Starting phenix.real_space_refine on Sun Aug 24 01:41:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j9p_36114/08_2025/8j9p_36114.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j9p_36114/08_2025/8j9p_36114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j9p_36114/08_2025/8j9p_36114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j9p_36114/08_2025/8j9p_36114.map" model { file = "/net/cci-nas-00/data/ceres_data/8j9p_36114/08_2025/8j9p_36114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j9p_36114/08_2025/8j9p_36114.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 83 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 10089 2.51 5 N 2705 2.21 5 O 3090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16013 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3618 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 25, 'TRANS': 422} Chain breaks: 1 Chain: "B" Number of atoms: 3529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3529 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 407} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 422 Classifications: {'DNA': 13, 'RNA': 8} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 20} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "F" Number of atoms: 432 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 21, 432 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "C" Number of atoms: 3646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3646 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 25, 'TRANS': 425} Chain breaks: 1 Chain: "D" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3531 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 14, 'TRANS': 407} Chain: "G" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 422 Classifications: {'DNA': 13, 'RNA': 8} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 20} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "H" Number of atoms: 411 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.97, per 1000 atoms: 0.19 Number of scatterers: 16013 At special positions: 0 Unit cell: (113.4, 168, 137.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 83 15.00 Mg 2 11.99 O 3090 8.00 N 2705 7.00 C 10089 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 629.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3310 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 23 sheets defined 34.9% alpha, 14.3% beta 26 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 22 through 30 Processing helix chain 'A' and resid 46 through 61 removed outlier: 3.978A pdb=" N GLN A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 102 through 107 removed outlier: 3.583A pdb=" N ASN A 107 " --> pdb=" O TYR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 132 removed outlier: 3.548A pdb=" N PHE A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 214 removed outlier: 3.670A pdb=" N LYS A 211 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 248 through 264 removed outlier: 3.547A pdb=" N ALA A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.501A pdb=" N TYR A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 375 Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 477 through 492 removed outlier: 3.606A pdb=" N ARG A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU A 488 " --> pdb=" O ASN A 484 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 removed outlier: 4.006A pdb=" N TYR A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 29 Processing helix chain 'B' and resid 44 through 56 removed outlier: 3.578A pdb=" N THR B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 89 removed outlier: 3.647A pdb=" N HIS B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN B 89 " --> pdb=" O LYS B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 139 Processing helix chain 'B' and resid 151 through 156 removed outlier: 3.945A pdb=" N GLN B 155 " --> pdb=" O ASN B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 203 removed outlier: 3.582A pdb=" N THR B 202 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.548A pdb=" N ASP B 222 " --> pdb=" O TRP B 219 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE B 223 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 248 Processing helix chain 'B' and resid 257 through 278 Processing helix chain 'B' and resid 300 through 304 removed outlier: 3.668A pdb=" N ASP B 303 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 366 Processing helix chain 'B' and resid 369 through 384 Processing helix chain 'C' and resid 15 through 17 No H-bonds generated for 'chain 'C' and resid 15 through 17' Processing helix chain 'C' and resid 22 through 30 Processing helix chain 'C' and resid 46 through 60 Processing helix chain 'C' and resid 77 through 82 Processing helix chain 'C' and resid 100 through 108 removed outlier: 3.759A pdb=" N TYR C 104 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N PHE C 106 " --> pdb=" O ARG C 103 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA C 108 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 132 removed outlier: 3.722A pdb=" N ARG C 113 " --> pdb=" O SER C 109 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE C 121 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 214 Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 248 through 265 removed outlier: 3.522A pdb=" N GLY C 265 " --> pdb=" O TYR C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 351 removed outlier: 4.062A pdb=" N LYS C 336 " --> pdb=" O PRO C 332 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA C 337 " --> pdb=" O LYS C 333 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR C 346 " --> pdb=" O ALA C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 375 removed outlier: 3.620A pdb=" N TRP C 370 " --> pdb=" O ASN C 366 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE C 373 " --> pdb=" O GLU C 369 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN C 374 " --> pdb=" O TRP C 370 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU C 375 " --> pdb=" O ASN C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 462 Processing helix chain 'C' and resid 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' Processing helix chain 'C' and resid 477 through 493 removed outlier: 4.071A pdb=" N ALA C 483 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN C 484 " --> pdb=" O LEU C 480 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU C 488 " --> pdb=" O ASN C 484 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE C 489 " --> pdb=" O LYS C 485 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER C 493 " --> pdb=" O ILE C 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 removed outlier: 3.699A pdb=" N LEU D 21 " --> pdb=" O PHE D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 52 Processing helix chain 'D' and resid 65 through 69 removed outlier: 3.923A pdb=" N GLY D 68 " --> pdb=" O SER D 65 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASN D 69 " --> pdb=" O THR D 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 65 through 69' Processing helix chain 'D' and resid 71 through 89 removed outlier: 3.845A pdb=" N LEU D 75 " --> pdb=" O ARG D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 115 removed outlier: 3.564A pdb=" N ARG D 114 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU D 115 " --> pdb=" O ILE D 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 111 through 115' Processing helix chain 'D' and resid 123 through 138 removed outlier: 3.511A pdb=" N GLY D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 158 removed outlier: 4.074A pdb=" N SER D 150 " --> pdb=" O ASP D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 248 Processing helix chain 'D' and resid 257 through 277 removed outlier: 3.731A pdb=" N CYS D 261 " --> pdb=" O ARG D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 353 through 366 Processing helix chain 'D' and resid 369 through 385 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 removed outlier: 5.429A pdb=" N ILE A 443 " --> pdb=" O THR A 389 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR A 389 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ILE A 445 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR A 387 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS A 447 " --> pdb=" O GLY A 385 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 384 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N CYS A 279 " --> pdb=" O PHE A 358 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N HIS A 360 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU A 281 " --> pdb=" O HIS A 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 13 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 95 removed outlier: 3.634A pdb=" N LYS A 94 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY A 45 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLY A 42 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ILE A 142 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 44 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 285 removed outlier: 3.766A pdb=" N VAL A 284 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 300 " --> pdb=" O VAL A 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 303 through 306 Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 398 Processing sheet with id=AA7, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.563A pdb=" N SER A 431 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 63 through 64 removed outlier: 3.842A pdb=" N ALA B 98 " --> pdb=" O ILE B 118 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 175 through 177 Processing sheet with id=AB1, first strand: chain 'B' and resid 175 through 177 Processing sheet with id=AB2, first strand: chain 'B' and resid 207 through 210 Processing sheet with id=AB3, first strand: chain 'B' and resid 390 through 394 Processing sheet with id=AB4, first strand: chain 'C' and resid 5 through 6 removed outlier: 6.875A pdb=" N GLY C 385 " --> pdb=" O ASN C 446 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C 358 " --> pdb=" O CYS C 279 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 12 through 13 Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 95 removed outlier: 3.610A pdb=" N LYS C 94 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY C 45 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY C 42 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ILE C 142 " --> pdb=" O GLY C 42 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL C 44 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N TRP C 139 " --> pdb=" O GLN C 222 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU C 224 " --> pdb=" O TRP C 139 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL C 141 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 300 through 306 Processing sheet with id=AB8, first strand: chain 'C' and resid 397 through 398 removed outlier: 4.678A pdb=" N GLU D 169 " --> pdb=" O GLY D 412 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY D 412 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 425 through 426 Processing sheet with id=AC1, first strand: chain 'D' and resid 63 through 64 Processing sheet with id=AC2, first strand: chain 'D' and resid 214 through 216 Processing sheet with id=AC3, first strand: chain 'D' and resid 283 through 285 Processing sheet with id=AC4, first strand: chain 'D' and resid 311 through 314 Processing sheet with id=AC5, first strand: chain 'D' and resid 390 through 394 517 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4149 1.33 - 1.45: 3466 1.45 - 1.57: 8732 1.57 - 1.69: 162 1.69 - 1.81: 68 Bond restraints: 16577 Sorted by residual: bond pdb=" CB LYS A 59 " pdb=" CG LYS A 59 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.45e+00 bond pdb=" CB LYS A 62 " pdb=" CG LYS A 62 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.55e+00 bond pdb=" CB ARG D 193 " pdb=" CG ARG D 193 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.47e+00 bond pdb=" C TYR D 330 " pdb=" N PRO D 331 " ideal model delta sigma weight residual 1.336 1.350 -0.014 1.20e-02 6.94e+03 1.35e+00 bond pdb=" CG LYS A 62 " pdb=" CD LYS A 62 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.34e+00 ... (remaining 16572 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 22276 1.91 - 3.81: 391 3.81 - 5.72: 59 5.72 - 7.62: 14 7.62 - 9.53: 4 Bond angle restraints: 22744 Sorted by residual: angle pdb=" CB LYS A 59 " pdb=" CG LYS A 59 " pdb=" CD LYS A 59 " ideal model delta sigma weight residual 111.30 120.39 -9.09 2.30e+00 1.89e-01 1.56e+01 angle pdb=" CA LYS A 59 " pdb=" CB LYS A 59 " pdb=" CG LYS A 59 " ideal model delta sigma weight residual 114.10 121.55 -7.45 2.00e+00 2.50e-01 1.39e+01 angle pdb=" CB LYS A 62 " pdb=" CG LYS A 62 " pdb=" CD LYS A 62 " ideal model delta sigma weight residual 111.30 119.84 -8.54 2.30e+00 1.89e-01 1.38e+01 angle pdb=" CA LYS D 59 " pdb=" CB LYS D 59 " pdb=" CG LYS D 59 " ideal model delta sigma weight residual 114.10 121.51 -7.41 2.00e+00 2.50e-01 1.37e+01 angle pdb=" N LEU B 310 " pdb=" CA LEU B 310 " pdb=" C LEU B 310 " ideal model delta sigma weight residual 114.56 110.17 4.39 1.27e+00 6.20e-01 1.19e+01 ... (remaining 22739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.16: 8974 29.16 - 58.31: 783 58.31 - 87.47: 68 87.47 - 116.62: 0 116.62 - 145.78: 6 Dihedral angle restraints: 9831 sinusoidal: 4709 harmonic: 5122 Sorted by residual: dihedral pdb=" CA ARG D 193 " pdb=" C ARG D 193 " pdb=" N LEU D 194 " pdb=" CA LEU D 194 " ideal model delta harmonic sigma weight residual 180.00 -156.35 -23.65 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA ARG B 189 " pdb=" C ARG B 189 " pdb=" N TYR B 190 " pdb=" CA TYR B 190 " ideal model delta harmonic sigma weight residual 180.00 159.46 20.54 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA TYR A 328 " pdb=" C TYR A 328 " pdb=" N HIS A 329 " pdb=" CA HIS A 329 " ideal model delta harmonic sigma weight residual 180.00 -159.63 -20.37 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 9828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2070 0.058 - 0.115: 345 0.115 - 0.173: 35 0.173 - 0.230: 3 0.230 - 0.288: 3 Chirality restraints: 2456 Sorted by residual: chirality pdb=" CG LEU D 227 " pdb=" CB LEU D 227 " pdb=" CD1 LEU D 227 " pdb=" CD2 LEU D 227 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C1' U E 1 " pdb=" O4' U E 1 " pdb=" C2' U E 1 " pdb=" N1 U E 1 " both_signs ideal model delta sigma weight residual False 2.46 2.19 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C1' U E 15 " pdb=" O4' U E 15 " pdb=" C2' U E 15 " pdb=" N1 U E 15 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 2453 not shown) Planarity restraints: 2595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 318 " -0.039 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO C 319 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 319 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 319 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 193 " 0.153 9.50e-02 1.11e+02 6.91e-02 3.54e+00 pdb=" NE ARG D 193 " -0.004 2.00e-02 2.50e+03 pdb=" CZ ARG D 193 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG D 193 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 193 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC F 4 " 0.001 2.00e-02 2.50e+03 1.25e-02 3.51e+00 pdb=" N1 DC F 4 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DC F 4 " 0.029 2.00e-02 2.50e+03 pdb=" O2 DC F 4 " -0.017 2.00e-02 2.50e+03 pdb=" N3 DC F 4 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DC F 4 " 0.011 2.00e-02 2.50e+03 pdb=" N4 DC F 4 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DC F 4 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DC F 4 " -0.005 2.00e-02 2.50e+03 ... (remaining 2592 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 188 2.60 - 3.17: 13089 3.17 - 3.75: 24642 3.75 - 4.32: 31554 4.32 - 4.90: 51641 Nonbonded interactions: 121114 Sorted by model distance: nonbonded pdb=" OP3 U G 1 " pdb="MG MG G 101 " model vdw 2.020 2.170 nonbonded pdb=" OP1 A G 3 " pdb="MG MG G 101 " model vdw 2.089 2.170 nonbonded pdb=" NE2 GLN A 302 " pdb=" O THR A 479 " model vdw 2.150 3.120 nonbonded pdb=" O4 U E 21 " pdb=" N7 DA F 3 " model vdw 2.154 2.496 nonbonded pdb=" OD1 ASN A 307 " pdb=" N GLY A 308 " model vdw 2.162 3.120 ... (remaining 121109 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 507) selection = (chain 'C' and (resid 1 through 144 or resid 204 through 507)) } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 1 through 421 or (resid 422 and (name N or name CA or name \ C or name O or name CB )))) } ncs_group { reference = chain 'E' selection = (chain 'G' and resid 1 through 21) } ncs_group { reference = (chain 'F' and resid 4 through 23) selection = chain 'H' } 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=0.95 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: 4.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.130 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 0.047 16577 Z= 0.125 Angle : 0.623 9.528 22744 Z= 0.323 Chirality : 0.044 0.288 2456 Planarity : 0.004 0.069 2595 Dihedral : 19.679 145.777 6521 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.26 % Allowed : 32.07 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.20), residues: 1731 helix: 0.74 (0.23), residues: 550 sheet: -0.58 (0.32), residues: 307 loop : -2.56 (0.18), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 193 TYR 0.019 0.001 TYR C 104 PHE 0.016 0.001 PHE D 273 TRP 0.021 0.001 TRP D 20 HIS 0.002 0.001 HIS D 320 Details of bonding type rmsd covalent geometry : bond 0.00267 (16577) covalent geometry : angle 0.62255 (22744) hydrogen bonds : bond 0.14069 ( 568) hydrogen bonds : angle 5.44009 ( 1571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.572 Fit side-chains REVERT: A 307 ASN cc_start: 0.7561 (t0) cc_final: 0.7329 (t0) REVERT: C 247 LYS cc_start: 0.8419 (mptt) cc_final: 0.7995 (mmtt) REVERT: D 219 TRP cc_start: 0.8151 (m100) cc_final: 0.7476 (m100) outliers start: 4 outliers final: 3 residues processed: 113 average time/residue: 0.1084 time to fit residues: 19.3642 Evaluate side-chains 105 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain B residue 156 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.0670 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.0470 chunk 149 optimal weight: 0.0570 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN A 296 ASN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 ASN ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS C 205 GLN C 295 GLN C 296 ASN C 302 GLN C 380 ASN D 405 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.097440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.074724 restraints weight = 54783.527| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 4.84 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16577 Z= 0.116 Angle : 0.581 8.848 22744 Z= 0.299 Chirality : 0.043 0.253 2456 Planarity : 0.004 0.051 2595 Dihedral : 16.869 150.630 2904 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.96 % Allowed : 29.37 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.20), residues: 1731 helix: 0.68 (0.23), residues: 563 sheet: -0.52 (0.31), residues: 334 loop : -2.56 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 193 TYR 0.014 0.001 TYR C 104 PHE 0.014 0.001 PHE D 273 TRP 0.012 0.001 TRP D 20 HIS 0.004 0.001 HIS D 188 Details of bonding type rmsd covalent geometry : bond 0.00247 (16577) covalent geometry : angle 0.58100 (22744) hydrogen bonds : bond 0.03881 ( 568) hydrogen bonds : angle 4.46189 ( 1571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 104 time to evaluate : 0.646 Fit side-chains REVERT: A 307 ASN cc_start: 0.7755 (t0) cc_final: 0.7381 (t0) REVERT: A 373 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8556 (m-10) REVERT: A 394 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8709 (tt) REVERT: A 506 TYR cc_start: 0.8963 (m-80) cc_final: 0.8706 (m-80) REVERT: C 111 HIS cc_start: 0.9044 (OUTLIER) cc_final: 0.8720 (p-80) REVERT: C 243 ARG cc_start: 0.9176 (tpp80) cc_final: 0.8451 (mmm160) REVERT: C 369 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8673 (pt0) REVERT: C 488 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8051 (pm20) REVERT: C 501 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.8931 (pp) REVERT: D 100 ASP cc_start: 0.7010 (p0) cc_final: 0.6806 (p0) REVERT: D 219 TRP cc_start: 0.8065 (m100) cc_final: 0.7283 (m100) outliers start: 46 outliers final: 15 residues processed: 145 average time/residue: 0.1028 time to fit residues: 22.9714 Evaluate side-chains 119 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 217 PHE Chi-restraints excluded: chain D residue 418 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 63 optimal weight: 0.4980 chunk 177 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 40 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.094807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.072187 restraints weight = 56454.185| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 4.81 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16577 Z= 0.166 Angle : 0.603 7.996 22744 Z= 0.311 Chirality : 0.044 0.317 2456 Planarity : 0.004 0.043 2595 Dihedral : 16.822 152.490 2897 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 4.56 % Allowed : 27.83 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.20), residues: 1731 helix: 0.59 (0.22), residues: 575 sheet: -0.53 (0.31), residues: 316 loop : -2.57 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 193 TYR 0.020 0.001 TYR D 213 PHE 0.015 0.001 PHE D 273 TRP 0.014 0.001 TRP D 124 HIS 0.022 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00379 (16577) covalent geometry : angle 0.60302 (22744) hydrogen bonds : bond 0.04441 ( 568) hydrogen bonds : angle 4.52090 ( 1571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 100 time to evaluate : 0.647 Fit side-chains REVERT: A 37 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.6070 (p90) REVERT: A 275 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7499 (mtm-85) REVERT: A 307 ASN cc_start: 0.7965 (t0) cc_final: 0.7581 (t0) REVERT: A 462 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9037 (tt) REVERT: A 506 TYR cc_start: 0.8967 (m-80) cc_final: 0.8678 (m-80) REVERT: B 217 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8011 (t80) REVERT: B 296 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8159 (tp30) REVERT: C 111 HIS cc_start: 0.9097 (m-70) cc_final: 0.8709 (p-80) REVERT: C 232 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8451 (mmm-85) REVERT: C 369 GLU cc_start: 0.9270 (OUTLIER) cc_final: 0.8872 (pt0) REVERT: C 388 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8942 (mp) REVERT: C 432 THR cc_start: 0.7896 (OUTLIER) cc_final: 0.7455 (t) REVERT: C 488 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8070 (pm20) REVERT: D 219 TRP cc_start: 0.8094 (m100) cc_final: 0.7381 (m100) REVERT: D 354 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7818 (mmtp) outliers start: 71 outliers final: 29 residues processed: 160 average time/residue: 0.1123 time to fit residues: 27.1425 Evaluate side-chains 135 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 95 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 275 ARG Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 217 PHE Chi-restraints excluded: chain D residue 225 HIS Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 418 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 138 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 chunk 148 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS A 296 ASN B 357 GLN C 111 HIS D 340 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.093374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.070791 restraints weight = 55878.731| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 4.74 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16577 Z= 0.195 Angle : 0.628 7.649 22744 Z= 0.326 Chirality : 0.045 0.352 2456 Planarity : 0.004 0.043 2595 Dihedral : 16.924 155.655 2897 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 5.85 % Allowed : 26.80 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.20), residues: 1731 helix: 0.58 (0.22), residues: 568 sheet: -0.64 (0.31), residues: 312 loop : -2.62 (0.19), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 243 TYR 0.026 0.001 TYR D 213 PHE 0.013 0.001 PHE A 365 TRP 0.017 0.001 TRP D 124 HIS 0.007 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00447 (16577) covalent geometry : angle 0.62783 (22744) hydrogen bonds : bond 0.04802 ( 568) hydrogen bonds : angle 4.62289 ( 1571) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 99 time to evaluate : 0.450 Fit side-chains REVERT: A 37 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.6315 (p90) REVERT: A 307 ASN cc_start: 0.8467 (t0) cc_final: 0.8126 (t0) REVERT: A 462 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9015 (tt) REVERT: A 506 TYR cc_start: 0.8945 (m-80) cc_final: 0.8650 (m-80) REVERT: B 92 MET cc_start: 0.5854 (OUTLIER) cc_final: 0.5575 (pmm) REVERT: B 217 PHE cc_start: 0.9178 (OUTLIER) cc_final: 0.8183 (t80) REVERT: B 296 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8193 (tp30) REVERT: B 345 MET cc_start: 0.8342 (tmm) cc_final: 0.8055 (tmm) REVERT: C 37 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.6415 (p90) REVERT: C 111 HIS cc_start: 0.9085 (OUTLIER) cc_final: 0.8824 (p90) REVERT: C 232 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8506 (mmm-85) REVERT: C 369 GLU cc_start: 0.9271 (OUTLIER) cc_final: 0.8699 (pt0) REVERT: C 388 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8969 (mp) REVERT: C 501 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9016 (pp) REVERT: D 219 TRP cc_start: 0.8123 (m100) cc_final: 0.7432 (m100) REVERT: D 354 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7871 (mmtp) REVERT: D 406 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8666 (mmtm) outliers start: 91 outliers final: 56 residues processed: 177 average time/residue: 0.1119 time to fit residues: 30.0890 Evaluate side-chains 162 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 93 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 217 PHE Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 418 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 92 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 48 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 357 GLN C 111 HIS D 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.094657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.072028 restraints weight = 55753.834| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 4.75 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16577 Z= 0.135 Angle : 0.602 10.480 22744 Z= 0.308 Chirality : 0.044 0.298 2456 Planarity : 0.004 0.043 2595 Dihedral : 16.844 156.989 2897 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 4.88 % Allowed : 28.15 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.20), residues: 1731 helix: 0.66 (0.22), residues: 568 sheet: -0.64 (0.30), residues: 323 loop : -2.53 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 193 TYR 0.019 0.001 TYR D 213 PHE 0.012 0.001 PHE D 273 TRP 0.017 0.001 TRP B 20 HIS 0.010 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00303 (16577) covalent geometry : angle 0.60237 (22744) hydrogen bonds : bond 0.04072 ( 568) hydrogen bonds : angle 4.44730 ( 1571) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 101 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8413 (OUTLIER) cc_final: 0.6332 (p90) REVERT: A 94 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8533 (ptpp) REVERT: A 307 ASN cc_start: 0.8510 (t0) cc_final: 0.8154 (t0) REVERT: A 369 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8582 (pt0) REVERT: A 506 TYR cc_start: 0.8903 (m-80) cc_final: 0.8594 (m-80) REVERT: B 217 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8171 (t80) REVERT: B 296 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7890 (tp30) REVERT: B 345 MET cc_start: 0.8297 (tmm) cc_final: 0.7994 (tmm) REVERT: C 37 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.6313 (p90) REVERT: C 232 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8502 (mmm-85) REVERT: C 302 GLN cc_start: 0.8477 (mp10) cc_final: 0.7703 (mp10) REVERT: C 369 GLU cc_start: 0.9243 (OUTLIER) cc_final: 0.8860 (pt0) REVERT: C 388 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8941 (mp) REVERT: C 488 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7987 (pm20) REVERT: C 501 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.8994 (pp) REVERT: D 219 TRP cc_start: 0.8097 (m100) cc_final: 0.7410 (m100) REVERT: D 354 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7838 (mmtp) outliers start: 76 outliers final: 46 residues processed: 167 average time/residue: 0.1123 time to fit residues: 28.6660 Evaluate side-chains 155 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 97 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 418 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 123 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 162 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.092821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.070246 restraints weight = 56095.795| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 4.69 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16577 Z= 0.213 Angle : 0.654 9.637 22744 Z= 0.337 Chirality : 0.046 0.359 2456 Planarity : 0.004 0.046 2595 Dihedral : 16.945 158.816 2897 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 5.85 % Allowed : 27.25 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.20), residues: 1731 helix: 0.55 (0.22), residues: 568 sheet: -0.69 (0.31), residues: 313 loop : -2.60 (0.19), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 250 TYR 0.027 0.001 TYR D 213 PHE 0.018 0.001 PHE D 17 TRP 0.016 0.001 TRP D 124 HIS 0.009 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00488 (16577) covalent geometry : angle 0.65419 (22744) hydrogen bonds : bond 0.04929 ( 568) hydrogen bonds : angle 4.67642 ( 1571) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 96 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.6634 (p90) REVERT: A 94 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8590 (ptpp) REVERT: A 369 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8608 (pt0) REVERT: A 462 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9053 (tt) REVERT: A 506 TYR cc_start: 0.8955 (m-80) cc_final: 0.8658 (m-80) REVERT: B 92 MET cc_start: 0.6222 (OUTLIER) cc_final: 0.5955 (pmm) REVERT: B 217 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8191 (t80) REVERT: C 37 TYR cc_start: 0.8238 (OUTLIER) cc_final: 0.6585 (p90) REVERT: C 111 HIS cc_start: 0.9078 (OUTLIER) cc_final: 0.8830 (p90) REVERT: C 232 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8518 (mmm-85) REVERT: C 369 GLU cc_start: 0.9227 (OUTLIER) cc_final: 0.8638 (pt0) REVERT: C 388 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8977 (mp) REVERT: C 488 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8012 (pm20) REVERT: C 501 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9049 (pp) REVERT: D 219 TRP cc_start: 0.8055 (m100) cc_final: 0.7356 (m100) REVERT: D 354 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7891 (mmtp) REVERT: D 406 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8684 (mmtm) outliers start: 91 outliers final: 61 residues processed: 173 average time/residue: 0.1040 time to fit residues: 28.0176 Evaluate side-chains 167 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 91 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 418 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 135 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 142 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 357 GLN C 111 HIS ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.093501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.070956 restraints weight = 55766.100| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 4.73 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16577 Z= 0.164 Angle : 0.630 8.089 22744 Z= 0.324 Chirality : 0.045 0.322 2456 Planarity : 0.004 0.044 2595 Dihedral : 16.919 159.983 2897 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 5.72 % Allowed : 27.83 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.20), residues: 1731 helix: 0.60 (0.22), residues: 568 sheet: -0.70 (0.30), residues: 315 loop : -2.55 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 102 TYR 0.022 0.001 TYR D 213 PHE 0.012 0.001 PHE D 273 TRP 0.016 0.001 TRP B 20 HIS 0.008 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00373 (16577) covalent geometry : angle 0.62954 (22744) hydrogen bonds : bond 0.04380 ( 568) hydrogen bonds : angle 4.56696 ( 1571) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 95 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.6663 (p90) REVERT: A 94 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8564 (ptpp) REVERT: A 369 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8577 (pt0) REVERT: A 462 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9049 (tt) REVERT: A 506 TYR cc_start: 0.8923 (m-80) cc_final: 0.8646 (m-80) REVERT: B 92 MET cc_start: 0.6199 (OUTLIER) cc_final: 0.5939 (pmm) REVERT: B 217 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.8157 (t80) REVERT: B 296 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7842 (tp30) REVERT: B 345 MET cc_start: 0.8539 (tmm) cc_final: 0.8113 (tmm) REVERT: C 37 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.6553 (p90) REVERT: C 111 HIS cc_start: 0.9056 (OUTLIER) cc_final: 0.8795 (p90) REVERT: C 203 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.7053 (t70) REVERT: C 232 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8502 (mmm-85) REVERT: C 369 GLU cc_start: 0.9231 (OUTLIER) cc_final: 0.8652 (pt0) REVERT: C 488 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8050 (pm20) REVERT: C 501 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9026 (pp) REVERT: D 219 TRP cc_start: 0.8006 (m100) cc_final: 0.7290 (m100) REVERT: D 354 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7854 (mmtp) outliers start: 89 outliers final: 61 residues processed: 171 average time/residue: 0.1154 time to fit residues: 30.3068 Evaluate side-chains 168 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 92 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 418 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 74 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN C 111 HIS ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.092440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.069905 restraints weight = 56042.266| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 4.73 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16577 Z= 0.216 Angle : 0.665 8.782 22744 Z= 0.343 Chirality : 0.046 0.360 2456 Planarity : 0.004 0.046 2595 Dihedral : 16.996 161.133 2897 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 5.91 % Allowed : 28.28 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.20), residues: 1731 helix: 0.55 (0.22), residues: 565 sheet: -0.76 (0.30), residues: 333 loop : -2.65 (0.19), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 102 TYR 0.027 0.001 TYR D 213 PHE 0.023 0.001 PHE D 17 TRP 0.019 0.001 TRP D 124 HIS 0.009 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00496 (16577) covalent geometry : angle 0.66486 (22744) hydrogen bonds : bond 0.04983 ( 568) hydrogen bonds : angle 4.71906 ( 1571) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 92 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.6897 (p90) REVERT: A 94 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8600 (ptpp) REVERT: A 363 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8779 (t) REVERT: A 369 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8607 (pt0) REVERT: A 432 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7499 (t) REVERT: A 462 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9056 (tt) REVERT: A 506 TYR cc_start: 0.8963 (m-80) cc_final: 0.8656 (m-80) REVERT: B 92 MET cc_start: 0.6213 (OUTLIER) cc_final: 0.5961 (pmm) REVERT: B 217 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8230 (t80) REVERT: B 345 MET cc_start: 0.8569 (tmm) cc_final: 0.8121 (tmm) REVERT: C 37 TYR cc_start: 0.8175 (OUTLIER) cc_final: 0.6557 (p90) REVERT: C 74 MET cc_start: 0.7549 (tpp) cc_final: 0.7256 (tpp) REVERT: C 203 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.7046 (t70) REVERT: C 232 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8514 (mmm-85) REVERT: C 369 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.8622 (pt0) REVERT: C 488 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8058 (pm20) REVERT: C 501 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9050 (pp) REVERT: D 219 TRP cc_start: 0.8023 (m100) cc_final: 0.7365 (m100) REVERT: D 354 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7861 (mmtp) outliers start: 92 outliers final: 63 residues processed: 172 average time/residue: 0.1183 time to fit residues: 31.2634 Evaluate side-chains 169 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 91 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 418 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 16 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 136 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 138 optimal weight: 0.1980 chunk 23 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.094581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.071957 restraints weight = 55777.117| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 4.78 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16577 Z= 0.126 Angle : 0.625 8.717 22744 Z= 0.319 Chirality : 0.044 0.285 2456 Planarity : 0.004 0.044 2595 Dihedral : 16.883 161.777 2897 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 4.82 % Allowed : 29.11 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.20), residues: 1731 helix: 0.62 (0.22), residues: 569 sheet: -0.66 (0.31), residues: 312 loop : -2.51 (0.19), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 201 TYR 0.017 0.001 TYR D 213 PHE 0.010 0.001 PHE A 206 TRP 0.015 0.001 TRP B 20 HIS 0.006 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00282 (16577) covalent geometry : angle 0.62503 (22744) hydrogen bonds : bond 0.03895 ( 568) hydrogen bonds : angle 4.43818 ( 1571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 98 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8447 (tpt) cc_final: 0.8212 (tpp) REVERT: A 37 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.6571 (p90) REVERT: A 94 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8535 (ptpp) REVERT: A 506 TYR cc_start: 0.8895 (m-80) cc_final: 0.8593 (m-80) REVERT: B 92 MET cc_start: 0.6115 (OUTLIER) cc_final: 0.5875 (pmm) REVERT: B 217 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8102 (t80) REVERT: B 296 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8096 (tp30) REVERT: B 345 MET cc_start: 0.8588 (tmm) cc_final: 0.8122 (tmm) REVERT: C 37 TYR cc_start: 0.8095 (OUTLIER) cc_final: 0.6361 (p90) REVERT: C 74 MET cc_start: 0.7634 (tpp) cc_final: 0.7360 (tpp) REVERT: C 203 ASP cc_start: 0.7225 (OUTLIER) cc_final: 0.6933 (t70) REVERT: C 232 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8482 (mmm-85) REVERT: C 302 GLN cc_start: 0.8510 (mp10) cc_final: 0.7746 (mp10) REVERT: C 369 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8638 (pt0) REVERT: C 488 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8074 (pm20) REVERT: C 501 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9033 (pp) REVERT: D 219 TRP cc_start: 0.8039 (m100) cc_final: 0.7367 (m100) REVERT: D 354 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7825 (mmtp) outliers start: 75 outliers final: 55 residues processed: 162 average time/residue: 0.1098 time to fit residues: 27.5814 Evaluate side-chains 158 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 91 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 418 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 128 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 49 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 164 optimal weight: 0.4980 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 296 ASN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.095369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.072820 restraints weight = 55688.807| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 4.78 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16577 Z= 0.122 Angle : 0.600 8.709 22744 Z= 0.305 Chirality : 0.044 0.276 2456 Planarity : 0.003 0.046 2595 Dihedral : 16.792 161.058 2897 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 4.37 % Allowed : 29.43 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.20), residues: 1731 helix: 0.70 (0.22), residues: 569 sheet: -0.53 (0.31), residues: 316 loop : -2.44 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 114 TYR 0.015 0.001 TYR D 213 PHE 0.020 0.001 PHE D 17 TRP 0.014 0.001 TRP B 20 HIS 0.005 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00275 (16577) covalent geometry : angle 0.59986 (22744) hydrogen bonds : bond 0.03567 ( 568) hydrogen bonds : angle 4.28632 ( 1571) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 99 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8497 (tpt) cc_final: 0.8289 (tpp) REVERT: A 37 TYR cc_start: 0.8366 (OUTLIER) cc_final: 0.6457 (p90) REVERT: A 94 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8512 (ptpp) REVERT: A 303 MET cc_start: 0.6748 (mmm) cc_final: 0.6451 (mmt) REVERT: A 506 TYR cc_start: 0.8907 (m-80) cc_final: 0.8610 (m-80) REVERT: B 92 MET cc_start: 0.6016 (OUTLIER) cc_final: 0.5791 (pmm) REVERT: B 217 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8048 (t80) REVERT: B 296 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7770 (tp30) REVERT: B 345 MET cc_start: 0.8619 (tmm) cc_final: 0.8105 (tmm) REVERT: C 37 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.6326 (p90) REVERT: C 74 MET cc_start: 0.7814 (tpp) cc_final: 0.7552 (tpp) REVERT: C 203 ASP cc_start: 0.7140 (OUTLIER) cc_final: 0.6811 (t70) REVERT: C 302 GLN cc_start: 0.8553 (mp10) cc_final: 0.7789 (mp10) REVERT: C 369 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8531 (pt0) REVERT: C 488 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8073 (pm20) REVERT: C 501 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9046 (pp) REVERT: D 219 TRP cc_start: 0.8016 (m100) cc_final: 0.7453 (m100) REVERT: D 354 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7801 (mmtp) outliers start: 68 outliers final: 54 residues processed: 156 average time/residue: 0.1053 time to fit residues: 25.5846 Evaluate side-chains 160 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 95 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 418 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 122 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 100 optimal weight: 0.0030 chunk 23 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 169 optimal weight: 0.2980 chunk 90 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.093068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.070736 restraints weight = 55898.795| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 4.61 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16577 Z= 0.203 Angle : 0.658 8.931 22744 Z= 0.337 Chirality : 0.046 0.350 2456 Planarity : 0.004 0.046 2595 Dihedral : 16.921 161.103 2897 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 4.82 % Allowed : 29.18 % Favored : 66.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.20), residues: 1731 helix: 0.60 (0.22), residues: 568 sheet: -0.74 (0.31), residues: 315 loop : -2.47 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 250 TYR 0.024 0.001 TYR D 213 PHE 0.025 0.001 PHE B 255 TRP 0.020 0.001 TRP D 124 HIS 0.008 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00466 (16577) covalent geometry : angle 0.65839 (22744) hydrogen bonds : bond 0.04633 ( 568) hydrogen bonds : angle 4.54232 ( 1571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3024.48 seconds wall clock time: 52 minutes 52.10 seconds (3172.10 seconds total)