Starting phenix.real_space_refine on Fri Jul 3 01:09:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dsx_30849/07_2026/7dsx_30849.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dsx_30849/07_2026/7dsx_30849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7dsx_30849/07_2026/7dsx_30849.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dsx_30849/07_2026/7dsx_30849.cif" model { file = "/net/cci-nas-00/data/ceres_data/7dsx_30849/07_2026/7dsx_30849.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dsx_30849/07_2026/7dsx_30849.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dsx_30849/07_2026/7dsx_30849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dsx_30849/07_2026/7dsx_30849.map" } resolution = 3.5 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= 0.087 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: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 7306 2.51 5 N 1804 2.21 5 O 1952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11106 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1450 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 178} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 4038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4038 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 16, 'TRANS': 492} Chain: "C" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1450 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 178} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 4038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4038 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 16, 'TRANS': 492} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {'HG0': 1, 'PGT': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PGT:plan-1': 3, 'PGT:plan-2': 3} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {'HG0': 1, 'PGT': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PGT:plan-1': 3, 'PGT:plan-2': 3} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 2.77, per 1000 atoms: 0.25 Number of scatterers: 11106 At special positions: 0 Unit cell: (146.64, 73.84, 98.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1952 8.00 N 1804 7.00 C 7306 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 423.2 milliseconds 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2576 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 0 sheets defined 67.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'D' and resid 14 through 22 Processing helix chain 'D' and resid 24 through 40 removed outlier: 3.846A pdb=" N ILE D 28 " --> pdb=" O SER D 24 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS D 40 " --> pdb=" O THR D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 53 Processing helix chain 'D' and resid 62 through 71 removed outlier: 4.405A pdb=" N PHE D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 89 removed outlier: 4.289A pdb=" N HIS D 89 " --> pdb=" O ARG D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 110 through 123 removed outlier: 4.169A pdb=" N ALA D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 143 Processing helix chain 'D' and resid 148 through 164 Processing helix chain 'D' and resid 173 through 181 removed outlier: 3.588A pdb=" N LYS D 178 " --> pdb=" O THR D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 189 Processing helix chain 'B' and resid 99 through 122 removed outlier: 3.570A pdb=" N ILE B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 129 removed outlier: 3.760A pdb=" N ILE B 128 " --> pdb=" O THR B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 147 removed outlier: 3.779A pdb=" N ILE B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 176 removed outlier: 4.219A pdb=" N ILE B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 185 removed outlier: 3.606A pdb=" N PHE B 182 " --> pdb=" O PRO B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 removed outlier: 3.723A pdb=" N ILE B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 198 removed outlier: 3.502A pdb=" N THR B 197 " --> pdb=" O ALA B 193 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 193 through 198' Processing helix chain 'B' and resid 199 through 214 Processing helix chain 'B' and resid 222 through 235 removed outlier: 4.173A pdb=" N ASP B 226 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE B 230 " --> pdb=" O ASP B 226 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 247 Processing helix chain 'B' and resid 252 through 267 removed outlier: 4.116A pdb=" N ASP B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 270 No H-bonds generated for 'chain 'B' and resid 268 through 270' Processing helix chain 'B' and resid 288 through 312 removed outlier: 3.553A pdb=" N GLY B 305 " --> pdb=" O VAL B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 328 No H-bonds generated for 'chain 'B' and resid 326 through 328' Processing helix chain 'B' and resid 329 through 334 removed outlier: 3.658A pdb=" N PHE B 333 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 329 through 334' Processing helix chain 'B' and resid 351 through 359 removed outlier: 3.749A pdb=" N ILE B 357 " --> pdb=" O ILE B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 368 Processing helix chain 'B' and resid 373 through 401 removed outlier: 3.937A pdb=" N MET B 385 " --> pdb=" O TYR B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 437 removed outlier: 3.842A pdb=" N ALA B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 455 Processing helix chain 'B' and resid 459 through 464 removed outlier: 3.566A pdb=" N PHE B 463 " --> pdb=" O GLY B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 494 removed outlier: 3.605A pdb=" N LEU B 481 " --> pdb=" O CYS B 477 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR B 482 " --> pdb=" O ASP B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 507 removed outlier: 3.821A pdb=" N ASP B 504 " --> pdb=" O ARG B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 539 removed outlier: 3.752A pdb=" N ASP B 536 " --> pdb=" O THR B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 557 Processing helix chain 'B' and resid 571 through 591 Processing helix chain 'C' and resid 14 through 22 Processing helix chain 'C' and resid 24 through 40 removed outlier: 3.847A pdb=" N ILE C 28 " --> pdb=" O SER C 24 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS C 40 " --> pdb=" O THR C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 53 Processing helix chain 'C' and resid 62 through 71 removed outlier: 4.404A pdb=" N PHE C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 94 through 100 Processing helix chain 'C' and resid 110 through 123 removed outlier: 4.168A pdb=" N ALA C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 143 Processing helix chain 'C' and resid 148 through 164 Processing helix chain 'C' and resid 173 through 181 removed outlier: 3.588A pdb=" N LYS C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 189 Processing helix chain 'A' and resid 99 through 122 removed outlier: 3.570A pdb=" N ILE A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.760A pdb=" N ILE A 128 " --> pdb=" O THR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 147 removed outlier: 3.780A pdb=" N ILE A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 176 removed outlier: 4.219A pdb=" N ILE A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 185 removed outlier: 3.605A pdb=" N PHE A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.724A pdb=" N ILE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 removed outlier: 3.503A pdb=" N THR A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 198 " --> pdb=" O VAL A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 193 through 198' Processing helix chain 'A' and resid 199 through 214 Processing helix chain 'A' and resid 222 through 235 removed outlier: 4.173A pdb=" N ASP A 226 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 247 Processing helix chain 'A' and resid 252 through 267 removed outlier: 4.115A pdb=" N ASP A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 270 No H-bonds generated for 'chain 'A' and resid 268 through 270' Processing helix chain 'A' and resid 288 through 312 removed outlier: 3.553A pdb=" N GLY A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 328 No H-bonds generated for 'chain 'A' and resid 326 through 328' Processing helix chain 'A' and resid 329 through 334 removed outlier: 3.658A pdb=" N PHE A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 334' Processing helix chain 'A' and resid 351 through 359 removed outlier: 3.750A pdb=" N ILE A 357 " --> pdb=" O ILE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 373 through 401 removed outlier: 3.937A pdb=" N MET A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 437 removed outlier: 3.842A pdb=" N ALA A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 455 Processing helix chain 'A' and resid 459 through 464 removed outlier: 3.567A pdb=" N PHE A 463 " --> pdb=" O GLY A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 494 removed outlier: 3.606A pdb=" N LEU A 481 " --> pdb=" O CYS A 477 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR A 482 " --> pdb=" O ASP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 507 removed outlier: 3.821A pdb=" N ASP A 504 " --> pdb=" O ARG A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 539 removed outlier: 3.753A pdb=" N ASP A 536 " --> pdb=" O THR A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 557 Processing helix chain 'A' and resid 571 through 591 578 hydrogen bonds defined for protein. 1734 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.65 Time building geometry restraints manager: 1.35 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: 1776 1.31 - 1.44: 3030 1.44 - 1.57: 6478 1.57 - 1.69: 0 1.69 - 1.82: 74 Bond restraints: 11358 Sorted by residual: bond pdb=" C12 HG0 B1003 " pdb=" N2 HG0 B1003 " ideal model delta sigma weight residual 1.387 1.245 0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" C12 HG0 A 604 " pdb=" N2 HG0 A 604 " ideal model delta sigma weight residual 1.387 1.245 0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" C12 HG0 A 604 " pdb=" N3 HG0 A 604 " ideal model delta sigma weight residual 1.375 1.243 0.132 2.00e-02 2.50e+03 4.37e+01 bond pdb=" C12 HG0 B1003 " pdb=" N3 HG0 B1003 " ideal model delta sigma weight residual 1.375 1.243 0.132 2.00e-02 2.50e+03 4.37e+01 bond pdb=" C1 HG0 B1003 " pdb=" C5 HG0 B1003 " ideal model delta sigma weight residual 1.537 1.415 0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 11353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.57: 15071 3.57 - 7.13: 252 7.13 - 10.70: 27 10.70 - 14.27: 6 14.27 - 17.83: 4 Bond angle restraints: 15360 Sorted by residual: angle pdb=" C PHE D 119 " pdb=" CA PHE D 119 " pdb=" CB PHE D 119 " ideal model delta sigma weight residual 110.67 127.47 -16.80 1.92e+00 2.71e-01 7.66e+01 angle pdb=" C PHE C 119 " pdb=" CA PHE C 119 " pdb=" CB PHE C 119 " ideal model delta sigma weight residual 110.67 127.46 -16.79 1.92e+00 2.71e-01 7.65e+01 angle pdb=" N LEU B 163 " pdb=" CA LEU B 163 " pdb=" C LEU B 163 " ideal model delta sigma weight residual 113.23 124.01 -10.78 1.24e+00 6.50e-01 7.56e+01 angle pdb=" N LEU A 163 " pdb=" CA LEU A 163 " pdb=" C LEU A 163 " ideal model delta sigma weight residual 113.23 124.00 -10.77 1.24e+00 6.50e-01 7.55e+01 angle pdb=" N GLU A 346 " pdb=" CA GLU A 346 " pdb=" C GLU A 346 " ideal model delta sigma weight residual 113.50 104.31 9.19 1.23e+00 6.61e-01 5.59e+01 ... (remaining 15355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 5928 17.05 - 34.09: 566 34.09 - 51.14: 152 51.14 - 68.18: 32 68.18 - 85.23: 14 Dihedral angle restraints: 6692 sinusoidal: 2696 harmonic: 3996 Sorted by residual: dihedral pdb=" C PHE D 119 " pdb=" N PHE D 119 " pdb=" CA PHE D 119 " pdb=" CB PHE D 119 " ideal model delta harmonic sigma weight residual -122.60 -146.60 24.00 0 2.50e+00 1.60e-01 9.22e+01 dihedral pdb=" C PHE C 119 " pdb=" N PHE C 119 " pdb=" CA PHE C 119 " pdb=" CB PHE C 119 " ideal model delta harmonic sigma weight residual -122.60 -146.58 23.98 0 2.50e+00 1.60e-01 9.20e+01 dihedral pdb=" N PHE D 119 " pdb=" C PHE D 119 " pdb=" CA PHE D 119 " pdb=" CB PHE D 119 " ideal model delta harmonic sigma weight residual 122.80 140.70 -17.90 0 2.50e+00 1.60e-01 5.13e+01 ... (remaining 6689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.168: 1736 0.168 - 0.336: 18 0.336 - 0.505: 4 0.505 - 0.673: 0 0.673 - 0.841: 2 Chirality restraints: 1760 Sorted by residual: chirality pdb=" CA PHE D 119 " pdb=" N PHE D 119 " pdb=" C PHE D 119 " pdb=" CB PHE D 119 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" CA PHE C 119 " pdb=" N PHE C 119 " pdb=" C PHE C 119 " pdb=" CB PHE C 119 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.76e+01 chirality pdb=" CA VAL A 160 " pdb=" N VAL A 160 " pdb=" C VAL A 160 " pdb=" CB VAL A 160 " both_signs ideal model delta sigma weight residual False 2.44 2.84 -0.40 2.00e-01 2.50e+01 4.00e+00 ... (remaining 1757 not shown) Planarity restraints: 1912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 182 " -0.023 2.00e-02 2.50e+03 1.88e-02 6.19e+00 pdb=" CG PHE B 182 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE B 182 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 182 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 182 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 182 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 182 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 182 " 0.023 2.00e-02 2.50e+03 1.88e-02 6.18e+00 pdb=" CG PHE A 182 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A 182 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 182 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 182 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 182 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 182 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 101 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO B 102 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 102 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 102 " -0.030 5.00e-02 4.00e+02 ... (remaining 1909 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2182 2.76 - 3.29: 11283 3.29 - 3.83: 17942 3.83 - 4.36: 21406 4.36 - 4.90: 35944 Nonbonded interactions: 88757 Sorted by model distance: nonbonded pdb=" OG1 THR A 197 " pdb=" OD1 ASN A 266 " model vdw 2.221 3.040 nonbonded pdb=" OG1 THR B 197 " pdb=" OD1 ASN B 266 " model vdw 2.222 3.040 nonbonded pdb=" OG1 THR B 433 " pdb=" OE1 GLN B 449 " model vdw 2.231 3.040 nonbonded pdb=" OG1 THR A 433 " pdb=" OE1 GLN A 449 " model vdw 2.231 3.040 nonbonded pdb=" NZ LYS B 116 " pdb=" OG SER B 388 " model vdw 2.265 3.120 ... (remaining 88752 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 85 through 593 or resid 602)) selection = (chain 'B' and (resid 85 through 593 or resid 1002)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.220 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.570 Find NCS groups from input model: 0.210 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 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 : 0.009 0.142 11358 Z= 0.430 Angle : 1.109 17.832 15360 Z= 0.625 Chirality : 0.067 0.841 1760 Planarity : 0.005 0.054 1912 Dihedral : 15.142 85.225 4116 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 0.34 % Allowed : 0.84 % Favored : 98.83 % Cbeta Deviations : 0.31 % 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: -2.95 (0.21), residues: 1380 helix: -1.60 (0.15), residues: 952 sheet: None (None), residues: 0 loop : -2.46 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 120 TYR 0.022 0.002 TYR A 209 PHE 0.043 0.003 PHE A 182 TRP 0.011 0.002 TRP A 434 HIS 0.009 0.002 HIS A 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00911 / 0.43 (11358) covalent geometry : angle 1.10933 / 0.62 (15360) hydrogen bonds : bond 0.12619 / 8.34 ( 578) hydrogen bonds : angle 6.83019 / 4.86 ( 1734) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 261 time to evaluate : 0.413 Fit side-chains REVERT: C 132 ARG cc_start: 0.7326 (mtp180) cc_final: 0.6927 (mtp180) REVERT: A 131 GLU cc_start: 0.8055 (pp20) cc_final: 0.7586 (pp20) REVERT: A 318 PHE cc_start: 0.8591 (t80) cc_final: 0.8379 (t80) outliers start: 4 outliers final: 1 residues processed: 263 average time/residue: 0.1255 time to fit residues: 45.1207 Evaluate side-chains 186 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.0170 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 HIS B 578 HIS A 376 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.208518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.173302 restraints weight = 13991.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.177288 restraints weight = 7606.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.179823 restraints weight = 5196.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.181200 restraints weight = 4122.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.182284 restraints weight = 3607.841| |-----------------------------------------------------------------------------| r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11358 Z= 0.143 Angle : 0.624 8.343 15360 Z= 0.329 Chirality : 0.043 0.175 1760 Planarity : 0.004 0.037 1912 Dihedral : 7.675 51.867 1573 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.01 % Allowed : 10.65 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.22), residues: 1380 helix: -0.53 (0.17), residues: 926 sheet: None (None), residues: 0 loop : -2.57 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 81 TYR 0.017 0.001 TYR B 577 PHE 0.025 0.002 PHE A 182 TRP 0.005 0.001 TRP A 411 HIS 0.004 0.001 HIS B 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (11358) covalent geometry : angle 0.62424 / 0.33 (15360) hydrogen bonds : bond 0.04089 / 2.81 ( 578) hydrogen bonds : angle 4.80952 / 3.48 ( 1734) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 210 time to evaluate : 0.409 Fit side-chains REVERT: D 189 MET cc_start: 0.8572 (tmm) cc_final: 0.8313 (tmm) REVERT: B 157 GLN cc_start: 0.7110 (mp10) cc_final: 0.6813 (mp10) REVERT: B 312 TYR cc_start: 0.7119 (m-10) cc_final: 0.6464 (m-10) REVERT: B 435 PHE cc_start: 0.7737 (t80) cc_final: 0.7517 (t80) REVERT: B 493 PHE cc_start: 0.8341 (m-10) cc_final: 0.7949 (m-80) REVERT: A 131 GLU cc_start: 0.7453 (pp20) cc_final: 0.7017 (pp20) REVERT: A 493 PHE cc_start: 0.8439 (m-10) cc_final: 0.8025 (m-80) REVERT: A 552 ARG cc_start: 0.7771 (ttp-170) cc_final: 0.7478 (mtm-85) outliers start: 12 outliers final: 9 residues processed: 217 average time/residue: 0.1067 time to fit residues: 33.2868 Evaluate side-chains 189 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 180 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 478 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 25 optimal weight: 0.0870 chunk 30 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 29 optimal weight: 0.6980 chunk 92 optimal weight: 0.0020 overall best weight: 0.4366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 ASN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 HIS B 578 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.211121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.175809 restraints weight = 14031.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.179916 restraints weight = 7459.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.182521 restraints weight = 5011.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.183945 restraints weight = 3943.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.185041 restraints weight = 3448.416| |-----------------------------------------------------------------------------| r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11358 Z= 0.120 Angle : 0.550 6.000 15360 Z= 0.291 Chirality : 0.041 0.142 1760 Planarity : 0.004 0.034 1912 Dihedral : 6.602 45.966 1572 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.85 % Allowed : 13.34 % Favored : 84.82 % 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: -1.20 (0.23), residues: 1380 helix: -0.02 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.39 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 53 TYR 0.013 0.001 TYR B 577 PHE 0.020 0.001 PHE A 119 TRP 0.005 0.001 TRP B 386 HIS 0.004 0.001 HIS B 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (11358) covalent geometry : angle 0.54967 / 0.29 (15360) hydrogen bonds : bond 0.03723 / 2.56 ( 578) hydrogen bonds : angle 4.32517 / 3.13 ( 1734) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 0.402 Fit side-chains REVERT: D 17 ILE cc_start: 0.7979 (mp) cc_final: 0.7568 (mp) REVERT: D 150 GLU cc_start: 0.7931 (pm20) cc_final: 0.7544 (tp30) REVERT: B 312 TYR cc_start: 0.6911 (m-10) cc_final: 0.6187 (m-10) REVERT: B 327 ARG cc_start: 0.7621 (mmt-90) cc_final: 0.7392 (mmp80) REVERT: B 432 LEU cc_start: 0.7949 (mt) cc_final: 0.7560 (mt) REVERT: C 189 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.6303 (tmm) REVERT: A 493 PHE cc_start: 0.8372 (m-10) cc_final: 0.7983 (m-80) REVERT: A 552 ARG cc_start: 0.7765 (ttp-170) cc_final: 0.7554 (mtm-85) outliers start: 22 outliers final: 11 residues processed: 208 average time/residue: 0.1020 time to fit residues: 30.8218 Evaluate side-chains 186 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain B residue 283 TYR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 478 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 60 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 0.0020 chunk 115 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 HIS ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 HIS A 543 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.208880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.174716 restraints weight = 14009.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.176496 restraints weight = 8664.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.178161 restraints weight = 6305.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.179079 restraints weight = 5091.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.179521 restraints weight = 4636.964| |-----------------------------------------------------------------------------| r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11358 Z= 0.127 Angle : 0.546 5.873 15360 Z= 0.286 Chirality : 0.041 0.143 1760 Planarity : 0.004 0.035 1912 Dihedral : 6.437 44.917 1572 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.52 % Allowed : 13.51 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.96 (0.23), residues: 1380 helix: 0.11 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.18 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 53 TYR 0.015 0.001 TYR B 577 PHE 0.018 0.001 PHE C 119 TRP 0.009 0.001 TRP A 386 HIS 0.007 0.001 HIS A 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (11358) covalent geometry : angle 0.54616 / 0.29 (15360) hydrogen bonds : bond 0.03612 / 2.49 ( 578) hydrogen bonds : angle 4.21495 / 3.05 ( 1734) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 0.267 Fit side-chains REVERT: D 77 GLN cc_start: 0.7167 (mp10) cc_final: 0.6811 (mm-40) REVERT: D 150 GLU cc_start: 0.7873 (pm20) cc_final: 0.7617 (tp30) REVERT: B 312 TYR cc_start: 0.6836 (m-10) cc_final: 0.6315 (m-10) REVERT: B 327 ARG cc_start: 0.7547 (mmt-90) cc_final: 0.7319 (mmp80) REVERT: C 150 GLU cc_start: 0.7929 (pm20) cc_final: 0.7546 (tp30) REVERT: C 189 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.5720 (tmm) REVERT: A 552 ARG cc_start: 0.7745 (ttp-170) cc_final: 0.7534 (mtm-85) outliers start: 30 outliers final: 15 residues processed: 219 average time/residue: 0.0908 time to fit residues: 29.0592 Evaluate side-chains 202 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 283 TYR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 478 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 130 optimal weight: 3.9990 chunk 87 optimal weight: 0.0060 chunk 59 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 92 optimal weight: 9.9990 chunk 82 optimal weight: 0.7980 chunk 122 optimal weight: 0.0170 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 HIS ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.211959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.176777 restraints weight = 13822.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.180652 restraints weight = 7527.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.183144 restraints weight = 5161.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.184623 restraints weight = 4113.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.185128 restraints weight = 3580.955| |-----------------------------------------------------------------------------| r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11358 Z= 0.113 Angle : 0.529 6.278 15360 Z= 0.280 Chirality : 0.040 0.151 1760 Planarity : 0.004 0.036 1912 Dihedral : 6.121 44.868 1572 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.43 % Allowed : 16.36 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.66 (0.24), residues: 1380 helix: 0.33 (0.17), residues: 938 sheet: None (None), residues: 0 loop : -2.05 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 53 TYR 0.012 0.001 TYR B 577 PHE 0.014 0.001 PHE C 119 TRP 0.008 0.001 TRP B 386 HIS 0.007 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (11358) covalent geometry : angle 0.52852 / 0.28 (15360) hydrogen bonds : bond 0.03475 / 2.39 ( 578) hydrogen bonds : angle 4.04754 / 2.93 ( 1734) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: D 77 GLN cc_start: 0.6993 (mp10) cc_final: 0.6685 (mm-40) REVERT: B 134 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7704 (mp) REVERT: B 141 LEU cc_start: 0.8267 (tp) cc_final: 0.7973 (tp) REVERT: B 312 TYR cc_start: 0.6729 (m-10) cc_final: 0.6164 (m-10) REVERT: B 454 TYR cc_start: 0.7055 (t80) cc_final: 0.6825 (t80) REVERT: C 129 LYS cc_start: 0.7225 (mmmt) cc_final: 0.6872 (mmmt) REVERT: C 177 VAL cc_start: 0.8061 (p) cc_final: 0.7784 (t) REVERT: C 189 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.5672 (tmm) REVERT: A 134 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7766 (mm) REVERT: A 312 TYR cc_start: 0.6824 (m-10) cc_final: 0.6270 (m-10) REVERT: A 493 PHE cc_start: 0.8381 (m-10) cc_final: 0.8002 (m-80) REVERT: A 552 ARG cc_start: 0.7784 (ttp-170) cc_final: 0.7529 (mtm-85) outliers start: 29 outliers final: 19 residues processed: 229 average time/residue: 0.0985 time to fit residues: 33.2992 Evaluate side-chains 209 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 283 TYR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 407 HIS Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 523 HIS Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 478 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 30 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 HIS A 218 GLN A 285 HIS A 578 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.210980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.175007 restraints weight = 13907.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.178823 restraints weight = 7706.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.181331 restraints weight = 5322.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.182853 restraints weight = 4245.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.183550 restraints weight = 3701.823| |-----------------------------------------------------------------------------| r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11358 Z= 0.123 Angle : 0.538 5.851 15360 Z= 0.283 Chirality : 0.041 0.160 1760 Planarity : 0.004 0.037 1912 Dihedral : 6.048 43.179 1572 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.10 % Allowed : 18.54 % Favored : 79.36 % 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: -0.61 (0.23), residues: 1380 helix: 0.34 (0.17), residues: 942 sheet: None (None), residues: 0 loop : -1.97 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 567 TYR 0.013 0.001 TYR B 577 PHE 0.025 0.001 PHE A 292 TRP 0.008 0.001 TRP B 386 HIS 0.006 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (11358) covalent geometry : angle 0.53831 / 0.28 (15360) hydrogen bonds : bond 0.03517 / 2.42 ( 578) hydrogen bonds : angle 4.01477 / 2.90 ( 1734) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: B 134 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7682 (mp) REVERT: B 141 LEU cc_start: 0.8288 (tp) cc_final: 0.7996 (tp) REVERT: B 312 TYR cc_start: 0.6757 (m-10) cc_final: 0.6272 (m-10) REVERT: B 454 TYR cc_start: 0.7131 (t80) cc_final: 0.6868 (t80) REVERT: C 189 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.5623 (tmm) REVERT: A 134 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7675 (mp) REVERT: A 312 TYR cc_start: 0.6802 (m-10) cc_final: 0.6308 (m-10) REVERT: A 493 PHE cc_start: 0.8428 (m-10) cc_final: 0.8033 (m-80) REVERT: A 552 ARG cc_start: 0.7796 (ttp-170) cc_final: 0.7547 (mtm-85) outliers start: 25 outliers final: 18 residues processed: 217 average time/residue: 0.0986 time to fit residues: 31.5006 Evaluate side-chains 204 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 283 TYR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 407 HIS Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 79 optimal weight: 0.2980 chunk 130 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 53 optimal weight: 0.0570 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 46 optimal weight: 0.0870 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 113 ASN B 578 HIS ** B 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.214274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.179830 restraints weight = 13781.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.183478 restraints weight = 7911.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.185835 restraints weight = 5575.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.187025 restraints weight = 4489.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.188081 restraints weight = 3971.944| |-----------------------------------------------------------------------------| r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11358 Z= 0.107 Angle : 0.523 8.068 15360 Z= 0.276 Chirality : 0.040 0.162 1760 Planarity : 0.004 0.037 1912 Dihedral : 5.825 43.735 1572 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.35 % Allowed : 19.04 % Favored : 78.61 % 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: -0.41 (0.24), residues: 1380 helix: 0.50 (0.17), residues: 944 sheet: None (None), residues: 0 loop : -1.92 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 53 TYR 0.012 0.001 TYR B 577 PHE 0.016 0.001 PHE C 83 TRP 0.008 0.001 TRP A 386 HIS 0.005 0.000 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (11358) covalent geometry : angle 0.52343 / 0.28 (15360) hydrogen bonds : bond 0.03350 / 2.30 ( 578) hydrogen bonds : angle 3.91650 / 2.83 ( 1734) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: D 189 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.5840 (tmm) REVERT: B 134 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7639 (mp) REVERT: B 141 LEU cc_start: 0.8280 (tp) cc_final: 0.7999 (tp) REVERT: B 218 GLN cc_start: 0.7968 (tt0) cc_final: 0.7739 (tt0) REVERT: B 312 TYR cc_start: 0.6603 (m-10) cc_final: 0.6042 (m-10) REVERT: A 134 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7652 (mp) REVERT: A 312 TYR cc_start: 0.6648 (m-10) cc_final: 0.6101 (m-10) REVERT: A 493 PHE cc_start: 0.8332 (m-10) cc_final: 0.7953 (m-80) REVERT: A 552 ARG cc_start: 0.7745 (ttp-170) cc_final: 0.7522 (mtm-85) outliers start: 28 outliers final: 19 residues processed: 215 average time/residue: 0.0965 time to fit residues: 30.6956 Evaluate side-chains 206 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 283 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 407 HIS Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 523 HIS Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 112 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 HIS ** B 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN A 578 HIS ** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.211064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.175064 restraints weight = 13745.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.178925 restraints weight = 7644.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.181386 restraints weight = 5269.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.182646 restraints weight = 4216.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.183593 restraints weight = 3712.353| |-----------------------------------------------------------------------------| r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11358 Z= 0.130 Angle : 0.558 8.813 15360 Z= 0.295 Chirality : 0.041 0.194 1760 Planarity : 0.004 0.038 1912 Dihedral : 5.881 41.232 1572 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.52 % Allowed : 19.04 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.23), residues: 1380 helix: 0.47 (0.17), residues: 942 sheet: None (None), residues: 0 loop : -1.96 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 327 TYR 0.014 0.001 TYR B 577 PHE 0.027 0.001 PHE A 292 TRP 0.008 0.001 TRP A 386 HIS 0.015 0.001 HIS B 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (11358) covalent geometry : angle 0.55821 / 0.30 (15360) hydrogen bonds : bond 0.03431 / 2.35 ( 578) hydrogen bonds : angle 3.94521 / 2.86 ( 1734) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: D 189 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.5900 (tmm) REVERT: B 134 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7672 (mp) REVERT: B 141 LEU cc_start: 0.8298 (tp) cc_final: 0.8019 (tp) REVERT: B 296 LEU cc_start: 0.7231 (mt) cc_final: 0.7031 (mt) REVERT: B 312 TYR cc_start: 0.6773 (m-10) cc_final: 0.6289 (m-10) REVERT: C 189 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.5506 (tmm) REVERT: A 134 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7633 (mp) REVERT: A 312 TYR cc_start: 0.6712 (m-10) cc_final: 0.6240 (m-10) REVERT: A 493 PHE cc_start: 0.8353 (m-10) cc_final: 0.8006 (m-80) REVERT: A 552 ARG cc_start: 0.7766 (ttp-170) cc_final: 0.7524 (mtm-85) outliers start: 30 outliers final: 24 residues processed: 211 average time/residue: 0.0893 time to fit residues: 27.6299 Evaluate side-chains 210 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 283 TYR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 407 HIS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 478 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 77 optimal weight: 0.0020 chunk 131 optimal weight: 0.7980 chunk 135 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 123 optimal weight: 0.4980 chunk 78 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 HIS B 584 GLN C 113 ASN A 349 HIS A 578 HIS A 584 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.213667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.178278 restraints weight = 13634.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.182217 restraints weight = 7517.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.184741 restraints weight = 5136.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.185958 restraints weight = 4086.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.187119 restraints weight = 3593.827| |-----------------------------------------------------------------------------| r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11358 Z= 0.114 Angle : 0.553 8.979 15360 Z= 0.291 Chirality : 0.041 0.205 1760 Planarity : 0.004 0.040 1912 Dihedral : 5.749 41.786 1572 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.60 % Allowed : 18.96 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.23), residues: 1380 helix: 0.60 (0.17), residues: 942 sheet: None (None), residues: 0 loop : -1.92 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 140 TYR 0.018 0.001 TYR A 577 PHE 0.015 0.001 PHE D 83 TRP 0.009 0.001 TRP B 386 HIS 0.018 0.001 HIS B 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (11358) covalent geometry : angle 0.55335 / 0.29 (15360) hydrogen bonds : bond 0.03338 / 2.29 ( 578) hydrogen bonds : angle 3.88659 / 2.82 ( 1734) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 189 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.5831 (tmm) REVERT: B 134 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7675 (mp) REVERT: B 141 LEU cc_start: 0.8302 (tp) cc_final: 0.8047 (tp) REVERT: B 267 ASP cc_start: 0.7429 (t70) cc_final: 0.7163 (t0) REVERT: B 312 TYR cc_start: 0.6632 (m-10) cc_final: 0.6076 (m-10) REVERT: C 90 PHE cc_start: 0.7702 (m-10) cc_final: 0.7183 (m-10) REVERT: C 129 LYS cc_start: 0.7398 (mmmt) cc_final: 0.7076 (mmtm) REVERT: C 189 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.5618 (tmm) REVERT: A 134 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7644 (mp) REVERT: A 312 TYR cc_start: 0.6580 (m-10) cc_final: 0.6079 (m-10) REVERT: A 349 HIS cc_start: 0.8065 (OUTLIER) cc_final: 0.7818 (m-70) REVERT: A 493 PHE cc_start: 0.8313 (m-10) cc_final: 0.7985 (m-80) REVERT: A 552 ARG cc_start: 0.7719 (ttp-170) cc_final: 0.7495 (mtm-85) outliers start: 31 outliers final: 22 residues processed: 209 average time/residue: 0.0900 time to fit residues: 27.5482 Evaluate side-chains 208 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 283 TYR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 407 HIS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 478 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 20.0000 chunk 74 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 86 optimal weight: 0.1980 chunk 62 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 HIS ** B 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 HIS ** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.213445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.177742 restraints weight = 13741.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.181641 restraints weight = 7625.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.184183 restraints weight = 5192.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.185542 restraints weight = 4128.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.186258 restraints weight = 3608.468| |-----------------------------------------------------------------------------| r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11358 Z= 0.118 Angle : 0.569 8.652 15360 Z= 0.298 Chirality : 0.041 0.207 1760 Planarity : 0.004 0.040 1912 Dihedral : 5.707 41.195 1572 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.18 % Allowed : 19.80 % Favored : 78.02 % 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: -0.26 (0.23), residues: 1380 helix: 0.62 (0.17), residues: 944 sheet: None (None), residues: 0 loop : -1.88 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 327 TYR 0.017 0.001 TYR A 577 PHE 0.018 0.001 PHE C 83 TRP 0.011 0.001 TRP B 386 HIS 0.016 0.001 HIS B 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (11358) covalent geometry : angle 0.56888 / 0.30 (15360) hydrogen bonds : bond 0.03349 / 2.31 ( 578) hydrogen bonds : angle 3.88898 / 2.81 ( 1734) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: D 189 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.5873 (tmm) REVERT: B 134 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7681 (mp) REVERT: B 141 LEU cc_start: 0.8315 (tp) cc_final: 0.8053 (tp) REVERT: B 267 ASP cc_start: 0.7442 (t70) cc_final: 0.7128 (t0) REVERT: B 312 TYR cc_start: 0.6621 (m-10) cc_final: 0.6075 (m-10) REVERT: C 90 PHE cc_start: 0.7676 (m-10) cc_final: 0.7148 (m-10) REVERT: C 129 LYS cc_start: 0.7397 (mmmt) cc_final: 0.7105 (mmtm) REVERT: C 189 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.5618 (tmm) REVERT: A 134 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7657 (mp) REVERT: A 312 TYR cc_start: 0.6668 (m-10) cc_final: 0.6155 (m-10) REVERT: A 493 PHE cc_start: 0.8304 (m-10) cc_final: 0.7992 (m-80) REVERT: A 552 ARG cc_start: 0.7726 (ttp-170) cc_final: 0.7515 (mtm-85) outliers start: 26 outliers final: 22 residues processed: 203 average time/residue: 0.0980 time to fit residues: 29.0112 Evaluate side-chains 207 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 283 TYR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 407 HIS Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 70 PHE Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 478 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 83 optimal weight: 8.9990 chunk 101 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 120 optimal weight: 0.6980 chunk 25 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 HIS ** B 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 HIS ** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.213447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.177804 restraints weight = 13756.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.181775 restraints weight = 7551.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.184259 restraints weight = 5169.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.185643 restraints weight = 4113.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.185895 restraints weight = 3594.970| |-----------------------------------------------------------------------------| r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11358 Z= 0.116 Angle : 0.556 8.384 15360 Z= 0.292 Chirality : 0.041 0.203 1760 Planarity : 0.004 0.040 1912 Dihedral : 5.645 40.728 1572 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.35 % Allowed : 19.71 % Favored : 77.94 % 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: -0.20 (0.23), residues: 1380 helix: 0.66 (0.17), residues: 944 sheet: None (None), residues: 0 loop : -1.85 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 327 TYR 0.017 0.001 TYR A 577 PHE 0.017 0.001 PHE C 83 TRP 0.011 0.001 TRP B 386 HIS 0.016 0.001 HIS B 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (11358) covalent geometry : angle 0.55572 / 0.29 (15360) hydrogen bonds : bond 0.03357 / 2.32 ( 578) hydrogen bonds : angle 3.88450 / 2.82 ( 1734) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1809.17 seconds wall clock time: 32 minutes 6.50 seconds (1926.50 seconds total)