Starting phenix.real_space_refine on Mon Dec 30 04:38:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cnw_45764/12_2024/9cnw_45764.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cnw_45764/12_2024/9cnw_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_45764/12_2024/9cnw_45764.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cnw_45764/12_2024/9cnw_45764.map" model { file = "/net/cci-nas-00/data/ceres_data/9cnw_45764/12_2024/9cnw_45764.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cnw_45764/12_2024/9cnw_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 6.95, per 1000 atoms: 0.60 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: 2.89 Conformation dependent library (CDL) restraints added in 1.8 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: 1.57 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: 4.35 Time building geometry restraints manager: 3.37 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 29.850 Find NCS groups from input model: 0.120 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:12.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.450 ------------------------------------------------------------------------------- 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 11899 Z= 0.192 Angle : 0.576 6.479 16176 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 *********************** 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 : 1.437 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: 1.3771 time to fit residues: 359.9692 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 : 1.639 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 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 11899 Z= 0.349 Angle : 0.672 6.748 16176 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 *********************** 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 : 1.263 Fit side-chains REVERT: A 338 ARG cc_start: 0.7591 (mtp-110) cc_final: 0.7323 (ttm-80) REVERT: A 369 MET cc_start: 0.8932 (mmp) cc_final: 0.8313 (mmp) REVERT: A 784 VAL cc_start: 0.9253 (t) cc_final: 0.8979 (t) REVERT: B 197 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8223 (mm-30) REVERT: B 221 MET cc_start: 0.8409 (mmm) cc_final: 0.7961 (mmm) REVERT: B 355 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6886 (ptt180) REVERT: D 160 THR cc_start: 0.8904 (m) cc_final: 0.8672 (p) REVERT: D 164 THR cc_start: 0.9379 (m) cc_final: 0.9116 (m) REVERT: D 199 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7986 (tt0) outliers start: 28 outliers final: 14 residues processed: 219 average time/residue: 1.3521 time to fit residues: 319.1892 Evaluate side-chains 209 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 73 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 110 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 143 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 131 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 B 175 ASN D 70 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11899 Z= 0.211 Angle : 0.557 5.856 16176 Z= 0.307 Chirality : 0.045 0.151 1769 Planarity : 0.004 0.050 2133 Dihedral : 4.837 21.392 1634 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.40 % Allowed : 11.06 % Favored : 86.54 % 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: 1.28 (0.22), residues: 1479 helix: 2.06 (0.28), residues: 325 sheet: 1.03 (0.23), residues: 470 loop : 0.21 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 546 HIS 0.006 0.001 HIS B 165 PHE 0.013 0.002 PHE A 169 TYR 0.025 0.002 TYR D 184 ARG 0.005 0.000 ARG D 135 *********************** 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: 30 poor density : 188 time to evaluate : 1.332 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.6755 (pt0) cc_final: 0.6164 (pt0) REVERT: A 212 ARG cc_start: 0.7980 (mtm180) cc_final: 0.7216 (mtm180) REVERT: A 267 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7639 (mtmm) REVERT: A 327 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7229 (pt0) REVERT: A 328 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.9102 (mm) REVERT: A 338 ARG cc_start: 0.7612 (mtp-110) cc_final: 0.7193 (ttm110) REVERT: A 369 MET cc_start: 0.8924 (mmp) cc_final: 0.8515 (mmp) REVERT: A 466 GLN cc_start: 0.6812 (tt0) cc_final: 0.6441 (mm110) REVERT: A 471 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8221 (tt) REVERT: A 784 VAL cc_start: 0.9236 (t) cc_final: 0.8961 (t) REVERT: B 221 MET cc_start: 0.8469 (mmm) cc_final: 0.7967 (mmm) REVERT: B 355 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6848 (ptt180) REVERT: C 81 ASP cc_start: 0.8652 (t0) cc_final: 0.8447 (t70) REVERT: D 164 THR cc_start: 0.9186 (m) cc_final: 0.8937 (m) outliers start: 30 outliers final: 14 residues processed: 206 average time/residue: 1.3688 time to fit residues: 303.6848 Evaluate side-chains 202 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 1.342 ------------------------------------------------------------------------------- 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 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 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 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 131 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 506 ASN D 70 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11899 Z= 0.185 Angle : 0.530 5.633 16176 Z= 0.290 Chirality : 0.044 0.149 1769 Planarity : 0.004 0.048 2133 Dihedral : 4.656 21.056 1634 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.24 % Allowed : 12.26 % 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: 1.38 (0.22), residues: 1479 helix: 2.25 (0.28), residues: 325 sheet: 1.07 (0.23), residues: 470 loop : 0.23 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 546 HIS 0.007 0.001 HIS B 165 PHE 0.012 0.001 PHE A 169 TYR 0.023 0.002 TYR D 184 ARG 0.006 0.000 ARG D 135 *********************** 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 218 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.6556 (pt0) cc_final: 0.5921 (pt0) REVERT: A 212 ARG cc_start: 0.7976 (mtm180) cc_final: 0.7173 (mtm180) REVERT: A 267 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7627 (mtmm) REVERT: A 369 MET cc_start: 0.8893 (mmp) cc_final: 0.8455 (mmp) REVERT: A 466 GLN cc_start: 0.6800 (tt0) cc_final: 0.6445 (mm110) REVERT: A 471 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8269 (tt) REVERT: A 784 VAL cc_start: 0.9233 (t) cc_final: 0.8963 (t) REVERT: B 197 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8167 (mm-30) REVERT: B 221 MET cc_start: 0.8572 (mmm) cc_final: 0.8077 (mmm) REVERT: B 355 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6872 (ptt180) REVERT: C 81 ASP cc_start: 0.8682 (t0) cc_final: 0.8449 (t70) outliers start: 28 outliers final: 12 residues processed: 204 average time/residue: 1.3933 time to fit residues: 306.6202 Evaluate side-chains 200 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 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 355 ARG Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain C residue 61 THR 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 117 optimal weight: 0.6980 chunk 80 optimal weight: 0.0970 chunk 2 optimal weight: 40.0000 chunk 105 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 chunk 72 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- 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 B 175 ASN B 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11899 Z= 0.299 Angle : 0.607 6.416 16176 Z= 0.331 Chirality : 0.046 0.155 1769 Planarity : 0.005 0.053 2133 Dihedral : 4.936 24.153 1634 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % 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 (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: 1.24 (0.22), residues: 1479 helix: 2.11 (0.28), residues: 326 sheet: 0.99 (0.23), residues: 470 loop : 0.14 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 546 HIS 0.016 0.002 HIS B 165 PHE 0.011 0.002 PHE A 169 TYR 0.027 0.002 TYR D 184 ARG 0.006 0.001 ARG D 135 *********************** 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 222 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 1.369 Fit side-chains revert: symmetry clash REVERT: A 212 ARG cc_start: 0.8037 (mtm180) cc_final: 0.7793 (mtm180) REVERT: A 267 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7740 (mtmt) REVERT: A 328 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9119 (mm) REVERT: A 338 ARG cc_start: 0.7650 (mtp-110) cc_final: 0.7297 (mtm-85) REVERT: A 369 MET cc_start: 0.8914 (mmp) cc_final: 0.8478 (mmp) REVERT: A 466 GLN cc_start: 0.6846 (tt0) cc_final: 0.6529 (mm110) REVERT: A 471 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8322 (tt) REVERT: A 784 VAL cc_start: 0.9262 (t) cc_final: 0.8969 (t) REVERT: B 221 MET cc_start: 0.8565 (mmm) cc_final: 0.8178 (mmm) REVERT: B 355 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6873 (ptt180) REVERT: C 81 ASP cc_start: 0.8697 (t0) cc_final: 0.8453 (t70) outliers start: 31 outliers final: 16 residues processed: 207 average time/residue: 1.3743 time to fit residues: 306.6059 Evaluate side-chains 209 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 1.334 ------------------------------------------------------------------------------- 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 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 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 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 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 47 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 74 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 D 70 GLN D 228 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11899 Z= 0.307 Angle : 0.623 8.508 16176 Z= 0.338 Chirality : 0.047 0.206 1769 Planarity : 0.005 0.051 2133 Dihedral : 4.980 24.212 1634 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.48 % Allowed : 14.10 % Favored : 83.41 % 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: 1.16 (0.22), residues: 1479 helix: 2.05 (0.28), residues: 326 sheet: 0.97 (0.23), residues: 470 loop : 0.08 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 546 HIS 0.017 0.002 HIS B 165 PHE 0.012 0.002 PHE A 675 TYR 0.027 0.002 TYR D 184 ARG 0.006 0.001 ARG D 135 *********************** 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 220 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.6685 (pt0) cc_final: 0.6055 (pt0) REVERT: A 212 ARG cc_start: 0.8059 (mtm180) cc_final: 0.7279 (mtm180) REVERT: A 237 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.7471 (mtp180) REVERT: A 267 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7755 (mtmt) REVERT: A 328 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.9112 (mm) REVERT: A 338 ARG cc_start: 0.7640 (mtp-110) cc_final: 0.7290 (mtm-85) REVERT: A 369 MET cc_start: 0.8885 (mmp) cc_final: 0.8430 (mmp) REVERT: A 466 GLN cc_start: 0.6854 (tt0) cc_final: 0.6560 (mm110) REVERT: A 471 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8257 (tt) REVERT: A 624 ASP cc_start: 0.7887 (m-30) cc_final: 0.7686 (m-30) REVERT: A 632 ARG cc_start: 0.8154 (mtp-110) cc_final: 0.7911 (mtp-110) REVERT: A 784 VAL cc_start: 0.9258 (t) cc_final: 0.8968 (t) REVERT: B 76 ASP cc_start: 0.8897 (OUTLIER) cc_final: 0.8668 (p0) REVERT: B 197 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8242 (mm-30) REVERT: B 221 MET cc_start: 0.8587 (mmm) cc_final: 0.8211 (mmm) REVERT: B 355 ARG cc_start: 0.7164 (OUTLIER) cc_final: 0.6875 (ptt180) REVERT: C 81 ASP cc_start: 0.8675 (t0) cc_final: 0.8441 (t70) REVERT: D 160 THR cc_start: 0.8852 (m) cc_final: 0.8640 (p) outliers start: 31 outliers final: 18 residues processed: 206 average time/residue: 1.4125 time to fit residues: 312.5694 Evaluate side-chains 212 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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 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 725 ILE Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain B residue 76 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 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 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 136 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11899 Z= 0.225 Angle : 0.570 6.897 16176 Z= 0.310 Chirality : 0.045 0.159 1769 Planarity : 0.004 0.047 2133 Dihedral : 4.760 22.383 1634 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.48 % Allowed : 14.26 % 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: 1.25 (0.22), residues: 1479 helix: 2.15 (0.28), residues: 325 sheet: 1.00 (0.23), residues: 467 loop : 0.14 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 546 HIS 0.011 0.001 HIS B 165 PHE 0.010 0.001 PHE A 675 TYR 0.024 0.002 TYR D 184 ARG 0.004 0.000 ARG D 135 *********************** 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: 31 poor density : 187 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.6655 (pt0) cc_final: 0.6056 (pt0) REVERT: A 212 ARG cc_start: 0.8060 (mtm180) cc_final: 0.7271 (mtm180) REVERT: A 237 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.7500 (mtp180) REVERT: A 267 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7718 (mtmt) REVERT: A 328 ILE cc_start: 0.9325 (OUTLIER) cc_final: 0.9115 (mm) REVERT: A 338 ARG cc_start: 0.7657 (mtp-110) cc_final: 0.7283 (mtm-85) REVERT: A 369 MET cc_start: 0.8865 (mmp) cc_final: 0.8422 (mmp) REVERT: A 466 GLN cc_start: 0.6812 (tt0) cc_final: 0.6576 (mm110) REVERT: A 471 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8271 (tt) REVERT: A 624 ASP cc_start: 0.7853 (m-30) cc_final: 0.7507 (m-30) REVERT: A 632 ARG cc_start: 0.8163 (mtp-110) cc_final: 0.7844 (mtm110) REVERT: A 784 VAL cc_start: 0.9254 (t) cc_final: 0.8941 (t) REVERT: B 221 MET cc_start: 0.8612 (mmm) cc_final: 0.8238 (mmm) REVERT: B 355 ARG cc_start: 0.7158 (OUTLIER) cc_final: 0.6863 (ptt180) REVERT: C 81 ASP cc_start: 0.8676 (t0) cc_final: 0.8449 (t70) REVERT: D 165 LYS cc_start: 0.8564 (mmtt) cc_final: 0.8310 (mmmt) outliers start: 31 outliers final: 20 residues processed: 205 average time/residue: 1.4371 time to fit residues: 318.4430 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 : 1.381 ------------------------------------------------------------------------------- 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 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 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 98 LEU Chi-restraints excluded: chain D residue 105 ILE 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 87 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 84 optimal weight: 0.0870 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 89 optimal weight: 0.0370 chunk 95 optimal weight: 0.8980 chunk 69 optimal weight: 0.4980 chunk 13 optimal weight: 20.0000 chunk 110 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11899 Z= 0.141 Angle : 0.507 6.973 16176 Z= 0.274 Chirality : 0.043 0.145 1769 Planarity : 0.004 0.044 2133 Dihedral : 4.378 19.915 1634 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.52 % Allowed : 15.46 % Favored : 83.01 % 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: 1.44 (0.22), residues: 1479 helix: 2.36 (0.28), residues: 327 sheet: 1.10 (0.24), residues: 462 loop : 0.24 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 228 HIS 0.004 0.001 HIS B 165 PHE 0.008 0.001 PHE A 738 TYR 0.022 0.001 TYR D 184 ARG 0.003 0.000 ARG A 634 *********************** 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 205 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.6600 (pt0) cc_final: 0.6167 (pt0) REVERT: A 212 ARG cc_start: 0.8113 (mtm180) cc_final: 0.7477 (mtm180) REVERT: A 237 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.7313 (mtp180) REVERT: A 267 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7715 (mtmt) REVERT: A 338 ARG cc_start: 0.7681 (mtp-110) cc_final: 0.7279 (mtm-85) REVERT: A 369 MET cc_start: 0.8845 (mmp) cc_final: 0.8350 (mmp) REVERT: A 466 GLN cc_start: 0.6809 (tt0) cc_final: 0.6594 (mm110) REVERT: A 471 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8270 (tt) REVERT: A 539 MET cc_start: 0.8532 (mtm) cc_final: 0.8160 (mtp) REVERT: A 632 ARG cc_start: 0.8137 (mtp-110) cc_final: 0.7843 (mtm110) REVERT: A 784 VAL cc_start: 0.9199 (t) cc_final: 0.8899 (t) REVERT: B 197 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8132 (mm-30) REVERT: B 221 MET cc_start: 0.8627 (mmm) cc_final: 0.8148 (mmm) REVERT: B 355 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6851 (ptt180) REVERT: C 81 ASP cc_start: 0.8622 (t0) cc_final: 0.8392 (t70) REVERT: D 165 LYS cc_start: 0.8386 (mmtt) cc_final: 0.8137 (mmmt) outliers start: 19 outliers final: 11 residues processed: 196 average time/residue: 1.5047 time to fit residues: 316.0424 Evaluate side-chains 197 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 1.374 ------------------------------------------------------------------------------- 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 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 503 ASP 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 D residue 58 LEU 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 134 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 130 optimal weight: 0.0370 chunk 86 optimal weight: 0.9980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN D 47 ASN D 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11899 Z= 0.158 Angle : 0.522 7.425 16176 Z= 0.283 Chirality : 0.043 0.143 1769 Planarity : 0.004 0.044 2133 Dihedral : 4.423 20.035 1634 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.44 % Allowed : 15.62 % Favored : 82.93 % 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: 1.51 (0.22), residues: 1479 helix: 2.42 (0.28), residues: 325 sheet: 1.19 (0.24), residues: 460 loop : 0.26 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 228 HIS 0.006 0.001 HIS B 165 PHE 0.009 0.001 PHE A 675 TYR 0.022 0.001 TYR D 184 ARG 0.004 0.000 ARG A 634 *********************** 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 200 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 1.376 Fit side-chains revert: symmetry clash REVERT: A 176 GLU cc_start: 0.6613 (pt0) cc_final: 0.6165 (pt0) REVERT: A 212 ARG cc_start: 0.8035 (mtm180) cc_final: 0.7126 (mtm180) REVERT: A 237 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.7323 (mtp180) REVERT: A 267 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7714 (mtmt) REVERT: A 338 ARG cc_start: 0.7682 (mtp-110) cc_final: 0.7307 (mtm-85) REVERT: A 369 MET cc_start: 0.8840 (mmp) cc_final: 0.8356 (mmp) REVERT: A 466 GLN cc_start: 0.6803 (tt0) cc_final: 0.6596 (mm110) REVERT: A 471 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8283 (tt) REVERT: A 539 MET cc_start: 0.8618 (mtm) cc_final: 0.8233 (mtp) REVERT: A 632 ARG cc_start: 0.8180 (mtp-110) cc_final: 0.7905 (mtm110) REVERT: A 784 VAL cc_start: 0.9198 (t) cc_final: 0.8895 (t) REVERT: B 221 MET cc_start: 0.8634 (mmm) cc_final: 0.8185 (mmm) REVERT: B 355 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6838 (ptt180) REVERT: C 81 ASP cc_start: 0.8593 (t0) cc_final: 0.8365 (t70) REVERT: D 47 ASN cc_start: 0.7888 (OUTLIER) cc_final: 0.7352 (t0) REVERT: D 152 ARG cc_start: 0.7870 (ptp90) cc_final: 0.7449 (mtt-85) REVERT: D 165 LYS cc_start: 0.8444 (mmtt) cc_final: 0.8154 (mmmt) outliers start: 18 outliers final: 11 residues processed: 191 average time/residue: 1.4711 time to fit residues: 301.8140 Evaluate side-chains 197 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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 425 SER 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 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 D residue 47 ASN Chi-restraints excluded: chain D residue 98 LEU 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 138 optimal weight: 1.9990 chunk 84 optimal weight: 0.0570 chunk 65 optimal weight: 0.4980 chunk 96 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN D 47 ASN D 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11899 Z= 0.176 Angle : 0.542 9.326 16176 Z= 0.292 Chirality : 0.043 0.146 1769 Planarity : 0.004 0.044 2133 Dihedral : 4.480 20.156 1634 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.52 % Allowed : 16.03 % 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 (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: 2.39 (0.28), residues: 326 sheet: 1.12 (0.23), residues: 470 loop : 0.26 (0.25), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 546 HIS 0.007 0.001 HIS B 165 PHE 0.009 0.001 PHE A 675 TYR 0.023 0.001 TYR D 184 ARG 0.003 0.000 ARG D 135 ********************** 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 202 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.6626 (pt0) cc_final: 0.6197 (pt0) REVERT: A 212 ARG cc_start: 0.8050 (mtm180) cc_final: 0.7147 (mtm180) REVERT: A 237 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.7329 (mtp180) REVERT: A 267 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7723 (mtmt) REVERT: A 338 ARG cc_start: 0.7697 (mtp-110) cc_final: 0.7304 (mtm-85) REVERT: A 369 MET cc_start: 0.8837 (mmp) cc_final: 0.8443 (mmp) REVERT: A 471 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8283 (tt) REVERT: A 539 MET cc_start: 0.8615 (mtm) cc_final: 0.8246 (mtp) REVERT: A 552 MET cc_start: 0.8634 (mmm) cc_final: 0.8394 (mmm) REVERT: A 632 ARG cc_start: 0.8160 (mtp-110) cc_final: 0.7883 (mtm110) REVERT: A 784 VAL cc_start: 0.9221 (t) cc_final: 0.8918 (t) REVERT: B 197 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8110 (mm-30) REVERT: B 221 MET cc_start: 0.8637 (mmm) cc_final: 0.8174 (mmm) REVERT: B 355 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6816 (ptt180) REVERT: C 81 ASP cc_start: 0.8595 (t0) cc_final: 0.8366 (t70) REVERT: D 47 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7570 (t0) REVERT: D 152 ARG cc_start: 0.7877 (ptp90) cc_final: 0.7466 (mtt-85) REVERT: D 165 LYS cc_start: 0.8457 (mmtt) cc_final: 0.8211 (mmmt) outliers start: 19 outliers final: 13 residues processed: 192 average time/residue: 1.4590 time to fit residues: 300.7550 Evaluate side-chains 200 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 1.466 ------------------------------------------------------------------------------- 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 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 503 ASP 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 D residue 47 ASN Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 98 LEU 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 123 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 0.2980 chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 116 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN ** A 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 678 GLN D 47 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 = 0.3805 r_free = 0.3805 target = 0.163997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.124337 restraints weight = 12130.466| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.88 r_work: 0.2958 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11899 Z= 0.203 Angle : 0.558 8.570 16176 Z= 0.302 Chirality : 0.044 0.186 1769 Planarity : 0.004 0.046 2133 Dihedral : 4.605 21.295 1634 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.68 % Allowed : 15.95 % 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: 1.43 (0.22), residues: 1479 helix: 2.34 (0.28), residues: 325 sheet: 1.03 (0.23), residues: 477 loop : 0.29 (0.25), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 546 HIS 0.009 0.001 HIS B 165 PHE 0.010 0.001 PHE A 675 TYR 0.024 0.002 TYR D 184 ARG 0.003 0.000 ARG D 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5095.94 seconds wall clock time: 91 minutes 42.49 seconds (5502.49 seconds total)