 0.221296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.131770 restraints weight = 13283.110| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.64 r_work: 0.3310 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12078 Z= 0.122 Angle : 0.586 14.412 16286 Z= 0.302 Chirality : 0.042 0.223 1772 Planarity : 0.004 0.033 2140 Dihedral : 4.220 20.748 1604 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.15 % Favored : 96.71 % Rotamer: Outliers : 1.85 % Allowed : 18.93 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.23), residues: 1460 helix: 1.08 (0.19), residues: 800 sheet: -0.27 (0.56), residues: 94 loop : -0.34 (0.28), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 338 HIS 0.008 0.001 HIS D 561 PHE 0.022 0.001 PHE C 11 TYR 0.038 0.002 TYR D 16 ARG 0.002 0.000 ARG D 423 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 592) hydrogen bonds : angle 4.20074 ( 1734) metal coordination : bond 0.00312 ( 4) covalent geometry : bond 0.00267 (12074) covalent geometry : angle 0.58642 (16286) *********************** 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 156 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.5374 (ppp) cc_final: 0.4354 (ttt) REVERT: A 95 LYS cc_start: 0.6827 (mptt) cc_final: 0.6273 (tptm) REVERT: D 24 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7231 (mm-30) REVERT: D 97 GLU cc_start: 0.7998 (tp30) cc_final: 0.7489 (mp0) REVERT: D 119 ARG cc_start: 0.8077 (mmt90) cc_final: 0.7672 (tpp-160) REVERT: D 194 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7401 (mpp80) REVERT: D 225 MET cc_start: 0.8948 (mmm) cc_final: 0.8167 (mmm) REVERT: D 470 MET cc_start: 0.2481 (OUTLIER) cc_final: 0.2057 (ppp) REVERT: B 95 LYS cc_start: 0.6824 (mptt) cc_final: 0.6273 (tptm) REVERT: C 97 GLU cc_start: 0.7975 (tp30) cc_final: 0.7483 (mp0) REVERT: C 119 ARG cc_start: 0.8075 (mmt90) cc_final: 0.7667 (tpp-160) REVERT: C 194 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7406 (mpp80) REVERT: C 470 MET cc_start: 0.2486 (OUTLIER) cc_final: 0.2057 (ppp) outliers start: 24 outliers final: 16 residues processed: 146 average time/residue: 1.5263 time to fit residues: 238.2456 Evaluate side-chains 150 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 194 ARG Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 470 MET Chi-restraints excluded: chain D residue 521 MET Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 470 MET Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 551 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 13 optimal weight: 0.0970 chunk 38 optimal weight: 0.9990 chunk 77 optimal weight: 0.2980 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 0.3980 chunk 135 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 42 optimal weight: 0.0570 chunk 82 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 601 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.223927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.142022 restraints weight = 13250.789| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.79 r_work: 0.3490 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12078 Z= 0.104 Angle : 0.563 15.797 16286 Z= 0.285 Chirality : 0.041 0.204 1772 Planarity : 0.003 0.031 2140 Dihedral : 4.040 21.960 1604 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.67 % Favored : 97.19 % Rotamer: Outliers : 1.24 % Allowed : 19.63 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.23), residues: 1460 helix: 1.08 (0.19), residues: 812 sheet: -0.12 (0.53), residues: 108 loop : -0.29 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 338 HIS 0.007 0.001 HIS D 561 PHE 0.016 0.001 PHE D 11 TYR 0.033 0.002 TYR C 16 ARG 0.002 0.000 ARG D 288 Details of bonding type rmsd hydrogen bonds : bond 0.03307 ( 592) hydrogen bonds : angle 4.10677 ( 1734) metal coordination : bond 0.00144 ( 4) covalent geometry : bond 0.00216 (12074) covalent geometry : angle 0.56345 (16286) ********************** 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 157 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.4970 (ppp) cc_final: 0.3444 (ttt) REVERT: A 95 LYS cc_start: 0.6732 (mptt) cc_final: 0.6043 (tptm) REVERT: D 119 ARG cc_start: 0.8071 (mmt90) cc_final: 0.7771 (tpp-160) REVERT: D 194 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7263 (mpp80) REVERT: B 73 MET cc_start: 0.5029 (ppp) cc_final: 0.3032 (ttt) REVERT: B 95 LYS cc_start: 0.6725 (mptt) cc_final: 0.6047 (tptm) REVERT: C 119 ARG cc_start: 0.8082 (mmt90) cc_final: 0.7788 (tpp-160) REVERT: C 194 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7261 (mpp80) outliers start: 16 outliers final: 15 residues processed: 149 average time/residue: 1.5235 time to fit residues: 243.2601 Evaluate side-chains 146 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 194 ARG Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 521 MET Chi-restraints excluded: chain D residue 551 PHE Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 551 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 47 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 19 optimal weight: 9.9990 chunk 116 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.4490 r_free = 0.4490 target = 0.223395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.138282 restraints weight = 13251.170| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.54 r_work: 0.3453 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12078 Z= 0.125 Angle : 0.593 17.067 16286 Z= 0.299 Chirality : 0.042 0.190 1772 Planarity : 0.004 0.033 2140 Dihedral : 4.099 19.110 1604 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.01 % Favored : 96.85 % Rotamer: Outliers : 1.70 % Allowed : 18.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.23), residues: 1460 helix: 1.07 (0.19), residues: 812 sheet: -0.37 (0.56), residues: 98 loop : -0.24 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 338 HIS 0.007 0.001 HIS D 561 PHE 0.009 0.001 PHE D 339 TYR 0.033 0.002 TYR D 49 ARG 0.002 0.000 ARG A 75 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 592) hydrogen bonds : angle 4.14366 ( 1734) metal coordination : bond 0.00339 ( 4) covalent geometry : bond 0.00278 (12074) covalent geometry : angle 0.59288 (16286) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11330.80 seconds wall clock time: 194 minutes 48.54 seconds (11688.54 seconds total)