Starting phenix.real_space_refine on Mon Dec 30 01:32:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jfy_36219/12_2024/8jfy_36219.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jfy_36219/12_2024/8jfy_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_36219/12_2024/8jfy_36219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jfy_36219/12_2024/8jfy_36219.map" model { file = "/net/cci-nas-00/data/ceres_data/8jfy_36219/12_2024/8jfy_36219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jfy_36219/12_2024/8jfy_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 10.56, 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: 3.15 Conformation dependent library (CDL) restraints added in 1.4 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: 1.52 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: 3.68 Time building geometry restraints manager: 3.60 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: 0.00 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: 3.740 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: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 34.730 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 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:13.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.950 ------------------------------------------------------------------------------- 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 : 0.003 0.059 12074 Z= 0.206 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 *********************** 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 : 1.378 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: 1.5127 time to fit residues: 222.3792 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 : 1.300 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 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 12074 Z= 0.258 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 *********************** 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 : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.2916 (OUTLIER) cc_final: 0.2394 (t0) REVERT: A 73 MET cc_start: 0.4906 (ppp) cc_final: 0.3623 (ttt) REVERT: A 95 LYS cc_start: 0.6512 (mptt) cc_final: 0.5999 (tppt) REVERT: D 119 ARG cc_start: 0.8139 (mmt90) cc_final: 0.7771 (tpp-160) REVERT: D 225 MET cc_start: 0.8999 (mmm) cc_final: 0.8173 (mmm) REVERT: D 470 MET cc_start: 0.2312 (OUTLIER) cc_final: 0.1657 (ppp) REVERT: B 3 ASP cc_start: 0.2919 (OUTLIER) cc_final: 0.2393 (t0) REVERT: B 73 MET cc_start: 0.4907 (ppp) cc_final: 0.3618 (ttt) REVERT: B 95 LYS cc_start: 0.6527 (mptt) cc_final: 0.6017 (tppt) REVERT: C 119 ARG cc_start: 0.8115 (mmt90) cc_final: 0.7737 (tpp-160) REVERT: C 225 MET cc_start: 0.8999 (mmm) cc_final: 0.8394 (mmt) REVERT: C 470 MET cc_start: 0.2343 (OUTLIER) cc_final: 0.1684 (ppp) outliers start: 32 outliers final: 12 residues processed: 146 average time/residue: 1.4968 time to fit residues: 235.4265 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 : 1.466 ------------------------------------------------------------------------------- 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 72 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12074 Z= 0.249 Angle : 0.561 7.625 16286 Z= 0.303 Chirality : 0.044 0.182 1772 Planarity : 0.004 0.039 2140 Dihedral : 4.352 21.246 1604 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.22 % Favored : 96.64 % Rotamer: Outliers : 2.55 % Allowed : 16.31 % Favored : 81.14 % 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: 0.52 (0.22), residues: 1460 helix: 1.00 (0.18), residues: 802 sheet: -0.10 (0.55), residues: 94 loop : -0.43 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 338 HIS 0.008 0.001 HIS D 561 PHE 0.017 0.002 PHE C 591 TYR 0.021 0.002 TYR D 49 ARG 0.003 0.000 ARG C 101 *********************** 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 158 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 1.413 Fit side-chains REVERT: A 3 ASP cc_start: 0.3097 (OUTLIER) cc_final: 0.2643 (t0) REVERT: A 95 LYS cc_start: 0.6481 (mptt) cc_final: 0.5977 (tptm) REVERT: D 24 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6994 (mm-30) REVERT: D 119 ARG cc_start: 0.8121 (mmt90) cc_final: 0.7700 (tpp-160) REVERT: D 194 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.6890 (mpp80) REVERT: D 225 MET cc_start: 0.9009 (mmm) cc_final: 0.8354 (mmt) REVERT: D 424 MET cc_start: 0.7127 (tpt) cc_final: 0.6914 (tpt) REVERT: D 470 MET cc_start: 0.2181 (OUTLIER) cc_final: 0.1613 (ppp) REVERT: B 3 ASP cc_start: 0.3046 (OUTLIER) cc_final: 0.2581 (t0) REVERT: B 95 LYS cc_start: 0.6457 (mptt) cc_final: 0.5953 (tptm) REVERT: C 24 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6999 (mm-30) REVERT: C 119 ARG cc_start: 0.8094 (mmt90) cc_final: 0.7693 (tpp-160) REVERT: C 194 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.6933 (mpp80) REVERT: C 225 MET cc_start: 0.9010 (mmm) cc_final: 0.8352 (mmt) REVERT: C 470 MET cc_start: 0.2178 (OUTLIER) cc_final: 0.1609 (ppp) outliers start: 33 outliers final: 19 residues processed: 142 average time/residue: 1.6603 time to fit residues: 252.2108 Evaluate side-chains 142 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP 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 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 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 402 MET 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 129 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 62 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 12074 Z= 0.499 Angle : 0.736 10.381 16286 Z= 0.392 Chirality : 0.051 0.252 1772 Planarity : 0.005 0.048 2140 Dihedral : 4.974 22.154 1604 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.32 % Favored : 95.55 % Rotamer: Outliers : 3.63 % Allowed : 15.77 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.19 (0.22), residues: 1460 helix: 0.33 (0.18), residues: 812 sheet: -0.33 (0.60), residues: 82 loop : -0.62 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP C 480 HIS 0.008 0.002 HIS C 561 PHE 0.019 0.003 PHE D 591 TYR 0.024 0.003 TYR D 49 ARG 0.006 0.001 ARG B 127 *********************** 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 165 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 118 time to evaluate : 1.419 Fit side-chains REVERT: A 3 ASP cc_start: 0.3085 (OUTLIER) cc_final: 0.2679 (t70) REVERT: A 95 LYS cc_start: 0.6318 (mptt) cc_final: 0.5890 (tptm) REVERT: D 193 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7746 (mppt) REVERT: D 194 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7361 (mpp80) REVERT: B 3 ASP cc_start: 0.3084 (OUTLIER) cc_final: 0.2675 (t70) REVERT: B 95 LYS cc_start: 0.6342 (mptt) cc_final: 0.5899 (tptm) REVERT: C 193 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7710 (mppt) REVERT: C 194 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7340 (mpp80) outliers start: 47 outliers final: 24 residues processed: 145 average time/residue: 1.5899 time to fit residues: 247.1406 Evaluate side-chains 142 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 1.463 ------------------------------------------------------------------------------- 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 120 LEU Chi-restraints excluded: chain D residue 193 LYS Chi-restraints excluded: chain D residue 194 ARG Chi-restraints excluded: chain D residue 201 LEU 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 415 THR Chi-restraints excluded: chain D residue 427 VAL 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 120 LEU Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 194 ARG Chi-restraints excluded: chain C residue 201 LEU 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 415 THR Chi-restraints excluded: chain C residue 427 VAL 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 115 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 71 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12074 Z= 0.163 Angle : 0.537 11.285 16286 Z= 0.284 Chirality : 0.042 0.181 1772 Planarity : 0.004 0.038 2140 Dihedral : 4.381 24.120 1604 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.22 % Favored : 96.64 % Rotamer: Outliers : 2.16 % Allowed : 18.32 % 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 (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: 0.22 (0.22), residues: 1460 helix: 0.71 (0.18), residues: 816 sheet: -0.34 (0.55), residues: 94 loop : -0.47 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 338 HIS 0.005 0.001 HIS C 561 PHE 0.017 0.001 PHE C 11 TYR 0.019 0.002 TYR C 49 ARG 0.003 0.000 ARG D 288 *********************** 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 152 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 1.434 Fit side-chains REVERT: A 73 MET cc_start: 0.5402 (ppp) cc_final: 0.3901 (ttt) REVERT: A 95 LYS cc_start: 0.6368 (mptt) cc_final: 0.5805 (tptm) REVERT: D 119 ARG cc_start: 0.8116 (mmt90) cc_final: 0.7623 (tpp-160) REVERT: D 193 LYS cc_start: 0.8292 (mppt) cc_final: 0.8032 (mtmm) REVERT: D 194 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.6933 (mpp80) REVERT: B 73 MET cc_start: 0.5403 (ppp) cc_final: 0.3900 (ttt) REVERT: B 95 LYS cc_start: 0.6352 (mptt) cc_final: 0.5785 (tptm) REVERT: C 119 ARG cc_start: 0.8116 (mmt90) cc_final: 0.7624 (tpp-160) REVERT: C 193 LYS cc_start: 0.8299 (mppt) cc_final: 0.8041 (mtmm) REVERT: C 194 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.6931 (mpp80) outliers start: 28 outliers final: 14 residues processed: 138 average time/residue: 1.6209 time to fit residues: 239.6673 Evaluate side-chains 136 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 1.423 ------------------------------------------------------------------------------- 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 263 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain B residue 30 THR 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 194 ARG Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 432 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 73 optimal weight: 5.9990 chunk 134 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12074 Z= 0.175 Angle : 0.561 10.220 16286 Z= 0.295 Chirality : 0.042 0.170 1772 Planarity : 0.004 0.034 2140 Dihedral : 4.269 21.860 1604 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.29 % Favored : 96.58 % Rotamer: Outliers : 2.70 % Allowed : 17.70 % 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 (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: 0.40 (0.23), residues: 1460 helix: 0.85 (0.19), residues: 816 sheet: -0.31 (0.56), residues: 94 loop : -0.38 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 338 HIS 0.006 0.001 HIS D 561 PHE 0.017 0.001 PHE D 11 TYR 0.039 0.002 TYR C 49 ARG 0.002 0.000 ARG C 101 *********************** 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 161 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2101 (tmm) cc_final: -0.0395 (ptp) REVERT: A 73 MET cc_start: 0.5393 (ppp) cc_final: 0.2920 (ttt) REVERT: A 95 LYS cc_start: 0.6389 (mptt) cc_final: 0.5814 (tptm) REVERT: D 16 TYR cc_start: 0.7515 (t80) cc_final: 0.7206 (t80) REVERT: D 119 ARG cc_start: 0.8113 (mmt90) cc_final: 0.7665 (tpp-160) REVERT: D 193 LYS cc_start: 0.8304 (mppt) cc_final: 0.8057 (mtmm) REVERT: D 194 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.6971 (mpp80) REVERT: D 470 MET cc_start: 0.2396 (OUTLIER) cc_final: 0.2003 (ppp) REVERT: B 1 MET cc_start: 0.2109 (tmm) cc_final: -0.0380 (ptp) REVERT: B 73 MET cc_start: 0.5422 (ppp) cc_final: 0.2975 (ttt) REVERT: B 95 LYS cc_start: 0.6383 (mptt) cc_final: 0.5809 (tptm) REVERT: C 16 TYR cc_start: 0.7534 (t80) cc_final: 0.7156 (t80) REVERT: C 119 ARG cc_start: 0.8112 (mmt90) cc_final: 0.7666 (tpp-160) REVERT: C 193 LYS cc_start: 0.8305 (mppt) cc_final: 0.8055 (mtmm) REVERT: C 194 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.6984 (mpp80) REVERT: C 470 MET cc_start: 0.2389 (OUTLIER) cc_final: 0.1995 (ppp) outliers start: 35 outliers final: 16 residues processed: 144 average time/residue: 1.6077 time to fit residues: 248.1181 Evaluate side-chains 144 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 1.309 ------------------------------------------------------------------------------- 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 85 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 194 ARG 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 85 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 194 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 4.9990 chunk 79 optimal weight: 0.0870 chunk 101 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 84 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.8160 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12074 Z= 0.164 Angle : 0.538 10.494 16286 Z= 0.281 Chirality : 0.041 0.170 1772 Planarity : 0.004 0.033 2140 Dihedral : 4.192 22.659 1604 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.49 % Favored : 96.37 % Rotamer: Outliers : 2.63 % Allowed : 17.54 % Favored : 79.83 % 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: 0.57 (0.23), residues: 1460 helix: 1.04 (0.19), residues: 806 sheet: -0.58 (0.55), residues: 98 loop : -0.29 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 338 HIS 0.006 0.001 HIS D 561 PHE 0.018 0.001 PHE D 11 TYR 0.036 0.002 TYR C 49 ARG 0.002 0.000 ARG D 101 *********************** 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 159 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2155 (tmm) cc_final: -0.0252 (ptp) REVERT: A 73 MET cc_start: 0.5357 (ppp) cc_final: 0.4505 (ttt) REVERT: A 95 LYS cc_start: 0.6439 (mptt) cc_final: 0.5868 (tptm) REVERT: D 119 ARG cc_start: 0.8097 (mmt90) cc_final: 0.7649 (tpp-160) REVERT: D 193 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.8070 (mtmm) REVERT: D 194 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.6966 (mpp80) REVERT: D 470 MET cc_start: 0.2450 (OUTLIER) cc_final: 0.2064 (ppp) REVERT: B 1 MET cc_start: 0.2180 (tmm) cc_final: -0.0237 (ptp) REVERT: B 73 MET cc_start: 0.5391 (ppp) cc_final: 0.4544 (ttt) REVERT: B 95 LYS cc_start: 0.6436 (mptt) cc_final: 0.5865 (tptm) REVERT: C 16 TYR cc_start: 0.7532 (t80) cc_final: 0.7118 (t80) REVERT: C 119 ARG cc_start: 0.8097 (mmt90) cc_final: 0.7650 (tpp-160) REVERT: C 193 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8071 (mtmm) REVERT: C 194 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.6964 (mpp80) REVERT: C 470 MET cc_start: 0.2468 (OUTLIER) cc_final: 0.2078 (ppp) outliers start: 34 outliers final: 17 residues processed: 143 average time/residue: 1.6156 time to fit residues: 247.9557 Evaluate side-chains 146 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 1.478 ------------------------------------------------------------------------------- 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 85 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 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 145 MET Chi-restraints excluded: chain C residue 85 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 0.0470 chunk 26 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 0.0370 chunk 68 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 126 optimal weight: 0.2980 overall best weight: 0.4156 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 12074 Z= 0.145 Angle : 0.561 12.121 16286 Z= 0.283 Chirality : 0.041 0.209 1772 Planarity : 0.003 0.031 2140 Dihedral : 4.045 21.133 1604 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.81 % Favored : 97.05 % Rotamer: Outliers : 1.85 % Allowed : 18.47 % 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: 0.65 (0.23), residues: 1460 helix: 1.08 (0.19), residues: 810 sheet: -0.38 (0.56), residues: 98 loop : -0.25 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 338 HIS 0.006 0.001 HIS D 561 PHE 0.016 0.001 PHE D 11 TYR 0.035 0.002 TYR D 16 ARG 0.002 0.000 ARG D 288 *********************** 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 156 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2140 (tmm) cc_final: -0.0127 (ptp) REVERT: A 73 MET cc_start: 0.4694 (ppp) cc_final: 0.3580 (ttt) REVERT: A 95 LYS cc_start: 0.6417 (mptt) cc_final: 0.5778 (tptm) REVERT: D 119 ARG cc_start: 0.8033 (mmt90) cc_final: 0.7792 (tpp-160) REVERT: D 193 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8030 (mtmm) REVERT: B 1 MET cc_start: 0.2148 (tmm) cc_final: -0.0109 (ptp) REVERT: B 73 MET cc_start: 0.4731 (ppp) cc_final: 0.3617 (ttt) REVERT: B 95 LYS cc_start: 0.6411 (mptt) cc_final: 0.5775 (tptm) REVERT: C 119 ARG cc_start: 0.8033 (mmt90) cc_final: 0.7794 (tpp-160) REVERT: C 193 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8030 (mtmm) outliers start: 24 outliers final: 16 residues processed: 140 average time/residue: 1.4831 time to fit residues: 223.7856 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 : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 193 LYS 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 B residue 145 MET Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 299 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 129 optimal weight: 0.6980 chunk 77 optimal weight: 0.0170 chunk 56 optimal weight: 6.9990 chunk 101 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 0.0570 chunk 122 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.4136 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12074 Z= 0.137 Angle : 0.568 12.910 16286 Z= 0.286 Chirality : 0.041 0.210 1772 Planarity : 0.003 0.030 2140 Dihedral : 4.005 21.325 1604 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.29 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 (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: 0.75 (0.23), residues: 1460 helix: 1.14 (0.19), residues: 812 sheet: -0.33 (0.56), residues: 98 loop : -0.19 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 338 HIS 0.007 0.001 HIS C 561 PHE 0.015 0.001 PHE C 11 TYR 0.043 0.002 TYR C 16 ARG 0.002 0.000 ARG D 101 *********************** 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 159 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2112 (tmm) cc_final: -0.0089 (ptp) REVERT: A 73 MET cc_start: 0.4931 (ppp) cc_final: 0.3289 (ttt) REVERT: A 95 LYS cc_start: 0.6421 (mptt) cc_final: 0.5802 (tptm) REVERT: D 119 ARG cc_start: 0.8018 (mmt90) cc_final: 0.7751 (tpp-160) REVERT: D 193 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8039 (mtmm) REVERT: B 1 MET cc_start: 0.2119 (tmm) cc_final: -0.0073 (ptp) REVERT: B 73 MET cc_start: 0.4932 (ppp) cc_final: 0.3285 (ttt) REVERT: B 95 LYS cc_start: 0.6419 (mptt) cc_final: 0.5798 (tptm) REVERT: C 119 ARG cc_start: 0.8016 (mmt90) cc_final: 0.7751 (tpp-160) REVERT: C 193 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8041 (mtmm) outliers start: 23 outliers final: 16 residues processed: 149 average time/residue: 1.4548 time to fit residues: 234.3978 Evaluate side-chains 143 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 193 LYS Chi-restraints excluded: chain D residue 244 LYS 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 145 MET Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 244 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 114 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12074 Z= 0.174 Angle : 0.607 18.006 16286 Z= 0.301 Chirality : 0.042 0.186 1772 Planarity : 0.004 0.033 2140 Dihedral : 4.056 20.001 1604 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.15 % Favored : 96.71 % Rotamer: Outliers : 1.85 % Allowed : 19.24 % Favored : 78.90 % 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: 0.74 (0.23), residues: 1460 helix: 1.16 (0.19), residues: 812 sheet: -0.42 (0.55), residues: 98 loop : -0.21 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 338 HIS 0.007 0.001 HIS C 561 PHE 0.012 0.001 PHE C 591 TYR 0.036 0.002 TYR D 16 ARG 0.002 0.000 ARG C 17 ********************** 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: 24 poor density : 130 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2151 (tmm) cc_final: -0.0008 (ptp) REVERT: A 95 LYS cc_start: 0.6452 (mptt) cc_final: 0.5821 (tptm) REVERT: A 112 ASN cc_start: 0.7102 (OUTLIER) cc_final: 0.6780 (t0) REVERT: D 119 ARG cc_start: 0.8054 (mmt90) cc_final: 0.7557 (tpp-160) REVERT: D 193 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8063 (mtmm) REVERT: B 1 MET cc_start: 0.2226 (tmm) cc_final: 0.0013 (ptp) REVERT: B 95 LYS cc_start: 0.6447 (mptt) cc_final: 0.5822 (tptm) REVERT: C 119 ARG cc_start: 0.8052 (mmt90) cc_final: 0.7558 (tpp-160) REVERT: C 193 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8062 (mtmm) outliers start: 24 outliers final: 16 residues processed: 143 average time/residue: 1.4805 time to fit residues: 227.9474 Evaluate side-chains 143 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 193 LYS Chi-restraints excluded: chain D residue 244 LYS 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 145 MET Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 244 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 21 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4487 r_free = 0.4487 target = 0.222551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.132258 restraints weight = 13137.396| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.43 r_work: 0.3379 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 12074 Z= 0.206 Angle : 0.854 59.200 16286 Z= 0.478 Chirality : 0.050 1.146 1772 Planarity : 0.004 0.110 2140 Dihedral : 4.056 20.200 1604 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.15 % Favored : 96.71 % Rotamer: Outliers : 1.55 % Allowed : 19.71 % Favored : 78.75 % Cbeta Deviations : 0.07 % 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: 0.75 (0.23), residues: 1460 helix: 1.17 (0.19), residues: 812 sheet: -0.42 (0.55), residues: 98 loop : -0.21 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 338 HIS 0.018 0.001 HIS C 561 PHE 0.011 0.001 PHE C 591 TYR 0.031 0.002 TYR C 49 ARG 0.001 0.000 ARG C 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4556.26 seconds wall clock time: 82 minutes 36.21 seconds (4956.21 seconds total)