Starting phenix.real_space_refine on Wed Jun 11 00:20:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cnw_45764/06_2025/9cnw_45764.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cnw_45764/06_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_45764/06_2025/9cnw_45764.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cnw_45764/06_2025/9cnw_45764.map" model { file = "/net/cci-nas-00/data/ceres_data/9cnw_45764/06_2025/9cnw_45764.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cnw_45764/06_2025/9cnw_45764.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.041 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.34, per 1000 atoms: 0.63 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: 2.86 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.97 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: 4.46 Time building geometry restraints manager: 3.45 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.300 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:13.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.880 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (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 TRP 0.011 0.002 TRP A 376 HIS 0.006 0.001 HIS A 533 PHE 0.032 0.002 PHE A 238 TYR 0.024 0.002 TYR D 184 ARG 0.003 0.001 ARG D 203 Details of bonding type rmsd hydrogen bonds : bond 0.17009 ( 528) hydrogen bonds : angle 6.48466 ( 1473) SS BOND : bond 0.00167 ( 1) SS BOND : angle 3.25289 ( 2) covalent geometry : bond 0.00306 (11899) covalent geometry : angle 0.57642 (16176) *********************** 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 : 1.178 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: 1.2616 time to fit residues: 329.0613 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 : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 286 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.162307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.127045 restraints weight = 11952.602| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.07 r_work: 0.3042 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11900 Z= 0.230 Angle : 0.673 6.748 16178 Z= 0.368 Chirality : 0.049 0.165 1769 Planarity : 0.006 0.074 2133 Dihedral : 5.270 26.258 1634 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.24 % Allowed : 8.65 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.22), residues: 1479 helix: 1.79 (0.28), residues: 325 sheet: 0.99 (0.23), residues: 466 loop : 0.22 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 546 HIS 0.009 0.002 HIS A 533 PHE 0.016 0.002 PHE A 169 TYR 0.029 0.003 TYR D 184 ARG 0.006 0.001 ARG A 367 Details of bonding type rmsd hydrogen bonds : bond 0.05972 ( 528) hydrogen bonds : angle 5.07637 ( 1473) SS BOND : bond 0.00275 ( 1) SS BOND : angle 3.01324 ( 2) covalent geometry : bond 0.00537 (11899) covalent geometry : angle 0.67194 (16176) *********************** 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 229 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 1.392 Fit side-chains REVERT: A 176 GLU cc_start: 0.7199 (pt0) cc_final: 0.6894 (pt0) REVERT: A 327 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7819 (pt0) REVERT: A 338 ARG cc_start: 0.8049 (mtp-110) cc_final: 0.7560 (ttm-80) REVERT: A 369 MET cc_start: 0.9108 (mmp) cc_final: 0.8499 (mmp) REVERT: A 784 VAL cc_start: 0.9277 (t) cc_final: 0.8992 (t) REVERT: B 197 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8475 (mm-30) REVERT: B 221 MET cc_start: 0.8627 (mmm) cc_final: 0.8208 (mmm) REVERT: B 355 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7499 (ptt180) REVERT: D 160 THR cc_start: 0.9060 (m) cc_final: 0.8855 (p) REVERT: D 164 THR cc_start: 0.9453 (m) cc_final: 0.9225 (m) REVERT: D 199 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8726 (tt0) outliers start: 28 outliers final: 14 residues processed: 219 average time/residue: 1.5408 time to fit residues: 364.0849 Evaluate side-chains 209 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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 755 SER 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 35 optimal weight: 0.5980 chunk 138 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.164802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.125426 restraints weight = 12233.407| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.04 r_work: 0.2962 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1675 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= 0.120 Angle : 0.527 5.543 16178 Z= 0.290 Chirality : 0.044 0.147 1769 Planarity : 0.004 0.048 2133 Dihedral : 4.688 21.230 1634 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.16 % Allowed : 11.22 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.22), residues: 1479 helix: 2.16 (0.28), residues: 325 sheet: 1.06 (0.23), residues: 470 loop : 0.26 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 228 HIS 0.005 0.001 HIS A 533 PHE 0.013 0.001 PHE A 169 TYR 0.023 0.002 TYR D 184 ARG 0.003 0.000 ARG A 634 Details of bonding type rmsd hydrogen bonds : bond 0.04467 ( 528) hydrogen bonds : angle 4.62805 ( 1473) SS BOND : bond 0.00549 ( 1) SS BOND : angle 3.06055 ( 2) covalent geometry : bond 0.00261 (11899) covalent geometry : angle 0.52558 (16176) *********************** 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 218 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 1.897 Fit side-chains REVERT: A 176 GLU cc_start: 0.7350 (pt0) cc_final: 0.7028 (pt0) REVERT: A 212 ARG cc_start: 0.8030 (mtm180) cc_final: 0.7485 (mtm180) REVERT: A 267 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7589 (mtmm) REVERT: A 327 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7854 (pt0) REVERT: A 338 ARG cc_start: 0.8192 (mtp-110) cc_final: 0.7635 (ttm-80) REVERT: A 369 MET cc_start: 0.9121 (mmp) cc_final: 0.8697 (mmp) REVERT: A 466 GLN cc_start: 0.6996 (tt0) cc_final: 0.6452 (mm110) REVERT: A 471 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8416 (tt) REVERT: A 784 VAL cc_start: 0.9268 (t) cc_final: 0.8992 (t) REVERT: B 221 MET cc_start: 0.8748 (mmm) cc_final: 0.8278 (mmm) REVERT: B 355 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7611 (ptt180) REVERT: C 81 ASP cc_start: 0.8921 (t0) cc_final: 0.8642 (t70) REVERT: D 165 LYS cc_start: 0.8905 (mmtt) cc_final: 0.8636 (mmmt) outliers start: 27 outliers final: 12 residues processed: 206 average time/residue: 1.6516 time to fit residues: 368.3935 Evaluate side-chains 199 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LYS 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 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 133 SER 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 72 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 20.0000 chunk 93 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 142 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 18 optimal weight: 20.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 D 70 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.164251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.129466 restraints weight = 12143.979| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.11 r_work: 0.3072 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1884 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= 0.133 Angle : 0.535 5.709 16178 Z= 0.293 Chirality : 0.044 0.148 1769 Planarity : 0.004 0.048 2133 Dihedral : 4.656 20.963 1634 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.16 % Allowed : 12.34 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.22), residues: 1479 helix: 2.25 (0.28), residues: 325 sheet: 1.05 (0.23), residues: 466 loop : 0.22 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 546 HIS 0.008 0.001 HIS B 165 PHE 0.012 0.001 PHE A 169 TYR 0.023 0.002 TYR D 184 ARG 0.004 0.000 ARG D 135 Details of bonding type rmsd hydrogen bonds : bond 0.04606 ( 528) hydrogen bonds : angle 4.56765 ( 1473) SS BOND : bond 0.00650 ( 1) SS BOND : angle 3.58068 ( 2) covalent geometry : bond 0.00296 (11899) covalent geometry : angle 0.53351 (16176) *********************** 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 214 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 1.365 Fit side-chains REVERT: A 176 GLU cc_start: 0.7178 (pt0) cc_final: 0.6884 (pt0) REVERT: A 267 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7621 (mtmm) REVERT: A 338 ARG cc_start: 0.8166 (mtp-110) cc_final: 0.7628 (ttm-80) REVERT: A 369 MET cc_start: 0.9063 (mmp) cc_final: 0.8607 (mmp) REVERT: A 466 GLN cc_start: 0.7002 (tt0) cc_final: 0.6496 (mm110) REVERT: A 471 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8396 (tt) REVERT: A 784 VAL cc_start: 0.9272 (t) cc_final: 0.8975 (t) REVERT: B 197 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8405 (mm-30) REVERT: B 221 MET cc_start: 0.8803 (mmm) cc_final: 0.8332 (mmm) REVERT: B 355 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7535 (ptt180) REVERT: C 81 ASP cc_start: 0.8938 (t0) cc_final: 0.8641 (t70) REVERT: D 165 LYS cc_start: 0.8893 (mmtt) cc_final: 0.8677 (mmmt) outliers start: 27 outliers final: 11 residues processed: 203 average time/residue: 1.8255 time to fit residues: 401.2190 Evaluate side-chains 196 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LYS 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 725 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 46 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 53 optimal weight: 0.0070 chunk 20 optimal weight: 0.7980 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN B 229 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 = 0.3806 r_free = 0.3806 target = 0.163920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.124299 restraints weight = 12031.731| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.89 r_work: 0.2943 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2014 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= 0.139 Angle : 0.539 5.751 16178 Z= 0.295 Chirality : 0.044 0.148 1769 Planarity : 0.004 0.047 2133 Dihedral : 4.650 21.055 1634 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.16 % Allowed : 13.46 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.22), residues: 1479 helix: 2.30 (0.28), residues: 324 sheet: 1.04 (0.23), residues: 470 loop : 0.25 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 546 HIS 0.009 0.001 HIS B 165 PHE 0.012 0.001 PHE A 169 TYR 0.024 0.002 TYR D 184 ARG 0.005 0.000 ARG D 135 Details of bonding type rmsd hydrogen bonds : bond 0.04627 ( 528) hydrogen bonds : angle 4.56971 ( 1473) SS BOND : bond 0.00582 ( 1) SS BOND : angle 3.90144 ( 2) covalent geometry : bond 0.00314 (11899) covalent geometry : angle 0.53761 (16176) *********************** 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 214 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7375 (pt0) cc_final: 0.7010 (pt0) REVERT: A 267 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7711 (mtmt) REVERT: A 338 ARG cc_start: 0.8253 (mtp-110) cc_final: 0.7644 (mtm-85) REVERT: A 369 MET cc_start: 0.9084 (mmp) cc_final: 0.8614 (mmp) REVERT: A 466 GLN cc_start: 0.7051 (tt0) cc_final: 0.6575 (mm110) REVERT: A 471 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8467 (tt) REVERT: A 552 MET cc_start: 0.8871 (mmm) cc_final: 0.8432 (mmm) REVERT: A 784 VAL cc_start: 0.9287 (t) cc_final: 0.8984 (t) REVERT: B 221 MET cc_start: 0.8866 (mmm) cc_final: 0.8522 (mmm) REVERT: B 355 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7666 (ptt180) REVERT: C 81 ASP cc_start: 0.8994 (t0) cc_final: 0.8689 (t70) REVERT: D 165 LYS cc_start: 0.8993 (mmtt) cc_final: 0.8767 (mmmt) outliers start: 27 outliers final: 15 residues processed: 202 average time/residue: 1.3065 time to fit residues: 284.7232 Evaluate side-chains 203 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LYS 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 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 C residue 61 THR Chi-restraints excluded: chain D residue 98 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 14 optimal weight: 8.9990 chunk 6 optimal weight: 40.0000 chunk 108 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.163874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.124611 restraints weight = 12159.800| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 3.07 r_work: 0.2956 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2098 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= 0.146 Angle : 0.554 7.798 16178 Z= 0.300 Chirality : 0.044 0.205 1769 Planarity : 0.004 0.047 2133 Dihedral : 4.675 21.815 1634 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.32 % Allowed : 13.62 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.22), residues: 1479 helix: 2.31 (0.28), residues: 324 sheet: 1.03 (0.23), residues: 470 loop : 0.25 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 546 HIS 0.010 0.001 HIS B 165 PHE 0.009 0.001 PHE E 77 TYR 0.024 0.002 TYR D 184 ARG 0.004 0.000 ARG D 135 Details of bonding type rmsd hydrogen bonds : bond 0.04686 ( 528) hydrogen bonds : angle 4.58351 ( 1473) SS BOND : bond 0.00809 ( 1) SS BOND : angle 4.44589 ( 2) covalent geometry : bond 0.00331 (11899) covalent geometry : angle 0.55178 (16176) *********************** 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 219 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7335 (pt0) cc_final: 0.6964 (pt0) REVERT: A 237 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.7812 (mtp180) REVERT: A 267 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7656 (mtmm) REVERT: A 328 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.9104 (mm) REVERT: A 338 ARG cc_start: 0.8168 (mtp-110) cc_final: 0.7680 (ttm110) REVERT: A 369 MET cc_start: 0.9066 (mmp) cc_final: 0.8598 (mmp) REVERT: A 466 GLN cc_start: 0.6973 (tt0) cc_final: 0.6525 (mm110) REVERT: A 471 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8460 (tt) REVERT: A 622 ASP cc_start: 0.7537 (t0) cc_final: 0.7008 (t0) REVERT: A 784 VAL cc_start: 0.9286 (t) cc_final: 0.8971 (t) REVERT: B 197 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8419 (mm-30) REVERT: B 221 MET cc_start: 0.8861 (mmm) cc_final: 0.8501 (mmm) REVERT: B 355 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7583 (ptt180) REVERT: C 81 ASP cc_start: 0.8962 (t0) cc_final: 0.8642 (t70) REVERT: D 165 LYS cc_start: 0.8982 (mmtt) cc_final: 0.8745 (mmmt) outliers start: 29 outliers final: 18 residues processed: 203 average time/residue: 1.4118 time to fit residues: 307.8857 Evaluate side-chains 211 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 583 ARG Chi-restraints excluded: chain A residue 596 THR 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 1 optimal weight: 30.0000 chunk 80 optimal weight: 0.0270 overall best weight: 1.7444 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.162256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.126952 restraints weight = 12194.531| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.10 r_work: 0.3032 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2156 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= 0.226 Angle : 0.648 7.004 16178 Z= 0.351 Chirality : 0.047 0.174 1769 Planarity : 0.005 0.055 2133 Dihedral : 5.024 25.464 1634 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.48 % Allowed : 13.94 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.22), residues: 1479 helix: 2.05 (0.28), residues: 325 sheet: 0.98 (0.23), residues: 477 loop : 0.13 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 546 HIS 0.017 0.002 HIS B 165 PHE 0.012 0.002 PHE A 675 TYR 0.027 0.003 TYR D 184 ARG 0.008 0.001 ARG D 135 Details of bonding type rmsd hydrogen bonds : bond 0.05643 ( 528) hydrogen bonds : angle 4.85455 ( 1473) SS BOND : bond 0.00885 ( 1) SS BOND : angle 5.52095 ( 2) covalent geometry : bond 0.00529 (11899) covalent geometry : angle 0.64509 (16176) *********************** 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 219 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 1.356 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7223 (pt0) cc_final: 0.6871 (pt0) REVERT: A 237 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.7891 (mtp180) REVERT: A 267 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7655 (mtmt) REVERT: A 328 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.9100 (mm) REVERT: A 338 ARG cc_start: 0.8124 (mtp-110) cc_final: 0.7500 (mtm-85) REVERT: A 369 MET cc_start: 0.9095 (mmp) cc_final: 0.8652 (mmp) REVERT: A 466 GLN cc_start: 0.6937 (tt0) cc_final: 0.6552 (mm110) REVERT: A 784 VAL cc_start: 0.9287 (t) cc_final: 0.8983 (t) REVERT: B 221 MET cc_start: 0.8824 (mmm) cc_final: 0.8458 (mmm) REVERT: B 225 GLN cc_start: 0.8598 (mp10) cc_final: 0.8245 (mp10) REVERT: B 355 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7506 (ptt180) REVERT: C 81 ASP cc_start: 0.8921 (t0) cc_final: 0.8614 (t70) outliers start: 31 outliers final: 21 residues processed: 204 average time/residue: 1.3685 time to fit residues: 300.0609 Evaluate side-chains 209 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 1.300 ------------------------------------------------------------------------------- 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 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 596 THR Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain B residue 229 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 73 optimal weight: 0.2980 chunk 100 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.164956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.126346 restraints weight = 12210.040| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.88 r_work: 0.2990 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11900 Z= 0.111 Angle : 0.532 6.892 16178 Z= 0.287 Chirality : 0.043 0.164 1769 Planarity : 0.004 0.045 2133 Dihedral : 4.522 20.177 1634 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.84 % Allowed : 14.82 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.22), residues: 1479 helix: 2.30 (0.28), residues: 325 sheet: 1.06 (0.24), residues: 462 loop : 0.19 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 228 HIS 0.006 0.001 HIS B 165 PHE 0.009 0.001 PHE A 738 TYR 0.022 0.001 TYR D 184 ARG 0.005 0.000 ARG A 634 Details of bonding type rmsd hydrogen bonds : bond 0.04124 ( 528) hydrogen bonds : angle 4.49314 ( 1473) SS BOND : bond 0.00548 ( 1) SS BOND : angle 5.25258 ( 2) covalent geometry : bond 0.00243 (11899) covalent geometry : angle 0.52834 (16176) *********************** 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 204 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7330 (pt0) cc_final: 0.6993 (pt0) REVERT: A 237 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.7788 (mtp180) REVERT: A 267 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7648 (mtmt) REVERT: A 328 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.9090 (mm) REVERT: A 338 ARG cc_start: 0.8173 (mtp-110) cc_final: 0.7648 (ttm110) REVERT: A 369 MET cc_start: 0.9036 (mmp) cc_final: 0.8565 (mmp) REVERT: A 466 GLN cc_start: 0.7029 (tt0) cc_final: 0.6627 (mm110) REVERT: A 471 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8398 (tt) REVERT: A 624 ASP cc_start: 0.8604 (m-30) cc_final: 0.8326 (m-30) REVERT: A 784 VAL cc_start: 0.9265 (t) cc_final: 0.8960 (t) REVERT: B 221 MET cc_start: 0.8878 (mmm) cc_final: 0.8432 (mmm) REVERT: B 355 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7542 (ptt180) REVERT: C 81 ASP cc_start: 0.8929 (t0) cc_final: 0.8621 (t70) REVERT: D 94 ARG cc_start: 0.8149 (ttp-170) cc_final: 0.7739 (ttt180) REVERT: D 165 LYS cc_start: 0.8874 (mmtt) cc_final: 0.8644 (mmmt) outliers start: 23 outliers final: 15 residues processed: 194 average time/residue: 1.3950 time to fit residues: 290.7173 Evaluate side-chains 201 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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 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 628 VAL Chi-restraints excluded: chain A residue 725 ILE 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 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 36 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 2 optimal weight: 50.0000 chunk 52 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 128 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 B 229 GLN B 302 ASN D 70 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.162068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.126661 restraints weight = 12143.305| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.15 r_work: 0.3021 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11900 Z= 0.232 Angle : 0.657 7.196 16178 Z= 0.356 Chirality : 0.048 0.160 1769 Planarity : 0.005 0.076 2133 Dihedral : 5.025 28.068 1634 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.24 % Allowed : 14.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.22), residues: 1479 helix: 2.03 (0.28), residues: 325 sheet: 1.00 (0.23), residues: 475 loop : 0.15 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 546 HIS 0.018 0.002 HIS B 165 PHE 0.013 0.002 PHE A 675 TYR 0.028 0.003 TYR D 184 ARG 0.014 0.001 ARG A 634 Details of bonding type rmsd hydrogen bonds : bond 0.05671 ( 528) hydrogen bonds : angle 4.84514 ( 1473) SS BOND : bond 0.00914 ( 1) SS BOND : angle 5.48291 ( 2) covalent geometry : bond 0.00543 (11899) covalent geometry : angle 0.65420 (16176) *********************** 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 212 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 1.341 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7236 (pt0) cc_final: 0.6963 (pt0) REVERT: A 237 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.7840 (mtp180) REVERT: A 267 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7718 (mtmt) REVERT: A 328 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.9138 (mm) REVERT: A 338 ARG cc_start: 0.8176 (mtp-110) cc_final: 0.7545 (mtm-85) REVERT: A 369 MET cc_start: 0.9073 (mmp) cc_final: 0.8629 (mmp) REVERT: A 466 GLN cc_start: 0.6968 (tt0) cc_final: 0.6588 (mm110) REVERT: A 624 ASP cc_start: 0.8545 (m-30) cc_final: 0.8320 (m-30) REVERT: A 784 VAL cc_start: 0.9289 (t) cc_final: 0.8990 (t) REVERT: B 197 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8507 (mm-30) REVERT: B 221 MET cc_start: 0.8865 (mmm) cc_final: 0.8519 (mmm) REVERT: B 355 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7522 (ptt180) REVERT: C 81 ASP cc_start: 0.8928 (t0) cc_final: 0.8629 (t70) outliers start: 28 outliers final: 20 residues processed: 200 average time/residue: 1.3483 time to fit residues: 289.8807 Evaluate side-chains 207 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 1.179 ------------------------------------------------------------------------------- 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 459 ASN 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 596 THR 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 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 98 LEU Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 160 THR 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 58 optimal weight: 1.9990 chunk 116 optimal weight: 0.0050 chunk 27 optimal weight: 4.9990 chunk 22 optimal weight: 0.0770 chunk 36 optimal weight: 0.9990 chunk 53 optimal weight: 0.0170 chunk 43 optimal weight: 0.9980 chunk 44 optimal weight: 0.2980 chunk 145 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN B 350 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 = 0.3848 r_free = 0.3848 target = 0.167762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.129183 restraints weight = 12196.014| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.71 r_work: 0.3046 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11900 Z= 0.094 Angle : 0.510 7.765 16178 Z= 0.273 Chirality : 0.042 0.141 1769 Planarity : 0.004 0.045 2133 Dihedral : 4.222 19.375 1634 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.52 % Allowed : 15.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.22), residues: 1479 helix: 2.44 (0.28), residues: 325 sheet: 1.15 (0.24), residues: 447 loop : 0.28 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 228 HIS 0.003 0.000 HIS B 324 PHE 0.008 0.001 PHE A 738 TYR 0.021 0.001 TYR D 184 ARG 0.010 0.000 ARG A 634 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 528) hydrogen bonds : angle 4.32180 ( 1473) SS BOND : bond 0.00037 ( 1) SS BOND : angle 5.38351 ( 2) covalent geometry : bond 0.00203 (11899) covalent geometry : angle 0.50666 (16176) ********************** 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: 19 poor density : 191 time to evaluate : 3.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7381 (pt0) cc_final: 0.7056 (pt0) REVERT: A 267 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7672 (mtmt) REVERT: A 338 ARG cc_start: 0.8289 (mtp-110) cc_final: 0.7765 (ttm110) REVERT: A 369 MET cc_start: 0.9016 (mmp) cc_final: 0.8477 (mmp) REVERT: A 466 GLN cc_start: 0.7118 (tt0) cc_final: 0.6714 (mm110) REVERT: A 471 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8436 (tt) REVERT: A 634 ARG cc_start: 0.9158 (ttt90) cc_final: 0.8926 (ttt90) REVERT: A 784 VAL cc_start: 0.9202 (t) cc_final: 0.8919 (t) REVERT: B 197 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8503 (mm-30) REVERT: B 221 MET cc_start: 0.8924 (mmm) cc_final: 0.8527 (mmm) REVERT: B 355 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7676 (ptt180) REVERT: C 81 ASP cc_start: 0.8992 (t0) cc_final: 0.8685 (t70) REVERT: D 152 ARG cc_start: 0.8288 (ptp90) cc_final: 0.7798 (mtt-85) REVERT: E 103 ASN cc_start: 0.8664 (t0) cc_final: 0.8418 (t0) outliers start: 19 outliers final: 11 residues processed: 200 average time/residue: 1.6641 time to fit residues: 360.6067 Evaluate side-chains 193 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 725 ILE 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 98 LEU 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 140 optimal weight: 0.5980 chunk 90 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN A 459 ASN A 678 GLN D 70 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.163595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.127272 restraints weight = 12048.739| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.06 r_work: 0.3079 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2370 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= 0.129 Angle : 0.563 9.592 16178 Z= 0.301 Chirality : 0.044 0.143 1769 Planarity : 0.004 0.060 2133 Dihedral : 4.486 20.728 1634 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.36 % Allowed : 16.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.22), residues: 1479 helix: 2.38 (0.28), residues: 325 sheet: 1.10 (0.24), residues: 460 loop : 0.31 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 228 HIS 0.009 0.001 HIS B 165 PHE 0.010 0.001 PHE A 675 TYR 0.022 0.002 TYR D 184 ARG 0.012 0.000 ARG A 634 Details of bonding type rmsd hydrogen bonds : bond 0.04333 ( 528) hydrogen bonds : angle 4.43551 ( 1473) SS BOND : bond 0.00742 ( 1) SS BOND : angle 5.69132 ( 2) covalent geometry : bond 0.00292 (11899) covalent geometry : angle 0.55940 (16176) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11615.26 seconds wall clock time: 206 minutes 34.51 seconds (12394.51 seconds total)