Starting phenix.real_space_refine on Thu Jul 2 21:48:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ias_52785/07_2026/9ias_52785.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ias_52785/07_2026/9ias_52785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ias_52785/07_2026/9ias_52785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ias_52785/07_2026/9ias_52785.map" model { file = "/net/cci-nas-00/data/ceres_data/9ias_52785/07_2026/9ias_52785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ias_52785/07_2026/9ias_52785.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 52 5.16 5 Cl 2 4.86 5 C 6642 2.51 5 N 1658 2.21 5 O 1820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10176 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4090 Classifications: {'peptide': 534} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 505} Chain breaks: 2 Chain: "B" Number of atoms: 4090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4090 Classifications: {'peptide': 534} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 505} Chain breaks: 2 Chain: "C" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 960 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "D" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 960 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 2.04, per 1000 atoms: 0.20 Number of scatterers: 10176 At special positions: 0 Unit cell: (84.194, 150.414, 123.926, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 52 16.00 P 2 15.00 O 1820 8.00 N 1658 7.00 C 6642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 328.8 milliseconds 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 10 sheets defined 63.6% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 44 through 74 removed outlier: 3.729A pdb=" N THR A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) Proline residue: A 64 - end of helix Processing helix chain 'A' and resid 77 through 83 removed outlier: 4.084A pdb=" N LEU A 81 " --> pdb=" O PRO A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 95 removed outlier: 3.966A pdb=" N PHE A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 116 Processing helix chain 'A' and resid 119 through 140 Processing helix chain 'A' and resid 142 through 149 removed outlier: 3.743A pdb=" N ILE A 149 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 169 Processing helix chain 'A' and resid 169 through 175 Processing helix chain 'A' and resid 182 through 193 Processing helix chain 'A' and resid 194 through 197 removed outlier: 3.686A pdb=" N THR A 197 " --> pdb=" O ILE A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 198 through 222 Processing helix chain 'A' and resid 236 through 246 Processing helix chain 'A' and resid 246 through 266 Processing helix chain 'A' and resid 299 through 307 Processing helix chain 'A' and resid 308 through 333 Proline residue: A 314 - end of helix Processing helix chain 'A' and resid 337 through 355 removed outlier: 3.746A pdb=" N LEU A 354 " --> pdb=" O MET A 350 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 373 Processing helix chain 'A' and resid 379 through 395 removed outlier: 4.308A pdb=" N VAL A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 402 removed outlier: 3.562A pdb=" N TYR A 401 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 402 " --> pdb=" O PHE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 416 Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 422 through 431 Processing helix chain 'A' and resid 434 through 445 removed outlier: 3.527A pdb=" N LEU A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 470 Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 493 through 506 Processing helix chain 'A' and resid 525 through 542 Processing helix chain 'A' and resid 552 through 563 removed outlier: 3.588A pdb=" N VAL A 558 " --> pdb=" O PRO A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 583 Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 44 through 73 removed outlier: 3.752A pdb=" N THR B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) Proline residue: B 64 - end of helix removed outlier: 3.692A pdb=" N GLU B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 removed outlier: 4.028A pdb=" N LEU B 81 " --> pdb=" O PRO B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 95 removed outlier: 4.063A pdb=" N PHE B 93 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 116 removed outlier: 3.515A pdb=" N TYR B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 140 Processing helix chain 'B' and resid 142 through 149 removed outlier: 3.650A pdb=" N ILE B 149 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 169 Processing helix chain 'B' and resid 169 through 175 Processing helix chain 'B' and resid 182 through 193 Processing helix chain 'B' and resid 194 through 197 removed outlier: 3.803A pdb=" N THR B 197 " --> pdb=" O ILE B 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 194 through 197' Processing helix chain 'B' and resid 198 through 222 Processing helix chain 'B' and resid 236 through 246 Processing helix chain 'B' and resid 246 through 266 Processing helix chain 'B' and resid 299 through 307 Processing helix chain 'B' and resid 308 through 333 Proline residue: B 314 - end of helix removed outlier: 3.740A pdb=" N SER B 321 " --> pdb=" O GLY B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 355 removed outlier: 3.742A pdb=" N LEU B 354 " --> pdb=" O MET B 350 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 373 Processing helix chain 'B' and resid 377 through 379 No H-bonds generated for 'chain 'B' and resid 377 through 379' Processing helix chain 'B' and resid 380 through 395 removed outlier: 3.533A pdb=" N THR B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 402 removed outlier: 3.549A pdb=" N TYR B 401 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 402 " --> pdb=" O PHE B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 416 Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 421 through 430 removed outlier: 4.343A pdb=" N ARG B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 433 No H-bonds generated for 'chain 'B' and resid 431 through 433' Processing helix chain 'B' and resid 434 through 445 removed outlier: 3.592A pdb=" N LEU B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 470 Processing helix chain 'B' and resid 490 through 492 No H-bonds generated for 'chain 'B' and resid 490 through 492' Processing helix chain 'B' and resid 493 through 506 Processing helix chain 'B' and resid 525 through 542 Processing helix chain 'B' and resid 552 through 563 removed outlier: 3.533A pdb=" N VAL B 558 " --> pdb=" O PRO B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'C' and resid 26 through 31 removed outlier: 3.527A pdb=" N PHE C 29 " --> pdb=" O GLY C 26 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG C 30 " --> pdb=" O ARG C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'D' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 103 removed outlier: 4.804A pdb=" N THR A 101 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 473 through 476 removed outlier: 8.279A pdb=" N PHE A 570 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N PHE A 548 " --> pdb=" O PHE A 570 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 103 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 477 removed outlier: 8.436A pdb=" N PHE B 570 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE B 548 " --> pdb=" O PHE B 570 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.579A pdb=" N LEU C 81 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.778A pdb=" N GLY C 10 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N MET C 34 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N SER C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.778A pdb=" N GLY C 10 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.567A pdb=" N LEU D 81 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.544A pdb=" N GLY D 10 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N MET D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.544A pdb=" N GLY D 10 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N CYS D 96 " --> pdb=" O TRP D 116 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TRP D 116 " --> pdb=" O CYS D 96 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG D 98 " --> pdb=" O ASP D 114 " (cutoff:3.500A) 645 hydrogen bonds defined for protein. 1809 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.43 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1584 1.31 - 1.44: 2763 1.44 - 1.56: 5937 1.56 - 1.69: 22 1.69 - 1.81: 82 Bond restraints: 10388 Sorted by residual: bond pdb=" C30 PEE A 601 " pdb=" O3 PEE A 601 " ideal model delta sigma weight residual 1.327 1.433 -0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C30 PEE C 700 " pdb=" O3 PEE C 700 " ideal model delta sigma weight residual 1.327 1.432 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C10 PEE A 601 " pdb=" O2 PEE A 601 " ideal model delta sigma weight residual 1.332 1.435 -0.103 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C10 PEE C 700 " pdb=" O2 PEE C 700 " ideal model delta sigma weight residual 1.332 1.434 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C10 PEE C 700 " pdb=" C11 PEE C 700 " ideal model delta sigma weight residual 1.504 1.573 -0.069 2.00e-02 2.50e+03 1.19e+01 ... (remaining 10383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 14049 3.31 - 6.63: 65 6.63 - 9.94: 7 9.94 - 13.25: 1 13.25 - 16.57: 2 Bond angle restraints: 14124 Sorted by residual: angle pdb=" O3P PEE C 700 " pdb=" P PEE C 700 " pdb=" O4P PEE C 700 " ideal model delta sigma weight residual 92.91 109.48 -16.57 3.00e+00 1.11e-01 3.05e+01 angle pdb=" O3P PEE A 601 " pdb=" P PEE A 601 " pdb=" O4P PEE A 601 " ideal model delta sigma weight residual 92.91 109.21 -16.30 3.00e+00 1.11e-01 2.95e+01 angle pdb=" O1P PEE A 601 " pdb=" P PEE A 601 " pdb=" O2P PEE A 601 " ideal model delta sigma weight residual 119.43 109.31 10.12 3.00e+00 1.11e-01 1.14e+01 angle pdb=" O1P PEE C 700 " pdb=" P PEE C 700 " pdb=" O2P PEE C 700 " ideal model delta sigma weight residual 119.43 109.54 9.89 3.00e+00 1.11e-01 1.09e+01 angle pdb=" C31 PEE A 601 " pdb=" C30 PEE A 601 " pdb=" O3 PEE A 601 " ideal model delta sigma weight residual 111.87 120.10 -8.23 3.00e+00 1.11e-01 7.52e+00 ... (remaining 14119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 6018 35.92 - 71.84: 114 71.84 - 107.76: 15 107.76 - 143.68: 6 143.68 - 179.60: 1 Dihedral angle restraints: 6154 sinusoidal: 2374 harmonic: 3780 Sorted by residual: dihedral pdb=" C4 PEE C 700 " pdb=" O4P PEE C 700 " pdb=" P PEE C 700 " pdb=" O1P PEE C 700 " ideal model delta sinusoidal sigma weight residual 57.28 -123.12 -179.60 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C4 PEE A 601 " pdb=" O4P PEE A 601 " pdb=" P PEE A 601 " pdb=" O1P PEE A 601 " ideal model delta sinusoidal sigma weight residual 57.28 -86.20 143.48 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" N PEE A 601 " pdb=" C4 PEE A 601 " pdb=" C5 PEE A 601 " pdb=" O4P PEE A 601 " ideal model delta sinusoidal sigma weight residual 303.03 176.05 126.98 1 3.00e+01 1.11e-03 1.71e+01 ... (remaining 6151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1313 0.047 - 0.094: 286 0.094 - 0.141: 61 0.141 - 0.188: 4 0.188 - 0.235: 2 Chirality restraints: 1666 Sorted by residual: chirality pdb=" C2 PEE A 601 " pdb=" C1 PEE A 601 " pdb=" C3 PEE A 601 " pdb=" O2 PEE A 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.56 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C2 PEE C 700 " pdb=" C1 PEE C 700 " pdb=" C3 PEE C 700 " pdb=" O2 PEE C 700 " both_signs ideal model delta sigma weight residual False -2.33 -2.54 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA PHE B 491 " pdb=" N PHE B 491 " pdb=" C PHE B 491 " pdb=" CB PHE B 491 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.31e-01 ... (remaining 1663 not shown) Planarity restraints: 1762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 509 " -0.048 5.00e-02 4.00e+02 7.26e-02 8.44e+00 pdb=" N PRO B 510 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 510 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 510 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 509 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.04e+00 pdb=" N PRO A 510 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 510 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 510 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 377 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO B 378 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 378 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 378 " 0.025 5.00e-02 4.00e+02 ... (remaining 1759 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2450 2.80 - 3.32: 9450 3.32 - 3.85: 16977 3.85 - 4.37: 19612 4.37 - 4.90: 34578 Nonbonded interactions: 83067 Sorted by model distance: nonbonded pdb=" OH TYR A 122 " pdb=" OD2 ASP A 305 " model vdw 2.270 3.040 nonbonded pdb=" OH TYR B 122 " pdb=" OD2 ASP B 305 " model vdw 2.278 3.040 nonbonded pdb=" O TRP C 2 " pdb=" OG SER C 115 " model vdw 2.287 3.040 nonbonded pdb=" NH1 ARG B 198 " pdb=" O PRO B 269 " model vdw 2.300 3.120 nonbonded pdb=" OH TYR B 43 " pdb=" OD2 ASP B 51 " model vdw 2.302 3.040 ... (remaining 83062 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' and resid 30 through 583) selection = (chain 'B' and resid 30 through 583) } ncs_group { reference = (chain 'C' and resid 1 through 124) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.010 Process input model: 8.630 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 10390 Z= 0.193 Angle : 0.614 16.567 14128 Z= 0.283 Chirality : 0.041 0.235 1666 Planarity : 0.005 0.073 1762 Dihedral : 15.096 179.596 3724 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.18 % Allowed : 10.26 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.24), residues: 1300 helix: 1.76 (0.19), residues: 758 sheet: 0.89 (0.44), residues: 154 loop : 0.14 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 198 TYR 0.022 0.001 TYR A 526 PHE 0.018 0.001 PHE B 328 TRP 0.011 0.001 TRP B 47 HIS 0.005 0.001 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 (10388) covalent geometry : angle 0.61382 / 0.28 (14124) SS BOND : bond 0.00197 / 0.10 ( 2) SS BOND : angle 0.17287 / 0.07 ( 4) hydrogen bonds : bond 0.15256 / 10.04 ( 637) hydrogen bonds : angle 5.67695 / 4.20 ( 1809) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 197 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.7822 (ttmt) cc_final: 0.7359 (tptt) REVERT: B 178 ASN cc_start: 0.8453 (p0) cc_final: 0.8243 (p0) REVERT: C 18 LEU cc_start: 0.8750 (tp) cc_final: 0.8449 (tm) REVERT: C 36 TRP cc_start: 0.8221 (m100) cc_final: 0.7813 (m100) REVERT: C 73 ASP cc_start: 0.8455 (m-30) cc_final: 0.8214 (t0) REVERT: C 83 MET cc_start: 0.8294 (mtt) cc_final: 0.7826 (mtp) REVERT: C 85 ILE cc_start: 0.8720 (mt) cc_final: 0.8516 (OUTLIER) REVERT: C 93 VAL cc_start: 0.7766 (t) cc_final: 0.7373 (p) REVERT: C 109 ASN cc_start: 0.8778 (t0) cc_final: 0.8536 (t0) REVERT: D 36 TRP cc_start: 0.8328 (m100) cc_final: 0.7867 (m100) REVERT: D 52 SER cc_start: 0.8457 (m) cc_final: 0.8221 (p) REVERT: D 83 MET cc_start: 0.8220 (mmt) cc_final: 0.7707 (mmt) outliers start: 2 outliers final: 2 residues processed: 198 average time/residue: 0.5208 time to fit residues: 110.4154 Evaluate side-chains 129 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 124 optimal weight: 0.0010 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 129 optimal weight: 0.0070 overall best weight: 0.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 GLN A 178 ASN A 333 ASN B 177 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.129958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.097602 restraints weight = 17185.445| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.71 r_work: 0.3229 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10390 Z= 0.123 Angle : 0.565 7.516 14128 Z= 0.288 Chirality : 0.040 0.163 1666 Planarity : 0.005 0.048 1762 Dihedral : 11.413 175.270 1477 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.42 % Allowed : 15.34 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.24), residues: 1300 helix: 1.99 (0.19), residues: 766 sheet: 0.89 (0.44), residues: 134 loop : -0.10 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 141 TYR 0.016 0.002 TYR A 526 PHE 0.022 0.001 PHE D 68 TRP 0.006 0.001 TRP D 2 HIS 0.003 0.001 HIS B 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (10388) covalent geometry : angle 0.56535 / 0.29 (14124) SS BOND : bond 0.00631 / 0.33 ( 2) SS BOND : angle 0.77869 / 0.38 ( 4) hydrogen bonds : bond 0.03863 / 2.56 ( 637) hydrogen bonds : angle 4.32007 / 3.17 ( 1809) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.5503 (mpp) REVERT: A 432 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7674 (mtt90) REVERT: B 581 ARG cc_start: 0.8676 (tpp-160) cc_final: 0.8335 (mmp80) REVERT: C 28 THR cc_start: 0.6707 (OUTLIER) cc_final: 0.6486 (t) REVERT: C 36 TRP cc_start: 0.8363 (m100) cc_final: 0.7434 (m100) REVERT: C 73 ASP cc_start: 0.8258 (m-30) cc_final: 0.7477 (t0) REVERT: C 82 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7140 (mm110) REVERT: C 83 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7752 (mtp) REVERT: C 109 ASN cc_start: 0.8858 (t0) cc_final: 0.8579 (t0) REVERT: C 112 ASP cc_start: 0.7278 (m-30) cc_final: 0.6982 (m-30) REVERT: D 36 TRP cc_start: 0.8527 (m100) cc_final: 0.7453 (m100) REVERT: D 52 SER cc_start: 0.8545 (m) cc_final: 0.7806 (p) REVERT: D 73 ASP cc_start: 0.7998 (t0) cc_final: 0.7606 (t0) REVERT: D 85 ILE cc_start: 0.8810 (pt) cc_final: 0.8451 (pp) REVERT: D 95 TYR cc_start: 0.7190 (m-80) cc_final: 0.6984 (m-80) outliers start: 37 outliers final: 12 residues processed: 162 average time/residue: 0.4646 time to fit residues: 81.4262 Evaluate side-chains 136 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 432 ARG Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain D residue 53 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 9 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 GLN D 39 GLN D 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.123478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.090834 restraints weight = 17487.580| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.74 r_work: 0.3131 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10390 Z= 0.218 Angle : 0.629 7.937 14128 Z= 0.319 Chirality : 0.044 0.183 1666 Planarity : 0.005 0.057 1762 Dihedral : 10.858 170.441 1476 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.71 % Allowed : 15.53 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.24), residues: 1300 helix: 1.77 (0.19), residues: 768 sheet: 1.00 (0.42), residues: 152 loop : -0.25 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 335 TYR 0.022 0.002 TYR A 358 PHE 0.019 0.002 PHE B 328 TRP 0.007 0.001 TRP D 2 HIS 0.005 0.002 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.22 (10388) covalent geometry : angle 0.62885 / 0.32 (14124) SS BOND : bond 0.00152 / 0.08 ( 2) SS BOND : angle 1.02395 / 0.55 ( 4) hydrogen bonds : bond 0.04487 / 2.96 ( 637) hydrogen bonds : angle 4.18160 / 3.07 ( 1809) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 134 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7823 (mtt90) REVERT: A 579 HIS cc_start: 0.7904 (OUTLIER) cc_final: 0.7648 (m90) REVERT: B 579 HIS cc_start: 0.7854 (OUTLIER) cc_final: 0.7534 (m90) REVERT: C 28 THR cc_start: 0.7052 (OUTLIER) cc_final: 0.6784 (t) REVERT: C 36 TRP cc_start: 0.8368 (m100) cc_final: 0.7285 (m100) REVERT: C 60 TYR cc_start: 0.7998 (m-80) cc_final: 0.7638 (m-80) REVERT: C 73 ASP cc_start: 0.8449 (m-30) cc_final: 0.7559 (t0) REVERT: C 95 TYR cc_start: 0.6798 (m-80) cc_final: 0.6244 (m-80) REVERT: C 109 ASN cc_start: 0.8902 (t0) cc_final: 0.8604 (t0) REVERT: D 36 TRP cc_start: 0.8538 (m100) cc_final: 0.7443 (m100) REVERT: D 52 SER cc_start: 0.8714 (m) cc_final: 0.8021 (p) REVERT: D 73 ASP cc_start: 0.8010 (t0) cc_final: 0.7318 (t0) REVERT: D 78 THR cc_start: 0.8299 (m) cc_final: 0.7912 (t) REVERT: D 95 TYR cc_start: 0.7271 (m-80) cc_final: 0.6993 (m-80) outliers start: 51 outliers final: 28 residues processed: 173 average time/residue: 0.4679 time to fit residues: 87.4980 Evaluate side-chains 154 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 254 PHE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 432 ARG Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 487 SER Chi-restraints excluded: chain B residue 579 HIS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 93 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 60 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 110 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 ASN B 582 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.126130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.093721 restraints weight = 17356.182| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.73 r_work: 0.3172 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10390 Z= 0.118 Angle : 0.557 10.306 14128 Z= 0.280 Chirality : 0.040 0.165 1666 Planarity : 0.004 0.043 1762 Dihedral : 10.453 168.823 1476 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.79 % Allowed : 17.93 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.24), residues: 1300 helix: 1.99 (0.19), residues: 768 sheet: 0.99 (0.44), residues: 134 loop : -0.35 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 335 TYR 0.021 0.002 TYR D 94 PHE 0.030 0.001 PHE C 68 TRP 0.006 0.001 TRP A 241 HIS 0.002 0.001 HIS B 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (10388) covalent geometry : angle 0.55657 / 0.28 (14124) SS BOND : bond 0.00359 / 0.18 ( 2) SS BOND : angle 0.54131 / 0.26 ( 4) hydrogen bonds : bond 0.03472 / 2.30 ( 637) hydrogen bonds : angle 3.98646 / 2.93 ( 1809) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 129 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 432 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7675 (mtt90) REVERT: A 579 HIS cc_start: 0.7816 (OUTLIER) cc_final: 0.7573 (m90) REVERT: B 432 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7643 (mtt90) REVERT: B 581 ARG cc_start: 0.8695 (tpp-160) cc_final: 0.8421 (mmp80) REVERT: C 28 THR cc_start: 0.6990 (OUTLIER) cc_final: 0.6774 (t) REVERT: C 36 TRP cc_start: 0.8249 (m100) cc_final: 0.7099 (m100) REVERT: C 60 TYR cc_start: 0.7886 (m-80) cc_final: 0.7624 (m-80) REVERT: C 73 ASP cc_start: 0.8432 (m-30) cc_final: 0.7518 (t0) REVERT: C 95 TYR cc_start: 0.6558 (m-80) cc_final: 0.6043 (m-80) REVERT: C 109 ASN cc_start: 0.8945 (t0) cc_final: 0.8676 (t0) REVERT: C 110 LYS cc_start: 0.8955 (mtmp) cc_final: 0.8679 (mtpp) REVERT: D 18 LEU cc_start: 0.8538 (tp) cc_final: 0.8236 (tt) REVERT: D 36 TRP cc_start: 0.8453 (m100) cc_final: 0.7284 (m100) REVERT: D 52 SER cc_start: 0.8555 (m) cc_final: 0.7827 (p) REVERT: D 73 ASP cc_start: 0.8014 (t0) cc_final: 0.7339 (t0) REVERT: D 78 THR cc_start: 0.8247 (m) cc_final: 0.7830 (t) REVERT: D 95 TYR cc_start: 0.7245 (m-80) cc_final: 0.6898 (m-80) outliers start: 41 outliers final: 19 residues processed: 156 average time/residue: 0.5097 time to fit residues: 85.7835 Evaluate side-chains 143 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 432 ARG Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 432 ARG Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 513 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 93 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 71 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 57 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.126056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.093516 restraints weight = 17295.147| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.74 r_work: 0.3168 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10390 Z= 0.127 Angle : 0.561 10.572 14128 Z= 0.281 Chirality : 0.040 0.167 1666 Planarity : 0.004 0.050 1762 Dihedral : 10.219 170.935 1476 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.60 % Allowed : 18.58 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.24), residues: 1300 helix: 2.05 (0.19), residues: 768 sheet: 1.11 (0.45), residues: 134 loop : -0.42 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 67 TYR 0.027 0.002 TYR C 94 PHE 0.016 0.001 PHE A 328 TRP 0.006 0.001 TRP A 241 HIS 0.004 0.001 HIS B 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (10388) covalent geometry : angle 0.56076 / 0.28 (14124) SS BOND : bond 0.00245 / 0.12 ( 2) SS BOND : angle 0.56221 / 0.29 ( 4) hydrogen bonds : bond 0.03460 / 2.28 ( 637) hydrogen bonds : angle 3.93981 / 2.90 ( 1809) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.6034 (pmt170) cc_final: 0.5821 (pmm-80) REVERT: A 579 HIS cc_start: 0.7837 (OUTLIER) cc_final: 0.7552 (m90) REVERT: B 432 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7690 (mtt90) REVERT: C 36 TRP cc_start: 0.8239 (m100) cc_final: 0.7108 (m100) REVERT: C 73 ASP cc_start: 0.8464 (m-30) cc_final: 0.7570 (t0) REVERT: C 95 TYR cc_start: 0.6642 (m-80) cc_final: 0.6029 (m-80) REVERT: C 109 ASN cc_start: 0.8971 (t0) cc_final: 0.8677 (t0) REVERT: D 17 SER cc_start: 0.8466 (m) cc_final: 0.8119 (p) REVERT: D 18 LEU cc_start: 0.8603 (tp) cc_final: 0.8249 (tt) REVERT: D 36 TRP cc_start: 0.8427 (m100) cc_final: 0.7265 (m100) REVERT: D 52 SER cc_start: 0.8563 (m) cc_final: 0.7820 (p) REVERT: D 73 ASP cc_start: 0.8026 (t0) cc_final: 0.7338 (t0) REVERT: D 78 THR cc_start: 0.8165 (m) cc_final: 0.7637 (t) REVERT: D 82 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7204 (mm110) REVERT: D 95 TYR cc_start: 0.7289 (m-80) cc_final: 0.6920 (m-80) outliers start: 39 outliers final: 23 residues processed: 167 average time/residue: 0.4748 time to fit residues: 85.9299 Evaluate side-chains 152 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 432 ARG Chi-restraints excluded: chain B residue 513 CYS Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 93 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 0.0270 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 ASN C 77 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.126677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.094327 restraints weight = 17368.099| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.73 r_work: 0.3177 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10390 Z= 0.115 Angle : 0.555 8.796 14128 Z= 0.279 Chirality : 0.040 0.303 1666 Planarity : 0.004 0.046 1762 Dihedral : 10.055 177.566 1476 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.33 % Allowed : 19.04 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.24), residues: 1300 helix: 2.12 (0.19), residues: 768 sheet: 1.13 (0.45), residues: 134 loop : -0.44 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 581 TYR 0.027 0.001 TYR C 94 PHE 0.015 0.001 PHE B 328 TRP 0.007 0.001 TRP A 241 HIS 0.003 0.001 HIS B 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (10388) covalent geometry : angle 0.55522 / 0.28 (14124) SS BOND : bond 0.00175 / 0.08 ( 2) SS BOND : angle 0.63933 / 0.34 ( 4) hydrogen bonds : bond 0.03282 / 2.17 ( 637) hydrogen bonds : angle 3.88095 / 2.86 ( 1809) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.8210 (tp) cc_final: 0.7900 (tp) REVERT: A 463 MET cc_start: 0.8403 (mtt) cc_final: 0.8074 (mtt) REVERT: A 579 HIS cc_start: 0.7791 (OUTLIER) cc_final: 0.7543 (m90) REVERT: B 432 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7731 (mtt90) REVERT: B 463 MET cc_start: 0.8396 (mtt) cc_final: 0.8115 (mtt) REVERT: B 581 ARG cc_start: 0.8731 (tpp-160) cc_final: 0.8375 (mmp80) REVERT: C 30 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7055 (ttt-90) REVERT: C 36 TRP cc_start: 0.8306 (m100) cc_final: 0.7289 (m100) REVERT: C 73 ASP cc_start: 0.8465 (m-30) cc_final: 0.7552 (t0) REVERT: C 95 TYR cc_start: 0.6993 (m-80) cc_final: 0.6269 (m-80) REVERT: C 109 ASN cc_start: 0.8973 (t0) cc_final: 0.8607 (t0) REVERT: D 17 SER cc_start: 0.8471 (m) cc_final: 0.8136 (p) REVERT: D 18 LEU cc_start: 0.8601 (tp) cc_final: 0.8279 (tt) REVERT: D 36 TRP cc_start: 0.8407 (m100) cc_final: 0.7262 (m100) REVERT: D 52 SER cc_start: 0.8499 (m) cc_final: 0.7734 (p) REVERT: D 73 ASP cc_start: 0.8030 (t0) cc_final: 0.7323 (t0) REVERT: D 78 THR cc_start: 0.8195 (m) cc_final: 0.7667 (t) REVERT: D 84 ASN cc_start: 0.8249 (m-40) cc_final: 0.7977 (m110) REVERT: D 95 TYR cc_start: 0.7180 (m-80) cc_final: 0.6948 (m-80) outliers start: 36 outliers final: 26 residues processed: 158 average time/residue: 0.4752 time to fit residues: 81.4457 Evaluate side-chains 153 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 432 ARG Chi-restraints excluded: chain B residue 513 CYS Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 93 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 48 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 0.0010 chunk 7 optimal weight: 0.9980 chunk 81 optimal weight: 0.0980 chunk 28 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.127338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.095092 restraints weight = 17187.485| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.71 r_work: 0.3192 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10390 Z= 0.110 Angle : 0.550 8.766 14128 Z= 0.278 Chirality : 0.040 0.172 1666 Planarity : 0.004 0.042 1762 Dihedral : 9.870 177.876 1476 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.42 % Allowed : 19.69 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.24), residues: 1300 helix: 2.21 (0.19), residues: 768 sheet: 1.12 (0.45), residues: 134 loop : -0.42 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 67 TYR 0.023 0.001 TYR C 94 PHE 0.020 0.001 PHE D 68 TRP 0.007 0.001 TRP A 241 HIS 0.002 0.000 HIS B 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (10388) covalent geometry : angle 0.54983 / 0.28 (14124) SS BOND : bond 0.00194 / 0.09 ( 2) SS BOND : angle 0.58825 / 0.30 ( 4) hydrogen bonds : bond 0.03137 / 2.07 ( 637) hydrogen bonds : angle 3.83784 / 2.83 ( 1809) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.8155 (tp) cc_final: 0.7836 (tp) REVERT: A 463 MET cc_start: 0.8401 (mtt) cc_final: 0.8088 (mtt) REVERT: B 432 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7698 (mtt90) REVERT: B 463 MET cc_start: 0.8387 (mtt) cc_final: 0.8099 (mtt) REVERT: B 581 ARG cc_start: 0.8733 (tpp-160) cc_final: 0.8510 (mmp80) REVERT: C 4 LEU cc_start: 0.8861 (mm) cc_final: 0.8525 (tp) REVERT: C 30 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7084 (ttt-90) REVERT: C 36 TRP cc_start: 0.8413 (m100) cc_final: 0.7350 (m100) REVERT: C 73 ASP cc_start: 0.8506 (m-30) cc_final: 0.7583 (t0) REVERT: C 95 TYR cc_start: 0.7120 (m-80) cc_final: 0.6420 (m-80) REVERT: C 109 ASN cc_start: 0.9037 (t0) cc_final: 0.8731 (t0) REVERT: D 17 SER cc_start: 0.8451 (m) cc_final: 0.8082 (p) REVERT: D 18 LEU cc_start: 0.8671 (tp) cc_final: 0.8405 (tt) REVERT: D 21 SER cc_start: 0.6982 (m) cc_final: 0.6607 (t) REVERT: D 36 TRP cc_start: 0.8418 (m100) cc_final: 0.7320 (m100) REVERT: D 52 SER cc_start: 0.8456 (m) cc_final: 0.7645 (p) REVERT: D 73 ASP cc_start: 0.8068 (t0) cc_final: 0.7368 (t0) REVERT: D 78 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.7688 (t) REVERT: D 95 TYR cc_start: 0.7238 (m-80) cc_final: 0.7026 (m-80) outliers start: 37 outliers final: 25 residues processed: 159 average time/residue: 0.4775 time to fit residues: 82.3465 Evaluate side-chains 152 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 432 ARG Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 513 CYS Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 93 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 111 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 GLN A 333 ASN D 77 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.124710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.092191 restraints weight = 17252.240| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.71 r_work: 0.3154 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10390 Z= 0.159 Angle : 0.588 9.482 14128 Z= 0.293 Chirality : 0.042 0.173 1666 Planarity : 0.004 0.051 1762 Dihedral : 9.744 172.916 1476 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.46 % Favored : 97.46 % Rotamer: Outliers : 4.34 % Allowed : 19.32 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.24), residues: 1300 helix: 2.06 (0.19), residues: 768 sheet: 1.05 (0.46), residues: 134 loop : -0.40 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 581 TYR 0.026 0.002 TYR C 94 PHE 0.018 0.001 PHE D 68 TRP 0.006 0.001 TRP C 116 HIS 0.003 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (10388) covalent geometry : angle 0.58813 / 0.29 (14124) SS BOND : bond 0.00114 / 0.06 ( 2) SS BOND : angle 0.71717 / 0.39 ( 4) hydrogen bonds : bond 0.03660 / 2.40 ( 637) hydrogen bonds : angle 3.89292 / 2.87 ( 1809) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 129 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 219 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7952 (tpt170) REVERT: A 461 LEU cc_start: 0.8227 (tp) cc_final: 0.7914 (tp) REVERT: A 463 MET cc_start: 0.8460 (mtt) cc_final: 0.8138 (mtt) REVERT: B 432 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7763 (mtt90) REVERT: B 463 MET cc_start: 0.8446 (mtt) cc_final: 0.8166 (mtt) REVERT: C 4 LEU cc_start: 0.8851 (mm) cc_final: 0.8502 (tp) REVERT: C 30 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7029 (ttt-90) REVERT: C 36 TRP cc_start: 0.8422 (m100) cc_final: 0.7366 (m100) REVERT: C 67 ARG cc_start: 0.7760 (mtm110) cc_final: 0.7479 (ptp-170) REVERT: C 73 ASP cc_start: 0.8569 (m-30) cc_final: 0.7675 (t0) REVERT: C 87 LYS cc_start: 0.9350 (mmtp) cc_final: 0.9096 (tmtm) REVERT: C 95 TYR cc_start: 0.7331 (m-80) cc_final: 0.6592 (m-80) REVERT: C 109 ASN cc_start: 0.9048 (t0) cc_final: 0.8765 (t0) REVERT: D 17 SER cc_start: 0.8452 (m) cc_final: 0.8087 (p) REVERT: D 18 LEU cc_start: 0.8691 (tp) cc_final: 0.8430 (tt) REVERT: D 36 TRP cc_start: 0.8427 (m100) cc_final: 0.7366 (m100) REVERT: D 38 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6909 (ptt180) REVERT: D 52 SER cc_start: 0.8558 (m) cc_final: 0.7760 (p) REVERT: D 73 ASP cc_start: 0.8106 (t0) cc_final: 0.7617 (t0) REVERT: D 95 TYR cc_start: 0.7265 (m-80) cc_final: 0.6965 (m-80) outliers start: 47 outliers final: 28 residues processed: 162 average time/residue: 0.4760 time to fit residues: 83.6954 Evaluate side-chains 158 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 513 CYS Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 432 ARG Chi-restraints excluded: chain B residue 513 CYS Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 93 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 81 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 87 optimal weight: 0.0670 chunk 124 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.126437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.094083 restraints weight = 17126.101| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.71 r_work: 0.3178 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10390 Z= 0.114 Angle : 0.562 7.683 14128 Z= 0.280 Chirality : 0.040 0.162 1666 Planarity : 0.004 0.038 1762 Dihedral : 9.571 169.739 1476 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.69 % Favored : 97.23 % Rotamer: Outliers : 3.60 % Allowed : 19.96 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.24), residues: 1300 helix: 2.20 (0.19), residues: 768 sheet: 1.05 (0.46), residues: 134 loop : -0.44 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 335 TYR 0.019 0.001 TYR C 94 PHE 0.017 0.001 PHE A 191 TRP 0.007 0.001 TRP C 116 HIS 0.002 0.001 HIS B 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (10388) covalent geometry : angle 0.56192 / 0.28 (14124) SS BOND : bond 0.00176 / 0.08 ( 2) SS BOND : angle 0.51117 / 0.26 ( 4) hydrogen bonds : bond 0.03207 / 2.11 ( 637) hydrogen bonds : angle 3.81644 / 2.81 ( 1809) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 30 LEU cc_start: 0.5169 (OUTLIER) cc_final: 0.4670 (pt) REVERT: A 209 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8257 (mtm) REVERT: A 219 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7945 (tpt170) REVERT: A 461 LEU cc_start: 0.8168 (tp) cc_final: 0.7851 (tp) REVERT: A 463 MET cc_start: 0.8427 (mtt) cc_final: 0.8161 (mtt) REVERT: B 167 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.8615 (t80) REVERT: B 209 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8200 (mtm) REVERT: B 432 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7791 (mtt90) REVERT: B 463 MET cc_start: 0.8417 (mtt) cc_final: 0.8140 (mtt) REVERT: C 4 LEU cc_start: 0.8857 (mm) cc_final: 0.8582 (tp) REVERT: C 30 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.6430 (ttt-90) REVERT: C 36 TRP cc_start: 0.8409 (m100) cc_final: 0.7381 (m100) REVERT: C 67 ARG cc_start: 0.7680 (mtm110) cc_final: 0.7383 (ptp-170) REVERT: C 73 ASP cc_start: 0.8525 (m-30) cc_final: 0.7476 (t0) REVERT: C 78 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7514 (t) REVERT: C 87 LYS cc_start: 0.9331 (mmtp) cc_final: 0.9070 (tmtm) REVERT: C 95 TYR cc_start: 0.7323 (m-80) cc_final: 0.6539 (m-80) REVERT: C 109 ASN cc_start: 0.9022 (t0) cc_final: 0.8742 (t0) REVERT: D 17 SER cc_start: 0.8508 (m) cc_final: 0.8240 (p) REVERT: D 18 LEU cc_start: 0.8665 (tp) cc_final: 0.8414 (tt) REVERT: D 36 TRP cc_start: 0.8391 (m100) cc_final: 0.7261 (m100) REVERT: D 52 SER cc_start: 0.8443 (m) cc_final: 0.7624 (p) REVERT: D 73 ASP cc_start: 0.8102 (t0) cc_final: 0.7400 (t0) REVERT: D 78 THR cc_start: 0.8275 (OUTLIER) cc_final: 0.7683 (t) REVERT: D 95 TYR cc_start: 0.7294 (m-80) cc_final: 0.7053 (m-80) outliers start: 39 outliers final: 24 residues processed: 154 average time/residue: 0.4779 time to fit residues: 80.1097 Evaluate side-chains 158 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 432 ARG Chi-restraints excluded: chain B residue 513 CYS Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 125 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 39 optimal weight: 0.0370 chunk 82 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.126754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.094539 restraints weight = 17089.685| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.71 r_work: 0.3187 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10390 Z= 0.113 Angle : 0.565 9.753 14128 Z= 0.280 Chirality : 0.040 0.162 1666 Planarity : 0.004 0.037 1762 Dihedral : 9.403 165.159 1476 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.62 % Favored : 97.31 % Rotamer: Outliers : 3.14 % Allowed : 20.06 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.24), residues: 1300 helix: 2.24 (0.19), residues: 768 sheet: 1.00 (0.45), residues: 134 loop : -0.43 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 67 TYR 0.017 0.001 TYR C 94 PHE 0.016 0.001 PHE B 328 TRP 0.008 0.001 TRP C 116 HIS 0.002 0.001 HIS B 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (10388) covalent geometry : angle 0.56542 / 0.28 (14124) SS BOND : bond 0.00196 / 0.09 ( 2) SS BOND : angle 0.46804 / 0.23 ( 4) hydrogen bonds : bond 0.03140 / 2.07 ( 637) hydrogen bonds : angle 3.77614 / 2.78 ( 1809) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 219 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7985 (tpt170) REVERT: A 461 LEU cc_start: 0.8152 (tp) cc_final: 0.7537 (mp) REVERT: A 463 MET cc_start: 0.8420 (mtt) cc_final: 0.8166 (mtt) REVERT: B 167 PHE cc_start: 0.8824 (OUTLIER) cc_final: 0.8613 (t80) REVERT: B 209 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8217 (mtm) REVERT: B 432 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7740 (mtt90) REVERT: B 463 MET cc_start: 0.8417 (mtt) cc_final: 0.8186 (mtt) REVERT: C 4 LEU cc_start: 0.8838 (mm) cc_final: 0.8561 (tp) REVERT: C 30 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.6479 (ttt-90) REVERT: C 32 TYR cc_start: 0.8928 (m-80) cc_final: 0.8728 (m-80) REVERT: C 36 TRP cc_start: 0.8449 (m100) cc_final: 0.7450 (m100) REVERT: C 46 GLU cc_start: 0.8625 (pt0) cc_final: 0.8214 (pm20) REVERT: C 73 ASP cc_start: 0.8562 (m-30) cc_final: 0.7440 (t0) REVERT: C 78 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7598 (t) REVERT: C 87 LYS cc_start: 0.9354 (mmtp) cc_final: 0.9049 (tptm) REVERT: C 95 TYR cc_start: 0.7340 (m-80) cc_final: 0.6592 (m-80) REVERT: C 109 ASN cc_start: 0.9001 (t0) cc_final: 0.8749 (t0) REVERT: D 17 SER cc_start: 0.8490 (m) cc_final: 0.8225 (p) REVERT: D 18 LEU cc_start: 0.8658 (tp) cc_final: 0.8439 (tt) REVERT: D 36 TRP cc_start: 0.8392 (m100) cc_final: 0.7323 (m100) REVERT: D 52 SER cc_start: 0.8411 (m) cc_final: 0.7590 (p) REVERT: D 73 ASP cc_start: 0.8126 (t0) cc_final: 0.7431 (t0) REVERT: D 78 THR cc_start: 0.8291 (OUTLIER) cc_final: 0.7715 (t) REVERT: D 84 ASN cc_start: 0.8042 (m-40) cc_final: 0.7835 (m110) outliers start: 34 outliers final: 24 residues processed: 152 average time/residue: 0.4849 time to fit residues: 80.0606 Evaluate side-chains 157 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 432 ARG Chi-restraints excluded: chain B residue 513 CYS Chi-restraints excluded: chain C residue 30 ARG Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 59 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.126622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.094224 restraints weight = 17261.650| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.73 r_work: 0.3184 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10390 Z= 0.115 Angle : 0.556 6.965 14128 Z= 0.278 Chirality : 0.040 0.167 1666 Planarity : 0.004 0.037 1762 Dihedral : 9.294 164.518 1476 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.54 % Favored : 97.38 % Rotamer: Outliers : 3.14 % Allowed : 20.15 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.24), residues: 1300 helix: 2.23 (0.19), residues: 768 sheet: 1.00 (0.45), residues: 134 loop : -0.44 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 335 TYR 0.017 0.001 TYR C 94 PHE 0.032 0.001 PHE D 68 TRP 0.007 0.001 TRP C 116 HIS 0.002 0.001 HIS B 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (10388) covalent geometry : angle 0.55613 / 0.28 (14124) SS BOND : bond 0.00178 / 0.09 ( 2) SS BOND : angle 0.52735 / 0.27 ( 4) hydrogen bonds : bond 0.03172 / 2.09 ( 637) hydrogen bonds : angle 3.76551 / 2.77 ( 1809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3199.04 seconds wall clock time: 55 minutes 23.47 seconds (3323.47 seconds total)