Starting phenix.real_space_refine on Mon Nov 18 09:35:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9p_36114/11_2024/8j9p_36114.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9p_36114/11_2024/8j9p_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9p_36114/11_2024/8j9p_36114.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9p_36114/11_2024/8j9p_36114.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9p_36114/11_2024/8j9p_36114.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j9p_36114/11_2024/8j9p_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 10.64, per 1000 atoms: 0.66 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: 4.07 Conformation dependent library (CDL) restraints added in 1.9 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: 5.57 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: 5.70 Time building geometry restraints manager: 4.71 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: 2.460 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: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 41.900 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.200 ------------------------------------------------------------------------------- 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= 0.166 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 *********************** 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 : 1.809 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: 0.3105 time to fit residues: 53.8519 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 : 1.921 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 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= 0.285 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 *********************** 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 : 1.831 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.6029 (p90) REVERT: A 275 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7615 (mtm-85) REVERT: A 307 ASN cc_start: 0.8035 (t0) cc_final: 0.7678 (t0) REVERT: A 462 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9009 (tt) REVERT: C 111 HIS cc_start: 0.9096 (OUTLIER) cc_final: 0.8739 (p-80) REVERT: C 283 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9160 (mt) REVERT: C 369 GLU cc_start: 0.9324 (OUTLIER) cc_final: 0.8911 (pt0) REVERT: C 388 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.9064 (mp) REVERT: C 432 THR cc_start: 0.7926 (OUTLIER) cc_final: 0.7484 (t) REVERT: D 219 TRP cc_start: 0.8159 (m100) cc_final: 0.7414 (m100) REVERT: D 354 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7882 (mmtp) outliers start: 73 outliers final: 31 residues processed: 162 average time/residue: 0.2846 time to fit residues: 69.9362 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 : 1.877 ------------------------------------------------------------------------------- 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 91 optimal weight: 0.1980 chunk 51 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 111 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 164 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 163 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16577 Z= 0.231 Angle : 0.616 8.102 22744 Z= 0.319 Chirality : 0.045 0.319 2456 Planarity : 0.004 0.046 2595 Dihedral : 16.939 153.505 2897 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 5.27 % Allowed : 28.53 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.80 (0.20), residues: 1731 helix: 0.44 (0.22), residues: 575 sheet: -0.77 (0.30), residues: 316 loop : -2.64 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 124 HIS 0.021 0.001 HIS C 111 PHE 0.021 0.001 PHE B 255 TYR 0.022 0.001 TYR D 213 ARG 0.006 0.000 ARG D 193 *********************** 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 181 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 99 time to evaluate : 1.593 Fit side-chains REVERT: A 37 TYR cc_start: 0.8370 (OUTLIER) cc_final: 0.5693 (p90) REVERT: A 275 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7576 (mtm-85) REVERT: A 307 ASN cc_start: 0.8174 (t0) cc_final: 0.7779 (t0) REVERT: A 432 THR cc_start: 0.7825 (OUTLIER) cc_final: 0.7255 (t) REVERT: A 462 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9038 (tt) REVERT: A 506 TYR cc_start: 0.9096 (m-80) cc_final: 0.8713 (m-80) REVERT: B 217 PHE cc_start: 0.9199 (OUTLIER) cc_final: 0.8129 (t80) REVERT: C 37 TYR cc_start: 0.8182 (OUTLIER) cc_final: 0.5727 (p90) REVERT: C 283 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9145 (mt) REVERT: C 369 GLU cc_start: 0.9335 (OUTLIER) cc_final: 0.8940 (pt0) REVERT: C 388 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.9060 (mp) REVERT: C 488 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8065 (pm20) REVERT: C 501 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9056 (pp) REVERT: D 219 TRP cc_start: 0.8187 (m100) cc_final: 0.7438 (m100) REVERT: D 354 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7878 (mmtp) outliers start: 82 outliers final: 44 residues processed: 168 average time/residue: 0.3210 time to fit residues: 80.9567 Evaluate side-chains 154 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 98 time to evaluate : 1.949 ------------------------------------------------------------------------------- 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 217 PHE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 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 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 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 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 418 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 162 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 85 optimal weight: 0.0170 chunk 18 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 174 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 156 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 overall best weight: 2.1624 ------------------------------------------------------------------------------- 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 111 HIS ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16577 Z= 0.333 Angle : 0.660 7.778 22744 Z= 0.344 Chirality : 0.047 0.372 2456 Planarity : 0.004 0.048 2595 Dihedral : 17.059 157.283 2897 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 6.11 % Allowed : 28.02 % Favored : 65.87 % 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: -1.91 (0.19), residues: 1731 helix: 0.40 (0.22), residues: 569 sheet: -0.91 (0.30), residues: 319 loop : -2.70 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 124 HIS 0.009 0.001 HIS C 67 PHE 0.020 0.002 PHE B 255 TYR 0.029 0.002 TYR D 213 ARG 0.002 0.000 ARG C 232 *********************** 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 191 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 96 time to evaluate : 2.041 Fit side-chains REVERT: A 37 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.6719 (p90) REVERT: A 307 ASN cc_start: 0.8639 (t0) cc_final: 0.8309 (t0) REVERT: A 432 THR cc_start: 0.8032 (OUTLIER) cc_final: 0.7490 (t) REVERT: A 462 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9043 (tt) REVERT: A 506 TYR cc_start: 0.9122 (m-80) cc_final: 0.8757 (m-80) REVERT: B 92 MET cc_start: 0.5861 (OUTLIER) cc_final: 0.5573 (pmm) REVERT: B 217 PHE cc_start: 0.9202 (OUTLIER) cc_final: 0.8338 (t80) REVERT: B 296 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8113 (tp30) REVERT: B 345 MET cc_start: 0.8433 (tmm) cc_final: 0.8151 (tmm) REVERT: C 37 TYR cc_start: 0.8192 (OUTLIER) cc_final: 0.6573 (p90) REVERT: C 111 HIS cc_start: 0.9120 (OUTLIER) cc_final: 0.8820 (p90) REVERT: C 283 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9183 (mt) REVERT: C 369 GLU cc_start: 0.9332 (OUTLIER) cc_final: 0.8904 (pt0) REVERT: C 388 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.9085 (mp) REVERT: C 488 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8067 (pm20) REVERT: C 501 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9109 (pp) REVERT: D 219 TRP cc_start: 0.8213 (m100) cc_final: 0.7479 (m100) REVERT: D 354 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7907 (mmtp) REVERT: D 406 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8780 (mmtm) outliers start: 95 outliers final: 56 residues processed: 178 average time/residue: 0.2804 time to fit residues: 77.1570 Evaluate side-chains 161 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 90 time to evaluate : 1.862 ------------------------------------------------------------------------------- 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 296 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 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 208 ILE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 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 111 HIS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 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 388 ILE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 179 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 406 LYS Chi-restraints excluded: chain D residue 418 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 357 GLN C 111 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16577 Z= 0.389 Angle : 0.695 9.164 22744 Z= 0.361 Chirality : 0.048 0.385 2456 Planarity : 0.004 0.051 2595 Dihedral : 17.109 159.101 2897 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 7.13 % Allowed : 27.38 % Favored : 65.49 % 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: -2.02 (0.19), residues: 1731 helix: 0.29 (0.21), residues: 565 sheet: -0.98 (0.29), residues: 337 loop : -2.76 (0.19), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 124 HIS 0.017 0.002 HIS C 111 PHE 0.021 0.002 PHE B 255 TYR 0.033 0.002 TYR D 213 ARG 0.004 0.000 ARG D 193 *********************** 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 201 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 90 time to evaluate : 1.953 Fit side-chains REVERT: A 37 TYR cc_start: 0.8594 (OUTLIER) cc_final: 0.6862 (p90) REVERT: A 309 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7748 (p0) REVERT: A 365 PHE cc_start: 0.7567 (OUTLIER) cc_final: 0.7111 (p90) REVERT: A 432 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7579 (t) REVERT: A 462 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9053 (tt) REVERT: B 92 MET cc_start: 0.5689 (OUTLIER) cc_final: 0.5405 (pmm) REVERT: B 217 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8329 (t80) REVERT: B 255 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7829 (p90) REVERT: C 37 TYR cc_start: 0.8180 (OUTLIER) cc_final: 0.6648 (p90) REVERT: C 111 HIS cc_start: 0.9139 (OUTLIER) cc_final: 0.8863 (p90) REVERT: C 283 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9173 (mt) REVERT: C 369 GLU cc_start: 0.9331 (OUTLIER) cc_final: 0.8902 (pt0) REVERT: C 388 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.9093 (mp) REVERT: C 488 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8098 (pm20) REVERT: C 501 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9109 (pp) REVERT: D 83 LYS cc_start: 0.8757 (mmtt) cc_final: 0.8534 (mmmt) REVERT: D 219 TRP cc_start: 0.8122 (m100) cc_final: 0.7421 (m100) REVERT: D 354 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7913 (mmtp) REVERT: D 406 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8773 (mmtm) outliers start: 111 outliers final: 67 residues processed: 186 average time/residue: 0.2624 time to fit residues: 75.5686 Evaluate side-chains 172 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 88 time to evaluate : 1.782 ------------------------------------------------------------------------------- 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 242 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 317 VAL 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 426 VAL 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 14 ASP 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 191 ASP 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 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 88 SER Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 216 GLU 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 388 ILE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 179 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 350 LEU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 406 LYS Chi-restraints excluded: chain D residue 418 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 0.0570 chunk 157 optimal weight: 3.9990 chunk 34 optimal weight: 0.2980 chunk 102 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 175 optimal weight: 0.8980 chunk 145 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 57 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 357 GLN C 122 ASN ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16577 Z= 0.158 Angle : 0.600 8.116 22744 Z= 0.309 Chirality : 0.044 0.260 2456 Planarity : 0.004 0.048 2595 Dihedral : 16.876 160.192 2897 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 4.11 % Allowed : 30.14 % Favored : 65.75 % 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: 0.60 (0.22), residues: 564 sheet: -0.79 (0.30), residues: 318 loop : -2.53 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 20 HIS 0.026 0.001 HIS C 111 PHE 0.018 0.001 PHE B 255 TYR 0.013 0.001 TYR C 104 ARG 0.004 0.000 ARG D 114 *********************** 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 164 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 100 time to evaluate : 1.878 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.6354 (p90) REVERT: A 303 MET cc_start: 0.7218 (mmm) cc_final: 0.6781 (mmt) REVERT: A 307 ASN cc_start: 0.7821 (t0) cc_final: 0.7587 (t0) REVERT: A 365 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.7137 (p90) REVERT: A 369 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8547 (pt0) REVERT: A 506 TYR cc_start: 0.9027 (m-80) cc_final: 0.8685 (m-80) REVERT: B 217 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.8235 (t80) REVERT: B 296 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7805 (tp30) REVERT: B 345 MET cc_start: 0.8397 (tmm) cc_final: 0.8148 (tmm) REVERT: C 37 TYR cc_start: 0.8053 (OUTLIER) cc_final: 0.6320 (p90) REVERT: C 369 GLU cc_start: 0.9228 (OUTLIER) cc_final: 0.8821 (pt0) REVERT: C 488 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8162 (pm20) REVERT: C 501 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9026 (pp) REVERT: D 83 LYS cc_start: 0.8732 (mmtt) cc_final: 0.8505 (mmmt) REVERT: D 219 TRP cc_start: 0.8155 (m100) cc_final: 0.7449 (m100) REVERT: D 354 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7851 (mmtp) outliers start: 64 outliers final: 35 residues processed: 154 average time/residue: 0.3088 time to fit residues: 72.9340 Evaluate side-chains 137 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 92 time to evaluate : 1.952 ------------------------------------------------------------------------------- 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 141 VAL Chi-restraints excluded: chain A residue 283 LEU 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 425 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 490 LEU 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 198 PHE Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 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 214 LEU 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 369 GLU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 126 LYS 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 354 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 97 optimal weight: 0.2980 chunk 174 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 111 HIS ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16577 Z= 0.246 Angle : 0.626 8.725 22744 Z= 0.323 Chirality : 0.045 0.324 2456 Planarity : 0.004 0.049 2595 Dihedral : 16.896 160.453 2897 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 5.59 % Allowed : 28.86 % Favored : 65.55 % 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: 0.60 (0.22), residues: 568 sheet: -0.75 (0.30), residues: 316 loop : -2.56 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 124 HIS 0.007 0.001 HIS C 67 PHE 0.020 0.001 PHE B 255 TYR 0.022 0.001 TYR D 213 ARG 0.003 0.000 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 97 time to evaluate : 1.874 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.6648 (p90) REVERT: A 307 ASN cc_start: 0.7829 (t0) cc_final: 0.7548 (t0) REVERT: A 363 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8758 (t) REVERT: A 365 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.6928 (p90) REVERT: A 506 TYR cc_start: 0.9101 (m-80) cc_final: 0.8766 (m-80) REVERT: B 92 MET cc_start: 0.6003 (OUTLIER) cc_final: 0.5735 (pmm) REVERT: B 217 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8270 (t80) REVERT: B 345 MET cc_start: 0.8365 (tmm) cc_final: 0.8108 (tmm) REVERT: C 37 TYR cc_start: 0.8172 (OUTLIER) cc_final: 0.6502 (p90) REVERT: C 203 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.6953 (t70) REVERT: C 283 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9144 (mt) REVERT: C 369 GLU cc_start: 0.9248 (OUTLIER) cc_final: 0.8818 (pt0) REVERT: C 488 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8106 (pm20) REVERT: C 501 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9027 (pp) REVERT: D 83 LYS cc_start: 0.8736 (mmtt) cc_final: 0.8507 (mmmt) REVERT: D 219 TRP cc_start: 0.8140 (m100) cc_final: 0.7444 (m100) REVERT: D 354 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7883 (mmtp) outliers start: 87 outliers final: 56 residues processed: 172 average time/residue: 0.2929 time to fit residues: 79.4772 Evaluate side-chains 160 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 92 time to evaluate : 1.832 ------------------------------------------------------------------------------- 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 363 THR Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 490 LEU 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 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 310 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 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 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 30 TYR Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 63 VAL 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 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 69 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 chunk 110 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16577 Z= 0.227 Angle : 0.631 9.442 22744 Z= 0.323 Chirality : 0.045 0.315 2456 Planarity : 0.004 0.047 2595 Dihedral : 16.899 160.979 2897 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 5.01 % Allowed : 29.56 % Favored : 65.42 % 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: 0.55 (0.22), residues: 569 sheet: -0.75 (0.30), residues: 319 loop : -2.52 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 124 HIS 0.007 0.001 HIS C 67 PHE 0.020 0.001 PHE B 255 TYR 0.020 0.001 TYR D 213 ARG 0.003 0.000 ARG D 114 *********************** 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 172 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 94 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.6668 (p90) REVERT: A 303 MET cc_start: 0.7386 (mmm) cc_final: 0.7059 (mmt) REVERT: A 307 ASN cc_start: 0.7790 (t0) cc_final: 0.7485 (t0) REVERT: A 363 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8742 (t) REVERT: A 365 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.7006 (p90) REVERT: A 506 TYR cc_start: 0.9081 (m-80) cc_final: 0.8750 (m-80) REVERT: B 217 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8250 (t80) REVERT: B 296 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7774 (tp30) REVERT: B 345 MET cc_start: 0.8356 (tmm) cc_final: 0.8096 (tmm) REVERT: C 37 TYR cc_start: 0.8135 (OUTLIER) cc_final: 0.6466 (p90) REVERT: C 203 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.6943 (t70) REVERT: C 369 GLU cc_start: 0.9247 (OUTLIER) cc_final: 0.8810 (pt0) REVERT: C 388 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.9062 (mp) REVERT: C 488 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8106 (pm20) REVERT: C 501 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9069 (pp) REVERT: D 83 LYS cc_start: 0.8736 (mmtt) cc_final: 0.8508 (mmmt) REVERT: D 219 TRP cc_start: 0.8155 (m100) cc_final: 0.7434 (m100) REVERT: D 354 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7852 (mmtp) outliers start: 78 outliers final: 60 residues processed: 161 average time/residue: 0.2644 time to fit residues: 66.8459 Evaluate side-chains 163 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 91 time to evaluate : 1.685 ------------------------------------------------------------------------------- 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 363 THR Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 490 LEU 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 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 282 VAL Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 369 GLU Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 504 LYS Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 63 VAL 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 354 LYS Chi-restraints excluded: chain D residue 370 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 167 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 153 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 111 HIS ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 16577 Z= 0.451 Angle : 0.757 14.179 22744 Z= 0.390 Chirality : 0.050 0.420 2456 Planarity : 0.004 0.050 2595 Dihedral : 17.184 161.916 2897 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 5.72 % Allowed : 29.24 % Favored : 65.04 % 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: -1.98 (0.19), residues: 1731 helix: 0.29 (0.21), residues: 566 sheet: -0.84 (0.30), residues: 320 loop : -2.73 (0.19), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 124 HIS 0.010 0.002 HIS C 67 PHE 0.025 0.002 PHE D 17 TYR 0.034 0.002 TYR D 213 ARG 0.003 0.000 ARG D 250 *********************** 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 176 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 87 time to evaluate : 1.745 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.7092 (p90) REVERT: A 275 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7674 (mtm-85) REVERT: A 307 ASN cc_start: 0.8117 (t0) cc_final: 0.7645 (t0) REVERT: A 363 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8799 (t) REVERT: A 365 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.7095 (p90) REVERT: B 92 MET cc_start: 0.6280 (OUTLIER) cc_final: 0.6013 (pmm) REVERT: B 217 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8321 (t80) REVERT: C 37 TYR cc_start: 0.8206 (OUTLIER) cc_final: 0.6735 (p90) REVERT: C 203 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.6940 (t70) REVERT: C 283 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9136 (mt) REVERT: C 369 GLU cc_start: 0.9309 (OUTLIER) cc_final: 0.8719 (pt0) REVERT: C 388 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.9096 (mp) REVERT: C 488 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8146 (pm20) REVERT: C 501 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9148 (pp) REVERT: D 83 LYS cc_start: 0.8770 (mmtt) cc_final: 0.8548 (mmmt) REVERT: D 219 TRP cc_start: 0.8171 (m100) cc_final: 0.7558 (m100) REVERT: D 354 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7906 (mmtp) outliers start: 89 outliers final: 64 residues processed: 164 average time/residue: 0.2893 time to fit residues: 73.4075 Evaluate side-chains 165 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 87 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP 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 317 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 363 THR 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 16 ASP 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 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 269 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 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 58 CYS Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 63 VAL 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 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 104 optimal weight: 0.2980 chunk 81 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 14 optimal weight: 0.1980 chunk 110 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN C 111 HIS ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16577 Z= 0.177 Angle : 0.641 12.402 22744 Z= 0.325 Chirality : 0.045 0.282 2456 Planarity : 0.004 0.048 2595 Dihedral : 16.973 163.241 2897 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 4.43 % Allowed : 30.59 % Favored : 64.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.68 (0.20), residues: 1731 helix: 0.61 (0.22), residues: 562 sheet: -0.86 (0.30), residues: 321 loop : -2.51 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 20 HIS 0.006 0.001 HIS C 67 PHE 0.023 0.001 PHE D 17 TYR 0.015 0.001 TYR D 213 ARG 0.002 0.000 ARG D 114 ********************** 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 163 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 94 time to evaluate : 2.130 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8412 (OUTLIER) cc_final: 0.6730 (p90) REVERT: A 307 ASN cc_start: 0.7998 (t0) cc_final: 0.7651 (t0) REVERT: A 363 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8729 (t) REVERT: A 365 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.6983 (p90) REVERT: A 506 TYR cc_start: 0.9041 (m-80) cc_final: 0.8679 (m-80) REVERT: B 92 MET cc_start: 0.6160 (OUTLIER) cc_final: 0.5896 (pmm) REVERT: B 217 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.8211 (t80) REVERT: B 296 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8103 (tp30) REVERT: B 345 MET cc_start: 0.8714 (tmm) cc_final: 0.8274 (tmm) REVERT: C 37 TYR cc_start: 0.8058 (OUTLIER) cc_final: 0.6467 (p90) REVERT: C 203 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.6896 (t70) REVERT: C 283 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9136 (mt) REVERT: C 369 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8773 (pt0) REVERT: C 488 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8103 (pm20) REVERT: C 501 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9120 (pp) REVERT: D 83 LYS cc_start: 0.8715 (mmtt) cc_final: 0.8484 (mmmt) REVERT: D 219 TRP cc_start: 0.8132 (m100) cc_final: 0.7472 (m100) REVERT: D 354 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7859 (mmtp) outliers start: 69 outliers final: 50 residues processed: 153 average time/residue: 0.2855 time to fit residues: 68.5363 Evaluate side-chains 154 residues out of total 1557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 91 time to evaluate : 1.930 ------------------------------------------------------------------------------- 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 292 LYS Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 458 ASP Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 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 217 PHE Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 67 HIS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 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 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 159 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 246 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 43 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 C 111 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.093125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.070488 restraints weight = 56309.072| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 4.75 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16577 Z= 0.246 Angle : 0.652 11.886 22744 Z= 0.331 Chirality : 0.045 0.320 2456 Planarity : 0.004 0.049 2595 Dihedral : 16.988 162.921 2897 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 4.63 % Allowed : 30.72 % Favored : 64.65 % 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: -1.72 (0.20), residues: 1731 helix: 0.58 (0.22), residues: 566 sheet: -0.92 (0.30), residues: 327 loop : -2.53 (0.19), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 124 HIS 0.007 0.001 HIS C 67 PHE 0.026 0.001 PHE D 17 TYR 0.021 0.001 TYR D 213 ARG 0.002 0.000 ARG D 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3137.43 seconds wall clock time: 59 minutes 12.17 seconds (3552.17 seconds total)