Starting phenix.real_space_refine on Sun Apr 5 12:26:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ias_52785/04_2026/9ias_52785.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ias_52785/04_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ias_52785/04_2026/9ias_52785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ias_52785/04_2026/9ias_52785.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ias_52785/04_2026/9ias_52785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ias_52785/04_2026/9ias_52785.map" } 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-2.1rc1-6017/lib/python3.9/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, 34 Unusual residues: {' CL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 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: 2.45, per 1000 atoms: 0.24 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: 0.72 Conformation dependent library (CDL) restraints added in 358.8 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: 0.27 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: 1.60 Time building geometry restraints manager: 0.97 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.950 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 covalent geometry : bond 0.00397 (10388) covalent geometry : angle 0.61382 (14124) SS BOND : bond 0.00197 ( 2) SS BOND : angle 0.17287 ( 4) hydrogen bonds : bond 0.15256 ( 637) hydrogen bonds : angle 5.67695 ( 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 : 0.367 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: 0.6075 time to fit residues: 128.2720 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 : 0.394 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.130073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.097725 restraints weight = 17208.724| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.72 r_work: 0.3222 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10390 Z= 0.120 Angle : 0.562 7.591 14128 Z= 0.286 Chirality : 0.040 0.162 1666 Planarity : 0.005 0.048 1762 Dihedral : 11.464 175.500 1477 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.51 % Allowed : 15.25 % 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: 1.98 (0.19), residues: 766 sheet: 0.90 (0.44), residues: 134 loop : -0.09 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 581 TYR 0.016 0.001 TYR A 526 PHE 0.020 0.001 PHE A 167 TRP 0.006 0.001 TRP D 2 HIS 0.002 0.001 HIS A 579 Details of bonding type rmsd covalent geometry : bond 0.00263 (10388) covalent geometry : angle 0.56175 (14124) SS BOND : bond 0.00554 ( 2) SS BOND : angle 0.76529 ( 4) hydrogen bonds : bond 0.03910 ( 637) hydrogen bonds : angle 4.34252 ( 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 174 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.5531 (mpp) REVERT: A 432 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7667 (mtt90) REVERT: B 581 ARG cc_start: 0.8682 (tpp-160) cc_final: 0.8433 (mmp80) REVERT: C 28 THR cc_start: 0.6650 (OUTLIER) cc_final: 0.6430 (t) REVERT: C 36 TRP cc_start: 0.8366 (m100) cc_final: 0.7448 (m100) REVERT: C 73 ASP cc_start: 0.8268 (m-30) cc_final: 0.7489 (t0) REVERT: C 82 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7222 (mm110) REVERT: C 83 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7613 (mtp) REVERT: C 109 ASN cc_start: 0.8857 (t0) cc_final: 0.8578 (t0) REVERT: C 112 ASP cc_start: 0.7290 (m-30) cc_final: 0.6998 (m-30) REVERT: D 36 TRP cc_start: 0.8539 (m100) cc_final: 0.7487 (m100) REVERT: D 52 SER cc_start: 0.8548 (m) cc_final: 0.7806 (p) REVERT: D 73 ASP cc_start: 0.7958 (t0) cc_final: 0.7566 (t0) REVERT: D 85 ILE cc_start: 0.8764 (pt) cc_final: 0.8410 (pp) REVERT: D 95 TYR cc_start: 0.7175 (m-80) cc_final: 0.6949 (m-80) outliers start: 38 outliers final: 13 residues processed: 161 average time/residue: 0.5441 time to fit residues: 94.3729 Evaluate side-chains 137 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 239 LEU 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: 0.7980 chunk 53 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3753 r_free = 0.3753 target = 0.123759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.091054 restraints weight = 17433.848| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.73 r_work: 0.3132 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10390 Z= 0.220 Angle : 0.631 8.749 14128 Z= 0.319 Chirality : 0.044 0.198 1666 Planarity : 0.005 0.050 1762 Dihedral : 10.887 170.740 1476 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.90 % Allowed : 15.53 % Favored : 79.57 % 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: 1.56 (0.24), residues: 1300 helix: 1.77 (0.19), residues: 768 sheet: 0.85 (0.44), residues: 134 loop : -0.28 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 141 TYR 0.021 0.002 TYR A 358 PHE 0.019 0.002 PHE B 328 TRP 0.008 0.001 TRP D 2 HIS 0.005 0.002 HIS A 466 Details of bonding type rmsd covalent geometry : bond 0.00538 (10388) covalent geometry : angle 0.63078 (14124) SS BOND : bond 0.00132 ( 2) SS BOND : angle 1.06057 ( 4) hydrogen bonds : bond 0.04466 ( 637) hydrogen bonds : angle 4.18627 ( 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 186 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 133 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7839 (mtt90) REVERT: A 579 HIS cc_start: 0.7907 (OUTLIER) cc_final: 0.7642 (m90) REVERT: B 579 HIS cc_start: 0.7837 (OUTLIER) cc_final: 0.7516 (m90) REVERT: C 28 THR cc_start: 0.6945 (OUTLIER) cc_final: 0.6670 (t) REVERT: C 36 TRP cc_start: 0.8368 (m100) cc_final: 0.7294 (m100) REVERT: C 60 TYR cc_start: 0.7970 (m-80) cc_final: 0.7594 (m-80) REVERT: C 73 ASP cc_start: 0.8434 (m-30) cc_final: 0.7556 (t0) REVERT: C 82 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7273 (mm-40) REVERT: C 90 ASP cc_start: 0.8007 (m-30) cc_final: 0.7365 (p0) REVERT: C 95 TYR cc_start: 0.6802 (m-80) cc_final: 0.6292 (m-80) REVERT: C 109 ASN cc_start: 0.8910 (t0) cc_final: 0.8612 (t0) REVERT: D 36 TRP cc_start: 0.8521 (m100) cc_final: 0.7411 (m100) REVERT: D 52 SER cc_start: 0.8718 (m) cc_final: 0.8020 (p) REVERT: D 73 ASP cc_start: 0.7998 (t0) cc_final: 0.7299 (t0) REVERT: D 78 THR cc_start: 0.8280 (m) cc_final: 0.7885 (t) REVERT: D 95 TYR cc_start: 0.7307 (m-80) cc_final: 0.7010 (m-80) outliers start: 53 outliers final: 29 residues processed: 174 average time/residue: 0.5368 time to fit residues: 100.8567 Evaluate side-chains 159 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 513 CYS 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 82 GLN 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: 0.5980 chunk 9 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN B 582 GLN C 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.126601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.094231 restraints weight = 17321.965| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.73 r_work: 0.3178 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10390 Z= 0.114 Angle : 0.546 10.505 14128 Z= 0.273 Chirality : 0.040 0.166 1666 Planarity : 0.004 0.046 1762 Dihedral : 10.427 168.718 1476 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.51 % Allowed : 17.74 % Favored : 78.74 % 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: 1.79 (0.24), residues: 1300 helix: 2.01 (0.19), residues: 768 sheet: 0.96 (0.44), residues: 134 loop : -0.33 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 335 TYR 0.020 0.001 TYR D 94 PHE 0.032 0.001 PHE C 68 TRP 0.007 0.001 TRP A 241 HIS 0.002 0.001 HIS B 579 Details of bonding type rmsd covalent geometry : bond 0.00261 (10388) covalent geometry : angle 0.54629 (14124) SS BOND : bond 0.00356 ( 2) SS BOND : angle 0.48430 ( 4) hydrogen bonds : bond 0.03415 ( 637) hydrogen bonds : angle 3.98318 ( 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 173 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 432 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7668 (mtt90) REVERT: A 579 HIS cc_start: 0.7848 (OUTLIER) cc_final: 0.7609 (m90) REVERT: B 209 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8311 (mtm) REVERT: B 350 MET cc_start: 0.8559 (mtp) cc_final: 0.8351 (mtm) REVERT: B 432 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7635 (mtt90) REVERT: B 581 ARG cc_start: 0.8696 (tpp-160) cc_final: 0.8416 (mmp80) REVERT: C 28 THR cc_start: 0.7036 (OUTLIER) cc_final: 0.6785 (t) REVERT: C 36 TRP cc_start: 0.8319 (m100) cc_final: 0.7132 (m100) REVERT: C 45 ARG cc_start: 0.6742 (ptp-170) cc_final: 0.6424 (ptp-170) REVERT: C 60 TYR cc_start: 0.7862 (m-80) cc_final: 0.7660 (m-80) REVERT: C 67 ARG cc_start: 0.7416 (mtm110) cc_final: 0.6972 (mtm110) REVERT: C 68 PHE cc_start: 0.7315 (m-80) cc_final: 0.7112 (m-80) REVERT: C 73 ASP cc_start: 0.8423 (m-30) cc_final: 0.7543 (t0) REVERT: C 82 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7264 (mm-40) REVERT: C 95 TYR cc_start: 0.6628 (m-80) cc_final: 0.6017 (m-80) REVERT: C 109 ASN cc_start: 0.8947 (t0) cc_final: 0.8664 (t0) REVERT: C 110 LYS cc_start: 0.8914 (mtmp) cc_final: 0.8663 (mtpp) REVERT: D 18 LEU cc_start: 0.8543 (tp) cc_final: 0.8274 (tt) REVERT: D 36 TRP cc_start: 0.8448 (m100) cc_final: 0.7306 (m100) REVERT: D 52 SER cc_start: 0.8545 (m) cc_final: 0.7817 (p) REVERT: D 73 ASP cc_start: 0.8008 (t0) cc_final: 0.7306 (t0) REVERT: D 78 THR cc_start: 0.8242 (m) cc_final: 0.7842 (t) REVERT: D 95 TYR cc_start: 0.7263 (m-80) cc_final: 0.6958 (m-80) outliers start: 38 outliers final: 14 residues processed: 162 average time/residue: 0.5331 time to fit residues: 92.7959 Evaluate side-chains 143 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 353 SER Chi-restraints excluded: chain A residue 432 ARG Chi-restraints excluded: chain A residue 513 CYS 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 432 ARG 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 85 ILE 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: 0.7980 chunk 102 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 123 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3783 r_free = 0.3783 target = 0.126207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.093731 restraints weight = 17269.345| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.73 r_work: 0.3171 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2500 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= 0.125 Angle : 0.558 10.954 14128 Z= 0.278 Chirality : 0.040 0.167 1666 Planarity : 0.004 0.039 1762 Dihedral : 10.210 169.907 1476 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.05 % Allowed : 19.13 % 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: 2.04 (0.19), residues: 768 sheet: 1.02 (0.45), residues: 134 loop : -0.38 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 335 TYR 0.016 0.001 TYR A 358 PHE 0.020 0.001 PHE C 68 TRP 0.005 0.001 TRP A 241 HIS 0.004 0.001 HIS B 579 Details of bonding type rmsd covalent geometry : bond 0.00297 (10388) covalent geometry : angle 0.55845 (14124) SS BOND : bond 0.00248 ( 2) SS BOND : angle 0.63848 ( 4) hydrogen bonds : bond 0.03458 ( 637) hydrogen bonds : angle 3.94099 ( 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 165 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.6027 (pmt170) cc_final: 0.5805 (pmm-80) REVERT: A 463 MET cc_start: 0.8425 (mtt) cc_final: 0.8069 (mtt) REVERT: B 302 MET cc_start: 0.7785 (mtp) cc_final: 0.7570 (mtp) REVERT: B 350 MET cc_start: 0.8549 (mtp) cc_final: 0.8346 (mtm) REVERT: B 432 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7687 (mtt90) REVERT: C 36 TRP cc_start: 0.8300 (m100) cc_final: 0.7141 (m100) REVERT: C 67 ARG cc_start: 0.7432 (mtm110) cc_final: 0.7231 (mtm110) REVERT: C 73 ASP cc_start: 0.8463 (m-30) cc_final: 0.7585 (t0) REVERT: C 85 ILE cc_start: 0.9185 (mp) cc_final: 0.8863 (tp) REVERT: C 95 TYR cc_start: 0.6676 (m-80) cc_final: 0.5998 (m-80) REVERT: C 109 ASN cc_start: 0.8980 (t0) cc_final: 0.8709 (t0) REVERT: D 17 SER cc_start: 0.8455 (m) cc_final: 0.8094 (p) REVERT: D 18 LEU cc_start: 0.8623 (tp) cc_final: 0.8308 (tt) REVERT: D 36 TRP cc_start: 0.8433 (m100) cc_final: 0.7330 (m100) REVERT: D 52 SER cc_start: 0.8567 (m) cc_final: 0.7831 (p) REVERT: D 73 ASP cc_start: 0.8032 (t0) cc_final: 0.7350 (t0) REVERT: D 78 THR cc_start: 0.8179 (m) cc_final: 0.7664 (t) REVERT: D 95 TYR cc_start: 0.7292 (m-80) cc_final: 0.6913 (m-80) outliers start: 33 outliers final: 22 residues processed: 158 average time/residue: 0.5385 time to fit residues: 91.7789 Evaluate side-chains 144 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 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 240 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 330 SER 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 93 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 69 optimal weight: 0.0000 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN C 77 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 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 = 0.3782 r_free = 0.3782 target = 0.126117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.093515 restraints weight = 17325.716| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.73 r_work: 0.3168 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2605 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= 0.125 Angle : 0.548 8.977 14128 Z= 0.274 Chirality : 0.040 0.166 1666 Planarity : 0.004 0.038 1762 Dihedral : 10.031 178.614 1476 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.69 % Favored : 97.23 % Rotamer: Outliers : 3.42 % Allowed : 19.50 % Favored : 77.08 % 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: 2.06 (0.19), residues: 768 sheet: 0.98 (0.45), residues: 134 loop : -0.39 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 581 TYR 0.016 0.001 TYR A 358 PHE 0.017 0.001 PHE C 68 TRP 0.007 0.001 TRP C 116 HIS 0.004 0.001 HIS B 579 Details of bonding type rmsd covalent geometry : bond 0.00297 (10388) covalent geometry : angle 0.54795 (14124) SS BOND : bond 0.00127 ( 2) SS BOND : angle 0.65715 ( 4) hydrogen bonds : bond 0.03387 ( 637) hydrogen bonds : angle 3.90020 ( 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 166 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.8214 (tp) cc_final: 0.7901 (tp) REVERT: A 463 MET cc_start: 0.8428 (mtt) cc_final: 0.8102 (mtt) REVERT: B 350 MET cc_start: 0.8546 (mtp) cc_final: 0.8316 (mtm) REVERT: B 432 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7729 (mtt90) REVERT: B 463 MET cc_start: 0.8418 (mtt) cc_final: 0.8131 (mtt) REVERT: B 581 ARG cc_start: 0.8717 (tpp-160) cc_final: 0.8456 (mmp80) REVERT: C 30 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7096 (ttt-90) REVERT: C 36 TRP cc_start: 0.8321 (m100) cc_final: 0.7224 (m100) REVERT: C 67 ARG cc_start: 0.7345 (mtm110) cc_final: 0.7143 (mtm110) REVERT: C 73 ASP cc_start: 0.8480 (m-30) cc_final: 0.7555 (t0) REVERT: C 85 ILE cc_start: 0.9234 (mp) cc_final: 0.8945 (tp) REVERT: C 95 TYR cc_start: 0.6827 (m-80) cc_final: 0.6167 (m-80) REVERT: C 109 ASN cc_start: 0.8977 (t0) cc_final: 0.8605 (t0) REVERT: C 110 LYS cc_start: 0.8024 (mtpp) cc_final: 0.7776 (mmmt) REVERT: D 17 SER cc_start: 0.8469 (m) cc_final: 0.8132 (p) REVERT: D 18 LEU cc_start: 0.8687 (tp) cc_final: 0.8413 (tt) REVERT: D 36 TRP cc_start: 0.8407 (m100) cc_final: 0.7259 (m100) REVERT: D 52 SER cc_start: 0.8527 (m) cc_final: 0.7767 (p) REVERT: D 73 ASP cc_start: 0.8032 (t0) cc_final: 0.7318 (t0) REVERT: D 78 THR cc_start: 0.8202 (m) cc_final: 0.7661 (t) REVERT: D 84 ASN cc_start: 0.8278 (m-40) cc_final: 0.8039 (m110) REVERT: D 95 TYR cc_start: 0.7248 (m-80) cc_final: 0.6960 (m-80) outliers start: 37 outliers final: 24 residues processed: 158 average time/residue: 0.5082 time to fit residues: 86.8014 Evaluate side-chains 146 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 330 SER Chi-restraints excluded: chain A residue 353 SER 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 240 VAL 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 432 ARG Chi-restraints excluded: chain B residue 473 THR 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 93 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3779 r_free = 0.3779 target = 0.125813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.093336 restraints weight = 17223.613| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.72 r_work: 0.3162 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10390 Z= 0.130 Angle : 0.550 6.723 14128 Z= 0.277 Chirality : 0.040 0.167 1666 Planarity : 0.004 0.038 1762 Dihedral : 9.819 176.155 1476 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.69 % Favored : 97.23 % Rotamer: Outliers : 3.60 % Allowed : 19.50 % 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: 1.82 (0.24), residues: 1300 helix: 2.06 (0.19), residues: 768 sheet: 0.99 (0.46), residues: 134 loop : -0.39 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 581 TYR 0.016 0.001 TYR A 358 PHE 0.015 0.001 PHE A 328 TRP 0.006 0.001 TRP C 116 HIS 0.003 0.001 HIS B 579 Details of bonding type rmsd covalent geometry : bond 0.00314 (10388) covalent geometry : angle 0.54973 (14124) SS BOND : bond 0.00129 ( 2) SS BOND : angle 0.67606 ( 4) hydrogen bonds : bond 0.03421 ( 637) hydrogen bonds : angle 3.90282 ( 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 165 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 LEU cc_start: 0.8179 (tp) cc_final: 0.7865 (tp) REVERT: A 463 MET cc_start: 0.8442 (mtt) cc_final: 0.8120 (mtt) REVERT: B 350 MET cc_start: 0.8548 (mtp) cc_final: 0.8321 (mtm) REVERT: B 432 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7717 (mtt90) REVERT: B 463 MET cc_start: 0.8423 (mtt) cc_final: 0.8144 (mtt) REVERT: B 581 ARG cc_start: 0.8707 (tpp-160) cc_final: 0.8478 (mmp80) REVERT: C 4 LEU cc_start: 0.8898 (mm) cc_final: 0.8565 (tp) REVERT: C 30 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7041 (ttt-90) REVERT: C 36 TRP cc_start: 0.8398 (m100) cc_final: 0.7324 (m100) REVERT: C 73 ASP cc_start: 0.8516 (m-30) cc_final: 0.7611 (t0) REVERT: C 87 LYS cc_start: 0.9264 (mmtp) cc_final: 0.8883 (tptm) REVERT: C 95 TYR cc_start: 0.6889 (m-80) cc_final: 0.6174 (m-80) REVERT: C 109 ASN cc_start: 0.8971 (t0) cc_final: 0.8589 (t0) REVERT: C 110 LYS cc_start: 0.7980 (mtpp) cc_final: 0.7768 (mmmt) REVERT: D 17 SER cc_start: 0.8470 (m) cc_final: 0.8125 (p) REVERT: D 18 LEU cc_start: 0.8672 (tp) cc_final: 0.8418 (tt) REVERT: D 36 TRP cc_start: 0.8414 (m100) cc_final: 0.7311 (m100) REVERT: D 52 SER cc_start: 0.8506 (m) cc_final: 0.7683 (p) REVERT: D 73 ASP cc_start: 0.8071 (t0) cc_final: 0.7558 (t0) REVERT: D 95 TYR cc_start: 0.7214 (m-80) cc_final: 0.6939 (m-80) outliers start: 39 outliers final: 28 residues processed: 157 average time/residue: 0.5290 time to fit residues: 89.9041 Evaluate side-chains 150 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 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 210 LEU 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 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 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: 0.5980 chunk 73 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 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 = 0.3764 r_free = 0.3764 target = 0.124542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.091944 restraints weight = 17249.409| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.72 r_work: 0.3146 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10390 Z= 0.157 Angle : 0.580 10.008 14128 Z= 0.290 Chirality : 0.041 0.172 1666 Planarity : 0.004 0.038 1762 Dihedral : 9.667 171.382 1476 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.69 % Favored : 97.23 % Rotamer: Outliers : 3.51 % Allowed : 19.41 % Favored : 77.08 % 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: 1.98 (0.19), residues: 768 sheet: 0.95 (0.46), residues: 134 loop : -0.41 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 581 TYR 0.019 0.002 TYR A 358 PHE 0.015 0.001 PHE A 328 TRP 0.006 0.001 TRP C 116 HIS 0.002 0.001 HIS A 579 Details of bonding type rmsd covalent geometry : bond 0.00382 (10388) covalent geometry : angle 0.58039 (14124) SS BOND : bond 0.00099 ( 2) SS BOND : angle 0.69659 ( 4) hydrogen bonds : bond 0.03681 ( 637) hydrogen bonds : angle 3.93096 ( 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 166 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 461 LEU cc_start: 0.8227 (tp) cc_final: 0.7916 (tp) REVERT: B 432 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7795 (mtt90) REVERT: B 463 MET cc_start: 0.8428 (mtt) cc_final: 0.8146 (mtt) REVERT: C 4 LEU cc_start: 0.8855 (mm) cc_final: 0.8572 (tp) REVERT: C 30 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.6466 (ttt-90) REVERT: C 36 TRP cc_start: 0.8464 (m100) cc_final: 0.7411 (m100) REVERT: C 73 ASP cc_start: 0.8557 (m-30) cc_final: 0.7673 (t0) REVERT: C 95 TYR cc_start: 0.6980 (m-80) cc_final: 0.6226 (m-80) REVERT: C 109 ASN cc_start: 0.8999 (t0) cc_final: 0.8641 (t0) REVERT: D 17 SER cc_start: 0.8521 (m) cc_final: 0.8196 (p) REVERT: D 18 LEU cc_start: 0.8675 (tp) cc_final: 0.8422 (tt) REVERT: D 36 TRP cc_start: 0.8467 (m100) cc_final: 0.7436 (m100) REVERT: D 52 SER cc_start: 0.8545 (m) cc_final: 0.7732 (p) REVERT: D 73 ASP cc_start: 0.8110 (t0) cc_final: 0.7590 (t0) outliers start: 38 outliers final: 26 residues processed: 159 average time/residue: 0.5328 time to fit residues: 91.5550 Evaluate side-chains 151 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 265 THR 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 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 81 optimal weight: 0.6980 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 87 optimal weight: 0.0670 chunk 124 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.126796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.094455 restraints weight = 17160.556| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.71 r_work: 0.3183 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10390 Z= 0.112 Angle : 0.563 9.247 14128 Z= 0.284 Chirality : 0.040 0.254 1666 Planarity : 0.004 0.037 1762 Dihedral : 9.457 167.695 1476 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.69 % Favored : 97.23 % Rotamer: Outliers : 2.50 % Allowed : 20.70 % Favored : 76.80 % Cbeta Deviations : 0.08 % 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: 1.93 (0.24), residues: 1300 helix: 2.18 (0.19), residues: 768 sheet: 1.03 (0.45), residues: 134 loop : -0.42 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 335 TYR 0.017 0.001 TYR A 122 PHE 0.018 0.001 PHE A 191 TRP 0.007 0.001 TRP C 116 HIS 0.001 0.000 HIS B 579 Details of bonding type rmsd covalent geometry : bond 0.00260 (10388) covalent geometry : angle 0.56258 (14124) SS BOND : bond 0.00214 ( 2) SS BOND : angle 0.56713 ( 4) hydrogen bonds : bond 0.03162 ( 637) hydrogen bonds : angle 3.83252 ( 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 156 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 178 ASN cc_start: 0.8848 (m-40) cc_final: 0.8500 (t0) REVERT: A 461 LEU cc_start: 0.8157 (tp) cc_final: 0.7840 (tp) REVERT: A 463 MET cc_start: 0.8404 (mtt) cc_final: 0.8081 (mtt) REVERT: B 167 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8621 (t80) REVERT: B 209 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8216 (mtm) REVERT: B 432 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7807 (mtt90) REVERT: B 463 MET cc_start: 0.8401 (mtt) cc_final: 0.8125 (mtt) REVERT: C 4 LEU cc_start: 0.8825 (mm) cc_final: 0.8593 (tp) REVERT: C 30 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.6501 (ttt-90) REVERT: C 36 TRP cc_start: 0.8300 (m100) cc_final: 0.7172 (m100) REVERT: C 67 ARG cc_start: 0.7558 (mtm110) cc_final: 0.7343 (ptp-170) REVERT: C 73 ASP cc_start: 0.8535 (m-30) cc_final: 0.7491 (t0) REVERT: C 78 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7606 (t) REVERT: C 87 LYS cc_start: 0.9408 (mmtm) cc_final: 0.8961 (tptm) REVERT: C 95 TYR cc_start: 0.7115 (m-80) cc_final: 0.6342 (m-80) REVERT: C 109 ASN cc_start: 0.9039 (t0) cc_final: 0.8759 (t0) REVERT: D 17 SER cc_start: 0.8518 (m) cc_final: 0.8255 (p) REVERT: D 18 LEU cc_start: 0.8660 (tp) cc_final: 0.8453 (tt) REVERT: D 36 TRP cc_start: 0.8417 (m100) cc_final: 0.7385 (m100) REVERT: D 52 SER cc_start: 0.8427 (m) cc_final: 0.7597 (p) REVERT: D 73 ASP cc_start: 0.8106 (t0) cc_final: 0.7404 (t0) REVERT: D 78 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.7705 (t) outliers start: 27 outliers final: 16 residues processed: 151 average time/residue: 0.4889 time to fit residues: 80.1923 Evaluate side-chains 144 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 330 SER Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain B residue 56 LEU 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 330 SER Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 432 ARG Chi-restraints excluded: chain B residue 473 THR 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 78 THR 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: 0.9990 chunk 124 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 ASN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 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 = 0.3778 r_free = 0.3778 target = 0.125557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.093164 restraints weight = 17137.628| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.70 r_work: 0.3168 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2920 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= 0.128 Angle : 0.579 9.154 14128 Z= 0.288 Chirality : 0.041 0.167 1666 Planarity : 0.004 0.037 1762 Dihedral : 9.346 164.695 1476 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.54 % Favored : 97.38 % Rotamer: Outliers : 2.87 % Allowed : 20.43 % 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: 1.89 (0.24), residues: 1300 helix: 2.14 (0.19), residues: 768 sheet: 1.01 (0.46), residues: 134 loop : -0.40 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 67 TYR 0.016 0.001 TYR A 358 PHE 0.031 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 covalent geometry : bond 0.00307 (10388) covalent geometry : angle 0.57903 (14124) SS BOND : bond 0.00136 ( 2) SS BOND : angle 0.57799 ( 4) hydrogen bonds : bond 0.03343 ( 637) hydrogen bonds : angle 3.84581 ( 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 154 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 461 LEU cc_start: 0.8163 (tp) cc_final: 0.7847 (tp) REVERT: A 463 MET cc_start: 0.8417 (mtt) cc_final: 0.8099 (mtt) REVERT: B 432 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7721 (mtt90) REVERT: B 463 MET cc_start: 0.8421 (mtt) cc_final: 0.8145 (mtt) REVERT: C 4 LEU cc_start: 0.8808 (mm) cc_final: 0.8555 (tp) REVERT: C 30 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.6499 (ttt-90) REVERT: C 67 ARG cc_start: 0.7579 (mtm110) cc_final: 0.7234 (ptp-170) REVERT: C 73 ASP cc_start: 0.8548 (m-30) cc_final: 0.7493 (t0) REVERT: C 78 THR cc_start: 0.8187 (OUTLIER) cc_final: 0.7587 (t) REVERT: C 95 TYR cc_start: 0.7076 (m-80) cc_final: 0.6617 (m-80) REVERT: C 109 ASN cc_start: 0.9013 (t0) cc_final: 0.8714 (t0) REVERT: D 17 SER cc_start: 0.8520 (m) cc_final: 0.8259 (p) REVERT: D 36 TRP cc_start: 0.8388 (m100) cc_final: 0.7391 (m100) REVERT: D 52 SER cc_start: 0.8439 (m) cc_final: 0.7613 (p) REVERT: D 73 ASP cc_start: 0.8115 (t0) cc_final: 0.7403 (t0) REVERT: D 78 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.7718 (t) REVERT: D 84 ASN cc_start: 0.8017 (m-40) cc_final: 0.7780 (m110) outliers start: 31 outliers final: 22 residues processed: 148 average time/residue: 0.4768 time to fit residues: 76.8522 Evaluate side-chains 146 residues out of total 1082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 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 353 SER 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 330 SER Chi-restraints excluded: chain B residue 348 THR 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 C residue 78 THR 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: 6.9990 chunk 11 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3786 r_free = 0.3786 target = 0.126146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.093736 restraints weight = 17300.637| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.72 r_work: 0.3178 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2974 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= 0.118 Angle : 0.576 9.438 14128 Z= 0.286 Chirality : 0.041 0.192 1666 Planarity : 0.004 0.038 1762 Dihedral : 9.213 165.273 1476 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.62 % Favored : 97.31 % Rotamer: Outliers : 2.68 % Allowed : 20.79 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.24), residues: 1300 helix: 2.17 (0.19), residues: 768 sheet: 1.05 (0.45), residues: 134 loop : -0.40 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 335 TYR 0.015 0.001 TYR A 122 PHE 0.034 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 covalent geometry : bond 0.00279 (10388) covalent geometry : angle 0.57565 (14124) SS BOND : bond 0.00193 ( 2) SS BOND : angle 0.51288 ( 4) hydrogen bonds : bond 0.03230 ( 637) hydrogen bonds : angle 3.81851 ( 1809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3119.56 seconds wall clock time: 53 minutes 53.48 seconds (3233.48 seconds total)