Starting phenix.real_space_refine on Tue Nov 18 07:39:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cnw_45764/11_2025/9cnw_45764.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cnw_45764/11_2025/9cnw_45764.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cnw_45764/11_2025/9cnw_45764.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cnw_45764/11_2025/9cnw_45764.map" model { file = "/net/cci-nas-00/data/ceres_data/9cnw_45764/11_2025/9cnw_45764.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cnw_45764/11_2025/9cnw_45764.cif" } resolution = 2.6 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= 0.000 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 771 atoms to isotropic. 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 32 5.16 5 C 7339 2.51 5 N 1987 2.21 5 O 2289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11647 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6207 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 29, 'TRANS': 755} Chain: "B" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2588 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 11, 'TRANS': 334} Chain breaks: 2 Chain: "C" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 406 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 7, 'TRANS': 49} Chain: "D" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1761 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 685 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Time building chain proxies: 3.19, per 1000 atoms: 0.27 Number of scatterers: 11647 At special positions: 0 Unit cell: (99.4423, 119.81, 140.178, 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 32 16.00 O 2289 8.00 N 1987 7.00 C 7339 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 698.9 milliseconds 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2728 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 18 sheets defined 25.7% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 106 through 117 removed outlier: 4.368A pdb=" N LEU A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 129 through 145 removed outlier: 3.951A pdb=" N LYS A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 215 through 233 removed outlier: 3.690A pdb=" N LEU A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.899A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.839A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 391 Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 691 through 695 Processing helix chain 'A' and resid 726 through 731 removed outlier: 5.110A pdb=" N ASN A 731 " --> pdb=" O LYS A 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 removed outlier: 4.470A pdb=" N TYR C 41 " --> pdb=" O ASP C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'D' and resid 31 through 46 removed outlier: 3.768A pdb=" N ILE D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 120 removed outlier: 3.660A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 135 removed outlier: 4.568A pdb=" N ASP D 134 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.536A pdb=" N LEU D 215 " --> pdb=" O THR D 211 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 242 Processing helix chain 'E' and resid 39 through 45 removed outlier: 3.689A pdb=" N LYS E 45 " --> pdb=" O ASN E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 79 removed outlier: 4.372A pdb=" N ASP A 74 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.131A pdb=" N LEU A 165 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE A 97 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU A 167 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE A 99 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N PHE A 169 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183 removed outlier: 7.462A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 276 removed outlier: 7.307A pdb=" N LEU A 337 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL A 271 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL A 339 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL A 273 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 341 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY A 275 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 334 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 375 through 376 removed outlier: 3.685A pdb=" N ALA A 375 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL A 412 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS A 351 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLN A 411 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ARG A 404 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ASP A 413 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR A 402 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 424 through 426 Processing sheet with id=AA7, first strand: chain 'A' and resid 424 through 426 removed outlier: 3.696A pdb=" N ASN A 448 " --> pdb=" O TYR A 454 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N TYR A 454 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 590 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.522A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 50 removed outlier: 6.764A pdb=" N SER B 389 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER B 49 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL B 387 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.859A pdb=" N VAL B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N SER B 94 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA B 83 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.777A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.578A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 201 through 203 removed outlier: 5.897A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N MET B 226 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.532A pdb=" N LEU B 267 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS B 280 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.678A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR B 309 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR B 315 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 331 through 333 removed outlier: 6.778A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 35 removed outlier: 4.010A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 32 through 35 534 hydrogen bonds defined for protein. 1473 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: 2.59 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3900 1.34 - 1.46: 2603 1.46 - 1.58: 5334 1.58 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 11899 Sorted by residual: bond pdb=" N PHE A 24 " pdb=" CA PHE A 24 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N LYS C 32 " pdb=" CA LYS C 32 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N GLU D 26 " pdb=" CA GLU D 26 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N VAL B 30 " pdb=" CA VAL B 30 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N GLU E 24 " pdb=" CA GLU E 24 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.74e+00 ... (remaining 11894 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 15590 1.30 - 2.59: 473 2.59 - 3.89: 85 3.89 - 5.18: 25 5.18 - 6.48: 3 Bond angle restraints: 16176 Sorted by residual: angle pdb=" N GLY A 584 " pdb=" CA GLY A 584 " pdb=" C GLY A 584 " ideal model delta sigma weight residual 112.49 118.32 -5.83 1.21e+00 6.83e-01 2.32e+01 angle pdb=" C ARG A 583 " pdb=" N GLY A 584 " pdb=" CA GLY A 584 " ideal model delta sigma weight residual 119.94 122.96 -3.02 1.09e+00 8.42e-01 7.67e+00 angle pdb=" N GLY B 113 " pdb=" CA GLY B 113 " pdb=" C GLY B 113 " ideal model delta sigma weight residual 113.18 106.70 6.48 2.37e+00 1.78e-01 7.47e+00 angle pdb=" CA TYR D 184 " pdb=" CB TYR D 184 " pdb=" CG TYR D 184 " ideal model delta sigma weight residual 113.90 109.19 4.71 1.80e+00 3.09e-01 6.85e+00 angle pdb=" CG MET A 46 " pdb=" SD MET A 46 " pdb=" CE MET A 46 " ideal model delta sigma weight residual 100.90 95.94 4.96 2.20e+00 2.07e-01 5.08e+00 ... (remaining 16171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6582 17.97 - 35.93: 352 35.93 - 53.90: 67 53.90 - 71.87: 17 71.87 - 89.84: 18 Dihedral angle restraints: 7036 sinusoidal: 2745 harmonic: 4291 Sorted by residual: dihedral pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual -86.00 -144.92 58.92 1 1.00e+01 1.00e-02 4.64e+01 dihedral pdb=" CA LYS A 106 " pdb=" C LYS A 106 " pdb=" N ASP A 107 " pdb=" CA ASP A 107 " ideal model delta harmonic sigma weight residual -180.00 -152.16 -27.84 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA VAL A 660 " pdb=" C VAL A 660 " pdb=" N ARG A 661 " pdb=" CA ARG A 661 " ideal model delta harmonic sigma weight residual 180.00 -159.52 -20.48 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 7033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 990 0.029 - 0.058: 513 0.058 - 0.087: 121 0.087 - 0.116: 113 0.116 - 0.145: 32 Chirality restraints: 1769 Sorted by residual: chirality pdb=" CA ILE C 67 " pdb=" N ILE C 67 " pdb=" C ILE C 67 " pdb=" CB ILE C 67 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA VAL A 744 " pdb=" N VAL A 744 " pdb=" C VAL A 744 " pdb=" CB VAL A 744 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ILE A 352 " pdb=" N ILE A 352 " pdb=" C ILE A 352 " pdb=" CB ILE A 352 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1766 not shown) Planarity restraints: 2133 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 66 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO E 67 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 67 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 67 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 238 " -0.014 2.00e-02 2.50e+03 1.44e-02 3.62e+00 pdb=" CG PHE A 238 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 238 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 238 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 238 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE A 238 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 238 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 203 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO A 204 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 204 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 204 " 0.024 5.00e-02 4.00e+02 ... (remaining 2130 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 162 2.69 - 3.24: 10968 3.24 - 3.79: 17530 3.79 - 4.35: 24585 4.35 - 4.90: 40358 Nonbonded interactions: 93603 Sorted by model distance: nonbonded pdb=" OH TYR A 468 " pdb=" OE1 GLU A 470 " model vdw 2.133 3.040 nonbonded pdb=" OE1 GLN A 198 " pdb=" NZ LYS A 218 " model vdw 2.199 3.120 nonbonded pdb=" NH1 ARG B 304 " pdb=" OG SER B 320 " model vdw 2.220 3.120 nonbonded pdb=" OD2 ASP E 66 " pdb=" OG1 THR E 70 " model vdw 2.237 3.040 nonbonded pdb=" OD1 ASN A 463 " pdb=" N ASP A 464 " model vdw 2.244 3.120 ... (remaining 93598 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.700 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11900 Z= 0.141 Angle : 0.578 6.479 16178 Z= 0.318 Chirality : 0.044 0.145 1769 Planarity : 0.004 0.060 2133 Dihedral : 12.855 89.835 4305 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.26 (0.22), residues: 1479 helix: 1.57 (0.28), residues: 324 sheet: 1.10 (0.22), residues: 476 loop : 0.40 (0.26), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 203 TYR 0.024 0.002 TYR D 184 PHE 0.032 0.002 PHE A 238 TRP 0.011 0.002 TRP A 376 HIS 0.006 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00306 (11899) covalent geometry : angle 0.57642 (16176) SS BOND : bond 0.00167 ( 1) SS BOND : angle 3.25289 ( 2) hydrogen bonds : bond 0.17009 ( 528) hydrogen bonds : angle 6.48466 ( 1473) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 369 MET cc_start: 0.8831 (mmp) cc_final: 0.8285 (mmp) REVERT: A 552 MET cc_start: 0.8542 (mmm) cc_final: 0.7923 (mmm) REVERT: A 784 VAL cc_start: 0.9342 (t) cc_final: 0.9074 (t) REVERT: D 72 GLN cc_start: 0.7776 (mt0) cc_final: 0.7551 (mt0) REVERT: D 164 THR cc_start: 0.9097 (m) cc_final: 0.8845 (m) REVERT: D 225 MET cc_start: 0.9169 (mtm) cc_final: 0.8830 (mtm) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.6628 time to fit residues: 172.4117 Evaluate side-chains 194 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 459 ASN A 523 ASN A 625 HIS B 85 ASN B 175 ASN B 266 ASN B 324 HIS D 70 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.162074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.126841 restraints weight = 12042.820| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.08 r_work: 0.3043 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 11900 Z= 0.239 Angle : 0.681 6.991 16178 Z= 0.373 Chirality : 0.049 0.167 1769 Planarity : 0.006 0.080 2133 Dihedral : 5.310 26.876 1634 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.16 % Allowed : 8.65 % Favored : 89.18 % 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: 1.15 (0.22), residues: 1479 helix: 1.81 (0.28), residues: 325 sheet: 0.97 (0.23), residues: 466 loop : 0.21 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 135 TYR 0.029 0.003 TYR D 184 PHE 0.016 0.002 PHE A 169 TRP 0.017 0.003 TRP A 546 HIS 0.009 0.002 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00558 (11899) covalent geometry : angle 0.68018 (16176) SS BOND : bond 0.00393 ( 1) SS BOND : angle 3.10361 ( 2) hydrogen bonds : bond 0.06087 ( 528) hydrogen bonds : angle 5.10685 ( 1473) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7201 (pt0) cc_final: 0.6884 (pt0) REVERT: A 327 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7847 (pt0) REVERT: A 338 ARG cc_start: 0.8061 (mtp-110) cc_final: 0.7599 (mtt90) REVERT: A 369 MET cc_start: 0.9110 (mmp) cc_final: 0.8516 (mmp) REVERT: A 784 VAL cc_start: 0.9281 (t) cc_final: 0.8999 (t) REVERT: B 221 MET cc_start: 0.8638 (mmm) cc_final: 0.8225 (mmm) REVERT: B 355 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7525 (ptt180) REVERT: D 199 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8717 (tt0) outliers start: 27 outliers final: 13 residues processed: 220 average time/residue: 0.6534 time to fit residues: 154.8394 Evaluate side-chains 202 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 98 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 1 optimal weight: 40.0000 chunk 58 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 96 optimal weight: 0.0670 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 135 optimal weight: 0.8980 chunk 10 optimal weight: 30.0000 chunk 45 optimal weight: 0.2980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN A 506 ASN A 523 ASN B 175 ASN D 70 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.165311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.125823 restraints weight = 12240.112| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.02 r_work: 0.2970 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11900 Z= 0.108 Angle : 0.512 5.437 16178 Z= 0.282 Chirality : 0.043 0.145 1769 Planarity : 0.004 0.045 2133 Dihedral : 4.617 20.061 1634 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.16 % Allowed : 11.06 % Favored : 86.78 % 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: 1.39 (0.22), residues: 1479 helix: 2.20 (0.28), residues: 325 sheet: 1.08 (0.23), residues: 465 loop : 0.27 (0.25), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 634 TYR 0.022 0.001 TYR D 184 PHE 0.013 0.001 PHE A 169 TRP 0.013 0.002 TRP B 228 HIS 0.004 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00228 (11899) covalent geometry : angle 0.51090 (16176) SS BOND : bond 0.00434 ( 1) SS BOND : angle 3.22901 ( 2) hydrogen bonds : bond 0.04250 ( 528) hydrogen bonds : angle 4.57828 ( 1473) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7391 (pt0) cc_final: 0.7074 (pt0) REVERT: A 212 ARG cc_start: 0.8062 (mtm180) cc_final: 0.7540 (mtm180) REVERT: A 327 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7894 (pt0) REVERT: A 338 ARG cc_start: 0.8208 (mtp-110) cc_final: 0.7739 (mtm-85) REVERT: A 369 MET cc_start: 0.9115 (mmp) cc_final: 0.8681 (mmp) REVERT: A 466 GLN cc_start: 0.7049 (tt0) cc_final: 0.6530 (mm110) REVERT: A 784 VAL cc_start: 0.9244 (t) cc_final: 0.8973 (t) REVERT: B 221 MET cc_start: 0.8750 (mmm) cc_final: 0.8300 (mmm) REVERT: B 355 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7613 (ptt180) REVERT: C 81 ASP cc_start: 0.8951 (t0) cc_final: 0.8658 (t70) REVERT: D 165 LYS cc_start: 0.8818 (mmtt) cc_final: 0.8581 (mmmt) outliers start: 27 outliers final: 12 residues processed: 204 average time/residue: 0.6590 time to fit residues: 144.5040 Evaluate side-chains 197 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 183 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 98 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 74 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN A 441 GLN A 523 ASN A 731 ASN B 175 ASN B 229 GLN D 41 GLN D 70 GLN D 72 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.162294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.126907 restraints weight = 12206.100| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.08 r_work: 0.3046 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11900 Z= 0.203 Angle : 0.612 6.154 16178 Z= 0.335 Chirality : 0.047 0.153 1769 Planarity : 0.005 0.059 2133 Dihedral : 4.998 25.858 1634 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.32 % Allowed : 12.42 % Favored : 85.26 % 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: 1.23 (0.22), residues: 1479 helix: 2.07 (0.28), residues: 325 sheet: 0.99 (0.23), residues: 470 loop : 0.16 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 135 TYR 0.027 0.002 TYR D 184 PHE 0.012 0.002 PHE A 169 TRP 0.017 0.002 TRP A 546 HIS 0.016 0.002 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00473 (11899) covalent geometry : angle 0.61108 (16176) SS BOND : bond 0.00664 ( 1) SS BOND : angle 3.74364 ( 2) hydrogen bonds : bond 0.05529 ( 528) hydrogen bonds : angle 4.82412 ( 1473) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7202 (pt0) cc_final: 0.6900 (pt0) REVERT: A 328 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.9125 (mm) REVERT: A 369 MET cc_start: 0.9095 (mmp) cc_final: 0.8685 (mmp) REVERT: A 466 GLN cc_start: 0.6897 (tt0) cc_final: 0.6444 (mm110) REVERT: A 622 ASP cc_start: 0.7487 (t0) cc_final: 0.6978 (t70) REVERT: A 784 VAL cc_start: 0.9295 (t) cc_final: 0.8991 (t) REVERT: B 221 MET cc_start: 0.8795 (mmm) cc_final: 0.8381 (mmm) REVERT: B 355 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7507 (ptt180) REVERT: C 81 ASP cc_start: 0.8917 (t0) cc_final: 0.8643 (t70) REVERT: D 199 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8738 (tt0) outliers start: 29 outliers final: 19 residues processed: 200 average time/residue: 0.6857 time to fit residues: 147.0427 Evaluate side-chains 205 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 98 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 109 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN A 538 ASN D 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.161516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.125843 restraints weight = 12053.557| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.09 r_work: 0.3016 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 11900 Z= 0.251 Angle : 0.668 7.027 16178 Z= 0.364 Chirality : 0.049 0.163 1769 Planarity : 0.006 0.063 2133 Dihedral : 5.180 25.543 1634 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.29 % Allowed : 12.90 % Favored : 83.81 % 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: 1.04 (0.22), residues: 1479 helix: 1.88 (0.28), residues: 326 sheet: 0.90 (0.23), residues: 475 loop : 0.03 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 135 TYR 0.029 0.003 TYR D 184 PHE 0.013 0.002 PHE A 675 TRP 0.019 0.003 TRP A 546 HIS 0.022 0.002 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00589 (11899) covalent geometry : angle 0.66682 (16176) SS BOND : bond 0.00849 ( 1) SS BOND : angle 4.18217 ( 2) hydrogen bonds : bond 0.05895 ( 528) hydrogen bonds : angle 4.94349 ( 1473) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 0.475 Fit side-chains REVERT: A 176 GLU cc_start: 0.7277 (pt0) cc_final: 0.6948 (pt0) REVERT: A 212 ARG cc_start: 0.8139 (mtm180) cc_final: 0.7549 (mtm180) REVERT: A 237 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.7862 (mtp180) REVERT: A 327 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7571 (pt0) REVERT: A 328 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9123 (mm) REVERT: A 338 ARG cc_start: 0.8129 (mtp-110) cc_final: 0.7499 (mtm-85) REVERT: A 369 MET cc_start: 0.9107 (mmp) cc_final: 0.8687 (mmp) REVERT: A 466 GLN cc_start: 0.7023 (tt0) cc_final: 0.6571 (mm110) REVERT: A 784 VAL cc_start: 0.9291 (t) cc_final: 0.8991 (t) REVERT: B 221 MET cc_start: 0.8827 (mmm) cc_final: 0.8472 (mmm) REVERT: B 355 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7537 (ptt180) REVERT: C 81 ASP cc_start: 0.8929 (t0) cc_final: 0.8648 (t70) REVERT: D 199 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8774 (tt0) outliers start: 41 outliers final: 20 residues processed: 210 average time/residue: 0.6747 time to fit residues: 152.4040 Evaluate side-chains 211 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 98 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 33 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 132 optimal weight: 0.5980 chunk 137 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 136 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN D 41 GLN D 70 GLN D 228 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.164454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.125636 restraints weight = 12115.771| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.63 r_work: 0.2940 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11900 Z= 0.124 Angle : 0.542 8.652 16178 Z= 0.294 Chirality : 0.044 0.216 1769 Planarity : 0.004 0.047 2133 Dihedral : 4.668 20.818 1634 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.48 % Allowed : 13.38 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.27 (0.22), residues: 1479 helix: 2.20 (0.28), residues: 325 sheet: 1.02 (0.24), residues: 460 loop : 0.14 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 135 TYR 0.023 0.002 TYR D 184 PHE 0.010 0.001 PHE A 738 TRP 0.014 0.002 TRP B 228 HIS 0.007 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00273 (11899) covalent geometry : angle 0.53928 (16176) SS BOND : bond 0.00744 ( 1) SS BOND : angle 4.43576 ( 2) hydrogen bonds : bond 0.04372 ( 528) hydrogen bonds : angle 4.57431 ( 1473) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7376 (pt0) cc_final: 0.7005 (pt0) REVERT: A 212 ARG cc_start: 0.8149 (mtm180) cc_final: 0.7550 (mtm180) REVERT: A 237 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.7795 (mtp180) REVERT: A 267 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7686 (mtmt) REVERT: A 328 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.9068 (mm) REVERT: A 338 ARG cc_start: 0.8231 (mtp-110) cc_final: 0.7618 (mtm-85) REVERT: A 369 MET cc_start: 0.9094 (mmp) cc_final: 0.8625 (mmp) REVERT: A 466 GLN cc_start: 0.7108 (tt0) cc_final: 0.6668 (mm110) REVERT: A 471 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8399 (tt) REVERT: A 624 ASP cc_start: 0.8746 (m-30) cc_final: 0.8425 (m-30) REVERT: A 784 VAL cc_start: 0.9292 (t) cc_final: 0.8971 (t) REVERT: B 221 MET cc_start: 0.8951 (mmm) cc_final: 0.8512 (mmm) REVERT: B 355 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7655 (ptt180) REVERT: C 81 ASP cc_start: 0.8968 (t0) cc_final: 0.8661 (t70) REVERT: D 94 ARG cc_start: 0.8231 (ttp-170) cc_final: 0.7799 (ttt180) REVERT: D 165 LYS cc_start: 0.8915 (mmtt) cc_final: 0.8694 (mmmt) outliers start: 31 outliers final: 14 residues processed: 204 average time/residue: 0.7012 time to fit residues: 153.4028 Evaluate side-chains 204 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 98 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 64 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 89 optimal weight: 0.5980 chunk 73 optimal weight: 0.2980 chunk 11 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN D 41 GLN D 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.163369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.123760 restraints weight = 12110.708| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.80 r_work: 0.2945 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11900 Z= 0.148 Angle : 0.569 6.294 16178 Z= 0.309 Chirality : 0.045 0.153 1769 Planarity : 0.005 0.050 2133 Dihedral : 4.745 22.480 1634 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.72 % Allowed : 13.46 % Favored : 83.81 % 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: 1.33 (0.22), residues: 1479 helix: 2.19 (0.28), residues: 325 sheet: 1.05 (0.23), residues: 476 loop : 0.20 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 634 TYR 0.024 0.002 TYR D 184 PHE 0.010 0.001 PHE A 675 TRP 0.014 0.002 TRP A 546 HIS 0.010 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00336 (11899) covalent geometry : angle 0.56622 (16176) SS BOND : bond 0.00708 ( 1) SS BOND : angle 4.87952 ( 2) hydrogen bonds : bond 0.04777 ( 528) hydrogen bonds : angle 4.62974 ( 1473) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7481 (pt0) cc_final: 0.7122 (pt0) REVERT: A 237 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.7860 (mtp180) REVERT: A 267 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7729 (mtmt) REVERT: A 268 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8528 (tt) REVERT: A 327 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7668 (pt0) REVERT: A 328 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.9070 (mm) REVERT: A 338 ARG cc_start: 0.8239 (mtp-110) cc_final: 0.7652 (mtm-85) REVERT: A 369 MET cc_start: 0.9078 (mmp) cc_final: 0.8664 (mmp) REVERT: A 466 GLN cc_start: 0.7128 (tt0) cc_final: 0.6746 (mm110) REVERT: A 471 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8424 (tt) REVERT: A 539 MET cc_start: 0.8889 (mtm) cc_final: 0.8640 (mtp) REVERT: A 624 ASP cc_start: 0.8740 (m-30) cc_final: 0.8466 (m-30) REVERT: A 784 VAL cc_start: 0.9296 (t) cc_final: 0.8976 (t) REVERT: B 221 MET cc_start: 0.8964 (mmm) cc_final: 0.8555 (mmm) REVERT: B 282 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8265 (mp0) REVERT: B 355 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7673 (ptt180) REVERT: C 81 ASP cc_start: 0.8938 (t0) cc_final: 0.8639 (t70) REVERT: E 24 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7431 (mm-30) outliers start: 34 outliers final: 19 residues processed: 203 average time/residue: 0.6992 time to fit residues: 152.3315 Evaluate side-chains 210 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 98 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 36 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 0 optimal weight: 60.0000 chunk 108 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN D 41 GLN D 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.161739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.126814 restraints weight = 12091.566| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.12 r_work: 0.3034 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11900 Z= 0.233 Angle : 0.660 7.791 16178 Z= 0.358 Chirality : 0.048 0.160 1769 Planarity : 0.005 0.055 2133 Dihedral : 5.052 25.619 1634 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.72 % Allowed : 14.02 % Favored : 83.25 % 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: 1.16 (0.22), residues: 1479 helix: 2.00 (0.28), residues: 325 sheet: 0.96 (0.23), residues: 477 loop : 0.10 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 135 TYR 0.029 0.003 TYR D 184 PHE 0.013 0.002 PHE A 675 TRP 0.020 0.002 TRP A 546 HIS 0.017 0.002 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00545 (11899) covalent geometry : angle 0.65615 (16176) SS BOND : bond 0.00965 ( 1) SS BOND : angle 6.09435 ( 2) hydrogen bonds : bond 0.05654 ( 528) hydrogen bonds : angle 4.86442 ( 1473) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7230 (pt0) cc_final: 0.6903 (pt0) REVERT: A 237 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.7880 (mtp180) REVERT: A 267 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7700 (mtmt) REVERT: A 328 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.9034 (mm) REVERT: A 338 ARG cc_start: 0.8136 (mtp-110) cc_final: 0.7503 (mtm-85) REVERT: A 369 MET cc_start: 0.9038 (mmp) cc_final: 0.8599 (mmp) REVERT: A 466 GLN cc_start: 0.6930 (tt0) cc_final: 0.6541 (mm110) REVERT: A 624 ASP cc_start: 0.8468 (m-30) cc_final: 0.8248 (m-30) REVERT: A 784 VAL cc_start: 0.9291 (t) cc_final: 0.8978 (t) REVERT: B 221 MET cc_start: 0.8905 (mmm) cc_final: 0.8470 (mmm) REVERT: B 282 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8252 (mp0) REVERT: B 355 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7483 (ptt180) REVERT: C 81 ASP cc_start: 0.8904 (t0) cc_final: 0.8606 (t70) outliers start: 34 outliers final: 22 residues processed: 201 average time/residue: 0.7142 time to fit residues: 153.8648 Evaluate side-chains 211 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 98 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 67 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 145 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 2 optimal weight: 50.0000 chunk 50 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN B 223 GLN D 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.163811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.124129 restraints weight = 12110.503| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.82 r_work: 0.2952 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11900 Z= 0.135 Angle : 0.561 7.587 16178 Z= 0.304 Chirality : 0.044 0.153 1769 Planarity : 0.004 0.048 2133 Dihedral : 4.685 21.566 1634 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.40 % Allowed : 14.98 % Favored : 82.61 % 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: 1.29 (0.22), residues: 1479 helix: 2.18 (0.28), residues: 325 sheet: 1.04 (0.23), residues: 465 loop : 0.16 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 634 TYR 0.024 0.002 TYR D 184 PHE 0.010 0.001 PHE A 738 TRP 0.015 0.002 TRP B 228 HIS 0.008 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00305 (11899) covalent geometry : angle 0.55886 (16176) SS BOND : bond 0.00631 ( 1) SS BOND : angle 4.51101 ( 2) hydrogen bonds : bond 0.04533 ( 528) hydrogen bonds : angle 4.61259 ( 1473) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7487 (pt0) cc_final: 0.7115 (pt0) REVERT: A 237 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.7811 (mtp180) REVERT: A 267 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7711 (mtmt) REVERT: A 327 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7639 (pt0) REVERT: A 328 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.9051 (mm) REVERT: A 338 ARG cc_start: 0.8288 (mtp-110) cc_final: 0.7665 (mtm-85) REVERT: A 369 MET cc_start: 0.9075 (mmp) cc_final: 0.8671 (mmp) REVERT: A 466 GLN cc_start: 0.7107 (tt0) cc_final: 0.6711 (mm110) REVERT: A 471 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8438 (tt) REVERT: A 784 VAL cc_start: 0.9287 (t) cc_final: 0.8969 (t) REVERT: B 221 MET cc_start: 0.8954 (mmm) cc_final: 0.8556 (mmm) REVERT: B 282 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8340 (mp0) REVERT: B 355 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7657 (ptt180) REVERT: C 81 ASP cc_start: 0.8964 (t0) cc_final: 0.8691 (t70) REVERT: D 165 LYS cc_start: 0.8962 (mmtt) cc_final: 0.8735 (mmmt) outliers start: 30 outliers final: 18 residues processed: 200 average time/residue: 0.7214 time to fit residues: 154.5758 Evaluate side-chains 206 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 98 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 58 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 89 optimal weight: 0.2980 chunk 53 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN D 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.163643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.124082 restraints weight = 12186.793| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.96 r_work: 0.2944 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11900 Z= 0.142 Angle : 0.582 8.346 16178 Z= 0.313 Chirality : 0.044 0.147 1769 Planarity : 0.004 0.048 2133 Dihedral : 4.714 21.913 1634 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.16 % Allowed : 15.38 % Favored : 82.45 % 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: 1.31 (0.22), residues: 1479 helix: 2.20 (0.28), residues: 325 sheet: 0.96 (0.23), residues: 473 loop : 0.23 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 321 TYR 0.024 0.002 TYR D 184 PHE 0.010 0.001 PHE A 738 TRP 0.013 0.002 TRP A 546 HIS 0.009 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00324 (11899) covalent geometry : angle 0.57786 (16176) SS BOND : bond 0.00864 ( 1) SS BOND : angle 6.24714 ( 2) hydrogen bonds : bond 0.04641 ( 528) hydrogen bonds : angle 4.61290 ( 1473) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7443 (pt0) cc_final: 0.7114 (pt0) REVERT: A 237 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.7862 (mtp180) REVERT: A 267 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7711 (mtmt) REVERT: A 327 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7578 (pt0) REVERT: A 328 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.9049 (mm) REVERT: A 338 ARG cc_start: 0.8260 (mtp-110) cc_final: 0.7636 (mtm-85) REVERT: A 369 MET cc_start: 0.9081 (mmp) cc_final: 0.8676 (mmp) REVERT: A 466 GLN cc_start: 0.7096 (tt0) cc_final: 0.6702 (mm110) REVERT: A 471 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8449 (tt) REVERT: A 539 MET cc_start: 0.8845 (mtm) cc_final: 0.8562 (mtp) REVERT: A 784 VAL cc_start: 0.9284 (t) cc_final: 0.8977 (t) REVERT: B 221 MET cc_start: 0.8962 (mmm) cc_final: 0.8557 (mmm) REVERT: B 282 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8328 (mp0) REVERT: B 355 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7646 (ptt180) REVERT: C 81 ASP cc_start: 0.8954 (t0) cc_final: 0.8684 (t70) REVERT: D 152 ARG cc_start: 0.8345 (ptp90) cc_final: 0.7822 (mtt-85) REVERT: D 165 LYS cc_start: 0.8982 (mmtt) cc_final: 0.8748 (mmmt) outliers start: 27 outliers final: 20 residues processed: 198 average time/residue: 0.7151 time to fit residues: 151.7525 Evaluate side-chains 207 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 98 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 94 optimal weight: 0.0870 chunk 15 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 144 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 129 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN D 41 GLN D 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.164712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.125288 restraints weight = 12192.600| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.90 r_work: 0.2979 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11900 Z= 0.116 Angle : 0.549 8.661 16178 Z= 0.296 Chirality : 0.044 0.165 1769 Planarity : 0.004 0.045 2133 Dihedral : 4.562 20.350 1634 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.08 % Allowed : 15.54 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.36 (0.22), residues: 1479 helix: 2.31 (0.28), residues: 325 sheet: 0.98 (0.23), residues: 468 loop : 0.24 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 634 TYR 0.022 0.001 TYR D 184 PHE 0.008 0.001 PHE A 738 TRP 0.016 0.002 TRP B 228 HIS 0.006 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00259 (11899) covalent geometry : angle 0.54554 (16176) SS BOND : bond 0.00666 ( 1) SS BOND : angle 5.49748 ( 2) hydrogen bonds : bond 0.04226 ( 528) hydrogen bonds : angle 4.50141 ( 1473) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5393.22 seconds wall clock time: 92 minutes 23.86 seconds (5543.86 seconds total)