Starting phenix.real_space_refine on Sat May 17 20:08:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j9p_36114/05_2025/8j9p_36114.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j9p_36114/05_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_36114/05_2025/8j9p_36114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j9p_36114/05_2025/8j9p_36114.map" model { file = "/net/cci-nas-00/data/ceres_data/8j9p_36114/05_2025/8j9p_36114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j9p_36114/05_2025/8j9p_36114.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.59, per 1000 atoms: 0.60 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: 3.66 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 5.14 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: 4.88 Time building geometry restraints manager: 4.19 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: 2.870 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 37.830 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.920 ------------------------------------------------------------------------------- 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 : 10.67 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (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 TRP 0.021 0.001 TRP D 20 HIS 0.002 0.001 HIS D 320 PHE 0.016 0.001 PHE D 273 TYR 0.019 0.001 TYR C 104 ARG 0.014 0.000 ARG D 193 Details of bonding type rmsd hydrogen bonds : bond 0.14069 ( 568) hydrogen bonds : angle 5.44009 ( 1571) covalent geometry : bond 0.00267 (16577) covalent geometry : angle 0.62255 (22744) *********************** 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 : 1.631 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: 0.2578 time to fit residues: 44.9697 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 : 1.565 ------------------------------------------------------------------------------- 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 152 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 295 GLN A 296 ASN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 405 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.093697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.071137 restraints weight = 55882.176| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 4.71 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 16577 Z= 0.200 Angle : 0.637 8.629 22744 Z= 0.331 Chirality : 0.045 0.341 2456 Planarity : 0.004 0.049 2595 Dihedral : 17.040 151.611 2904 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.67 % Favored : 91.28 % Rotamer: Outliers : 4.69 % Allowed : 28.92 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.20), residues: 1731 helix: 0.48 (0.22), residues: 571 sheet: -0.67 (0.30), residues: 324 loop : -2.67 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 124 HIS 0.006 0.001 HIS C 207 PHE 0.019 0.001 PHE D 273 TYR 0.023 0.001 TYR D 213 ARG 0.011 0.000 ARG D 193 Details of bonding type rmsd hydrogen bonds : bond 0.05022 ( 568) hydrogen bonds : angle 4.77055 ( 1571) covalent geometry : bond 0.00456 (16577) covalent geometry : angle 0.63715 (22744) *********************** 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 173 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 100 time to evaluate : 1.600 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.5993 (p90) REVERT: A 275 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7580 (mtm-85) REVERT: A 307 ASN cc_start: 0.7908 (t0) cc_final: 0.7561 (t0) REVERT: A 462 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.8992 (tt) REVERT: C 111 HIS cc_start: 0.9090 (OUTLIER) cc_final: 0.8734 (p-80) REVERT: C 283 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9092 (mt) REVERT: C 369 GLU cc_start: 0.9287 (OUTLIER) cc_final: 0.8876 (pt0) REVERT: C 388 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8960 (mp) REVERT: C 432 THR cc_start: 0.7801 (OUTLIER) cc_final: 0.7371 (t) REVERT: D 219 TRP cc_start: 0.8079 (m100) cc_final: 0.7342 (m100) REVERT: D 354 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7861 (mmtp) outliers start: 73 outliers final: 31 residues processed: 162 average time/residue: 0.2590 time to fit residues: 63.5236 Evaluate side-chains 134 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 94 time to evaluate : 1.617 ------------------------------------------------------------------------------- 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 423 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 18 THR Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 283 LEU 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 490 LEU 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 159 LEU 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 269 ILE Chi-restraints excluded: chain D residue 354 LYS 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 57 optimal weight: 9.9990 chunk 106 optimal weight: 0.0980 chunk 53 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS A 251 HIS ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.093454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.070862 restraints weight = 55851.206| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 4.70 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1276 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= 0.185 Angle : 0.629 8.032 22744 Z= 0.326 Chirality : 0.045 0.334 2456 Planarity : 0.004 0.046 2595 Dihedral : 16.974 153.771 2897 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 5.72 % Allowed : 28.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.20), residues: 1731 helix: 0.41 (0.22), residues: 575 sheet: -0.80 (0.30), residues: 322 loop : -2.67 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 124 HIS 0.017 0.001 HIS C 111 PHE 0.021 0.001 PHE B 255 TYR 0.024 0.001 TYR D 213 ARG 0.005 0.000 ARG D 193 Details of bonding type rmsd hydrogen bonds : bond 0.04783 ( 568) hydrogen bonds : angle 4.68698 ( 1571) covalent geometry : bond 0.00423 (16577) covalent geometry : angle 0.62889 (22744) *********************** 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 186 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 97 time to evaluate : 1.747 Fit side-chains REVERT: A 37 TYR cc_start: 0.8372 (OUTLIER) cc_final: 0.5936 (p90) REVERT: A 275 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7551 (mtm-85) REVERT: A 307 ASN cc_start: 0.8124 (t0) cc_final: 0.7741 (t0) REVERT: A 432 THR cc_start: 0.7843 (OUTLIER) cc_final: 0.7289 (t) REVERT: A 462 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9010 (tt) REVERT: A 506 TYR cc_start: 0.8966 (m-80) cc_final: 0.8678 (m-80) REVERT: B 217 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8114 (t80) REVERT: C 37 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.6004 (p90) REVERT: C 232 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8505 (mmm-85) REVERT: C 283 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9113 (mt) REVERT: C 369 GLU cc_start: 0.9290 (OUTLIER) cc_final: 0.8867 (pt0) REVERT: C 388 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8962 (mp) REVERT: C 488 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8025 (pm20) REVERT: C 501 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9025 (pp) REVERT: D 219 TRP cc_start: 0.8115 (m100) cc_final: 0.7400 (m100) REVERT: D 354 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7875 (mmtp) REVERT: D 406 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8671 (mmtm) outliers start: 89 outliers final: 50 residues processed: 173 average time/residue: 0.2818 time to fit residues: 72.3833 Evaluate side-chains 159 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 95 time to evaluate : 1.734 ------------------------------------------------------------------------------- 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 292 LYS Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 317 VAL 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 45 PHE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 95 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 310 LEU Chi-restraints excluded: chain B residue 357 GLN 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 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 283 LEU 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 490 LEU 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 140 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 56 optimal weight: 0.2980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 357 GLN ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.094543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.071980 restraints weight = 55270.268| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 4.76 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 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 = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16577 Z= 0.136 Angle : 0.588 7.719 22744 Z= 0.305 Chirality : 0.044 0.292 2456 Planarity : 0.004 0.044 2595 Dihedral : 16.883 155.294 2897 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 4.82 % Allowed : 28.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.20), residues: 1731 helix: 0.63 (0.22), residues: 568 sheet: -0.73 (0.30), residues: 322 loop : -2.60 (0.19), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 124 HIS 0.006 0.001 HIS C 67 PHE 0.019 0.001 PHE B 255 TYR 0.019 0.001 TYR D 213 ARG 0.002 0.000 ARG C 243 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 568) hydrogen bonds : angle 4.48927 ( 1571) covalent geometry : bond 0.00303 (16577) covalent geometry : angle 0.58785 (22744) *********************** 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 174 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 99 time to evaluate : 1.692 Fit side-chains REVERT: A 37 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.5955 (p90) REVERT: A 307 ASN cc_start: 0.8435 (t0) cc_final: 0.8091 (t0) REVERT: A 373 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.8443 (m-10) REVERT: A 506 TYR cc_start: 0.8906 (m-80) cc_final: 0.8600 (m-80) REVERT: B 217 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8192 (t80) REVERT: B 296 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7900 (tp30) REVERT: B 345 MET cc_start: 0.8293 (tmm) cc_final: 0.8043 (tmm) REVERT: C 37 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.5994 (p90) REVERT: C 111 HIS cc_start: 0.9054 (OUTLIER) cc_final: 0.8716 (p90) REVERT: C 232 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8492 (mmm-85) REVERT: C 369 GLU cc_start: 0.9269 (OUTLIER) cc_final: 0.8883 (pt0) REVERT: C 388 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8924 (mp) REVERT: C 488 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7991 (pm20) REVERT: C 501 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.8984 (pp) REVERT: D 219 TRP cc_start: 0.8101 (m100) cc_final: 0.7349 (m100) REVERT: D 354 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7825 (mmtp) outliers start: 75 outliers final: 43 residues processed: 163 average time/residue: 0.2770 time to fit residues: 68.2763 Evaluate side-chains 148 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 93 time to evaluate : 1.806 ------------------------------------------------------------------------------- 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 292 LYS Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 373 PHE 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 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 95 ILE 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 290 THR Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 370 ASN 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 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 369 GLU Chi-restraints excluded: chain C residue 388 ILE 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 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 246 ILE Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 354 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 82 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 172 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.095028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.072433 restraints weight = 56140.005| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 4.77 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 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 = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16577 Z= 0.124 Angle : 0.590 10.383 22744 Z= 0.302 Chirality : 0.044 0.283 2456 Planarity : 0.004 0.045 2595 Dihedral : 16.812 156.411 2897 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 4.95 % Allowed : 28.21 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.20), residues: 1731 helix: 0.68 (0.22), residues: 568 sheet: -0.71 (0.30), residues: 326 loop : -2.54 (0.19), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 124 HIS 0.012 0.001 HIS C 111 PHE 0.018 0.001 PHE B 255 TYR 0.017 0.001 TYR D 213 ARG 0.004 0.000 ARG D 193 Details of bonding type rmsd hydrogen bonds : bond 0.03852 ( 568) hydrogen bonds : angle 4.41790 ( 1571) covalent geometry : bond 0.00276 (16577) covalent geometry : angle 0.59001 (22744) *********************** 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 179 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 102 time to evaluate : 1.605 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8359 (OUTLIER) cc_final: 0.5901 (p90) REVERT: A 369 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8591 (pt0) REVERT: A 373 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.8469 (m-10) REVERT: A 506 TYR cc_start: 0.8908 (m-80) cc_final: 0.8598 (m-80) REVERT: B 92 MET cc_start: 0.5848 (OUTLIER) cc_final: 0.5581 (pmm) REVERT: B 217 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8195 (t80) REVERT: B 296 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7876 (tp30) REVERT: B 345 MET cc_start: 0.8289 (tmm) cc_final: 0.8058 (tmm) REVERT: C 37 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.5993 (p90) REVERT: C 111 HIS cc_start: 0.9110 (m-70) cc_final: 0.8744 (p-80) REVERT: C 369 GLU cc_start: 0.9243 (OUTLIER) cc_final: 0.8638 (pt0) REVERT: C 488 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7975 (pm20) REVERT: C 501 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.8949 (pp) REVERT: D 219 TRP cc_start: 0.8052 (m100) cc_final: 0.7311 (m100) REVERT: D 354 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7814 (mmtp) outliers start: 77 outliers final: 49 residues processed: 167 average time/residue: 0.2698 time to fit residues: 68.8466 Evaluate side-chains 157 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 97 time to evaluate : 1.724 ------------------------------------------------------------------------------- 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 283 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 292 LYS 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 373 PHE 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 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 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 290 THR Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 370 ASN 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 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 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 405 ILE 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 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 246 ILE Chi-restraints excluded: chain D residue 265 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 114 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS ** C 302 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 = 0.3666 r_free = 0.3666 target = 0.094669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.072056 restraints weight = 55972.902| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 4.76 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16577 Z= 0.140 Angle : 0.593 8.028 22744 Z= 0.305 Chirality : 0.044 0.299 2456 Planarity : 0.003 0.045 2595 Dihedral : 16.792 157.772 2897 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 5.59 % Allowed : 27.83 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.20), residues: 1731 helix: 0.70 (0.22), residues: 568 sheet: -0.64 (0.29), residues: 342 loop : -2.56 (0.19), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 124 HIS 0.006 0.001 HIS C 67 PHE 0.019 0.001 PHE B 255 TYR 0.018 0.001 TYR D 213 ARG 0.002 0.000 ARG C 243 Details of bonding type rmsd hydrogen bonds : bond 0.04015 ( 568) hydrogen bonds : angle 4.43304 ( 1571) covalent geometry : bond 0.00319 (16577) covalent geometry : angle 0.59337 (22744) *********************** 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 190 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 103 time to evaluate : 1.534 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.6119 (p90) REVERT: A 365 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.7036 (p90) REVERT: A 369 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8575 (pt0) REVERT: A 506 TYR cc_start: 0.8927 (m-80) cc_final: 0.8602 (m-80) REVERT: B 92 MET cc_start: 0.6004 (OUTLIER) cc_final: 0.5736 (pmm) REVERT: B 217 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.8174 (t80) REVERT: B 296 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7804 (tp30) REVERT: C 37 TYR cc_start: 0.8189 (OUTLIER) cc_final: 0.6193 (p90) REVERT: C 111 HIS cc_start: 0.9056 (m90) cc_final: 0.8782 (p90) REVERT: C 369 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8860 (pt0) REVERT: C 388 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8920 (mp) REVERT: C 488 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7972 (pm20) REVERT: C 501 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.8956 (pp) REVERT: D 219 TRP cc_start: 0.8060 (m100) cc_final: 0.7311 (m100) REVERT: D 354 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7815 (mmtp) outliers start: 87 outliers final: 62 residues processed: 178 average time/residue: 0.2535 time to fit residues: 70.1194 Evaluate side-chains 167 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 93 time to evaluate : 1.697 ------------------------------------------------------------------------------- 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 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 317 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 365 PHE 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 215 CYS 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 357 GLN Chi-restraints excluded: chain B residue 370 ASN 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 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 388 ILE 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 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 225 HIS 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 418 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 96 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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** B 357 GLN ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.092592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.070125 restraints weight = 56285.391| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 4.70 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 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 = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16577 Z= 0.218 Angle : 0.665 9.230 22744 Z= 0.342 Chirality : 0.047 0.367 2456 Planarity : 0.004 0.046 2595 Dihedral : 16.964 159.643 2897 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 6.23 % Allowed : 28.15 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.20), residues: 1731 helix: 0.55 (0.22), residues: 568 sheet: -0.70 (0.30), residues: 334 loop : -2.62 (0.19), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 124 HIS 0.009 0.001 HIS C 67 PHE 0.020 0.002 PHE B 255 TYR 0.026 0.001 TYR D 213 ARG 0.003 0.000 ARG D 114 Details of bonding type rmsd hydrogen bonds : bond 0.05042 ( 568) hydrogen bonds : angle 4.70705 ( 1571) covalent geometry : bond 0.00502 (16577) covalent geometry : angle 0.66539 (22744) *********************** 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 191 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 94 time to evaluate : 2.049 Fit side-chains REVERT: A 37 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.6586 (p90) REVERT: A 275 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7543 (mtm-85) REVERT: A 365 PHE cc_start: 0.7383 (OUTLIER) cc_final: 0.7132 (p90) REVERT: A 369 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8593 (pt0) REVERT: A 432 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7500 (t) REVERT: A 462 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9032 (tt) REVERT: A 506 TYR cc_start: 0.8965 (m-80) cc_final: 0.8656 (m-80) REVERT: B 92 MET cc_start: 0.6225 (OUTLIER) cc_final: 0.5977 (pmm) REVERT: B 217 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8280 (t80) REVERT: B 345 MET cc_start: 0.8592 (tmm) cc_final: 0.8150 (tmm) REVERT: C 37 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.6367 (p90) REVERT: C 111 HIS cc_start: 0.9079 (m90) cc_final: 0.8821 (p90) REVERT: C 203 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.7025 (t70) REVERT: C 283 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9158 (mp) REVERT: C 369 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.8656 (pt0) REVERT: C 388 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8961 (mp) REVERT: C 488 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7994 (pm20) REVERT: C 501 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9019 (pp) REVERT: D 219 TRP cc_start: 0.8081 (m100) cc_final: 0.7326 (m100) REVERT: D 354 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7852 (mmtp) outliers start: 97 outliers final: 62 residues processed: 178 average time/residue: 0.2556 time to fit residues: 70.6388 Evaluate side-chains 170 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 92 time to evaluate : 1.608 ------------------------------------------------------------------------------- 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 271 LEU Chi-restraints excluded: chain A residue 275 ARG 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 303 MET Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 365 PHE 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 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 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 234 PHE Chi-restraints excluded: chain C residue 283 LEU 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 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 78 LEU 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 265 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 169 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.094600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.072040 restraints weight = 55586.539| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 4.74 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 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 = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16577 Z= 0.130 Angle : 0.613 9.215 22744 Z= 0.313 Chirality : 0.044 0.290 2456 Planarity : 0.004 0.046 2595 Dihedral : 16.867 160.439 2897 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 5.27 % Allowed : 28.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.20), residues: 1731 helix: 0.66 (0.22), residues: 564 sheet: -0.61 (0.30), residues: 318 loop : -2.47 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 124 HIS 0.006 0.001 HIS C 67 PHE 0.018 0.001 PHE B 255 TYR 0.017 0.001 TYR D 213 ARG 0.002 0.000 ARG C 232 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 568) hydrogen bonds : angle 4.44354 ( 1571) covalent geometry : bond 0.00295 (16577) covalent geometry : angle 0.61262 (22744) *********************** 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 178 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 96 time to evaluate : 1.797 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.6276 (p90) REVERT: A 365 PHE cc_start: 0.7304 (OUTLIER) cc_final: 0.7044 (p90) REVERT: A 369 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8568 (pt0) REVERT: A 506 TYR cc_start: 0.8905 (m-80) cc_final: 0.8596 (m-80) REVERT: B 92 MET cc_start: 0.6128 (OUTLIER) cc_final: 0.5891 (pmm) REVERT: B 217 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8119 (t80) REVERT: B 296 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7766 (tp30) REVERT: B 345 MET cc_start: 0.8588 (tmm) cc_final: 0.8107 (tmm) REVERT: C 37 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.6174 (p90) REVERT: C 111 HIS cc_start: 0.9058 (m90) cc_final: 0.8831 (p90) REVERT: C 203 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6986 (t70) REVERT: C 369 GLU cc_start: 0.9200 (OUTLIER) cc_final: 0.8782 (pt0) REVERT: C 488 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7964 (pm20) REVERT: C 501 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9014 (pp) REVERT: D 219 TRP cc_start: 0.8042 (m100) cc_final: 0.7332 (m100) REVERT: D 354 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7834 (mmtp) outliers start: 82 outliers final: 58 residues processed: 167 average time/residue: 0.2525 time to fit residues: 65.1713 Evaluate side-chains 162 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 92 time to evaluate : 1.786 ------------------------------------------------------------------------------- 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 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 365 PHE 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 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 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 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 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 225 HIS Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 265 ILE Chi-restraints excluded: chain D residue 353 SER 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 163 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 122 optimal weight: 0.0770 chunk 150 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 177 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- 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** B 357 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 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 = 0.3655 r_free = 0.3655 target = 0.094049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.071473 restraints weight = 55617.095| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 4.76 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 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 = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16577 Z= 0.151 Angle : 0.629 13.518 22744 Z= 0.319 Chirality : 0.045 0.308 2456 Planarity : 0.004 0.047 2595 Dihedral : 16.858 160.579 2897 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 4.76 % Allowed : 29.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.20), residues: 1731 helix: 0.66 (0.22), residues: 568 sheet: -0.61 (0.30), residues: 336 loop : -2.52 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 124 HIS 0.007 0.001 HIS C 67 PHE 0.021 0.001 PHE D 17 TYR 0.020 0.001 TYR D 213 ARG 0.002 0.000 ARG C 232 Details of bonding type rmsd hydrogen bonds : bond 0.04142 ( 568) hydrogen bonds : angle 4.47704 ( 1571) covalent geometry : bond 0.00345 (16577) covalent geometry : angle 0.62895 (22744) *********************** 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 165 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 91 time to evaluate : 1.786 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8477 (tpt) cc_final: 0.8187 (tpp) REVERT: A 37 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.6471 (p90) REVERT: A 365 PHE cc_start: 0.7323 (OUTLIER) cc_final: 0.7060 (p90) REVERT: A 369 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8544 (pt0) REVERT: A 462 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9050 (tt) REVERT: A 506 TYR cc_start: 0.8929 (m-80) cc_final: 0.8607 (m-80) REVERT: B 92 MET cc_start: 0.6159 (OUTLIER) cc_final: 0.5920 (pmm) REVERT: B 217 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8182 (t80) REVERT: B 296 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7773 (tp30) REVERT: B 345 MET cc_start: 0.8608 (tmm) cc_final: 0.8115 (tmm) REVERT: C 37 TYR cc_start: 0.8162 (OUTLIER) cc_final: 0.6362 (p90) REVERT: C 111 HIS cc_start: 0.9067 (m90) cc_final: 0.8840 (p90) REVERT: C 203 ASP cc_start: 0.7172 (OUTLIER) cc_final: 0.6894 (t70) REVERT: C 369 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.8622 (pt0) REVERT: C 488 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7971 (pm20) REVERT: C 501 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.8994 (pp) REVERT: D 219 TRP cc_start: 0.8057 (m100) cc_final: 0.7338 (m100) REVERT: D 354 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7824 (mmtp) outliers start: 74 outliers final: 57 residues processed: 155 average time/residue: 0.2598 time to fit residues: 62.7743 Evaluate side-chains 159 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 89 time to evaluate : 1.813 ------------------------------------------------------------------------------- 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 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 365 PHE 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 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 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 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 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 265 ILE Chi-restraints excluded: chain D residue 353 SER 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 94 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 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 = 0.3644 r_free = 0.3644 target = 0.093439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.070820 restraints weight = 56125.804| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 4.74 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 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 = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16577 Z= 0.181 Angle : 0.644 13.642 22744 Z= 0.328 Chirality : 0.045 0.334 2456 Planarity : 0.004 0.046 2595 Dihedral : 16.915 160.960 2897 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 5.14 % Allowed : 28.60 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.20), residues: 1731 helix: 0.62 (0.22), residues: 568 sheet: -0.62 (0.30), residues: 334 loop : -2.54 (0.19), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 124 HIS 0.008 0.001 HIS C 67 PHE 0.019 0.001 PHE B 255 TYR 0.023 0.001 TYR D 213 ARG 0.002 0.000 ARG C 232 Details of bonding type rmsd hydrogen bonds : bond 0.04446 ( 568) hydrogen bonds : angle 4.54994 ( 1571) covalent geometry : bond 0.00415 (16577) covalent geometry : angle 0.64445 (22744) ********************** 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 171 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 91 time to evaluate : 1.678 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8494 (tpt) cc_final: 0.8294 (tpp) REVERT: A 37 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.6661 (p90) REVERT: A 94 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8648 (ptpp) REVERT: A 365 PHE cc_start: 0.7360 (OUTLIER) cc_final: 0.7072 (p90) REVERT: A 369 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8570 (pt0) REVERT: A 462 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9086 (tt) REVERT: A 506 TYR cc_start: 0.8943 (m-80) cc_final: 0.8654 (m-80) REVERT: B 92 MET cc_start: 0.6163 (OUTLIER) cc_final: 0.5923 (pmm) REVERT: B 217 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.8180 (t80) REVERT: B 296 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7781 (tp30) REVERT: B 345 MET cc_start: 0.8627 (tmm) cc_final: 0.8132 (tmm) REVERT: C 37 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.6419 (p90) REVERT: C 111 HIS cc_start: 0.9070 (m90) cc_final: 0.8834 (p90) REVERT: C 203 ASP cc_start: 0.7175 (OUTLIER) cc_final: 0.6891 (t70) REVERT: C 369 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8634 (pt0) REVERT: C 488 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7974 (pm20) REVERT: C 501 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9099 (pp) REVERT: D 219 TRP cc_start: 0.8044 (m100) cc_final: 0.7311 (m100) REVERT: D 354 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7837 (mmtp) outliers start: 80 outliers final: 61 residues processed: 161 average time/residue: 0.2577 time to fit residues: 64.6766 Evaluate side-chains 165 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 90 time to evaluate : 1.592 ------------------------------------------------------------------------------- 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 365 PHE 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 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 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 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 58 CYS Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 78 LEU 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 265 ILE Chi-restraints excluded: chain D residue 353 SER 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 55 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 chunk 150 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 24 optimal weight: 0.0670 chunk 105 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.094947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.072389 restraints weight = 55468.956| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 4.75 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1849 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= 0.124 Angle : 0.620 13.615 22744 Z= 0.313 Chirality : 0.044 0.281 2456 Planarity : 0.004 0.047 2595 Dihedral : 16.844 160.978 2897 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 4.76 % Allowed : 28.98 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.20), residues: 1731 helix: 0.75 (0.22), residues: 565 sheet: -0.58 (0.30), residues: 321 loop : -2.43 (0.19), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 124 HIS 0.006 0.001 HIS C 67 PHE 0.022 0.001 PHE D 17 TYR 0.015 0.001 TYR D 213 ARG 0.002 0.000 ARG D 114 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 568) hydrogen bonds : angle 4.36972 ( 1571) covalent geometry : bond 0.00279 (16577) covalent geometry : angle 0.61988 (22744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6639.80 seconds wall clock time: 117 minutes 1.98 seconds (7021.98 seconds total)